U.S. patent application number 14/991083 was filed with the patent office on 2016-04-28 for crispr-cas component systems, methods and compositions for sequence manipulation.
The applicant listed for this patent is THE BROAD INSTITUTE INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, THE ROCKEFELLER UNIVERSITY. Invention is credited to David Olivier Bikard, David Benjamin Turitz Cox, Wenyan Jiang, Luciano Marraffini, Neville Espi Sanjana, Feng Zhang.
Application Number | 20160115489 14/991083 |
Document ID | / |
Family ID | 49881125 |
Filed Date | 2016-04-28 |
United States Patent
Application |
20160115489 |
Kind Code |
A1 |
Zhang; Feng ; et
al. |
April 28, 2016 |
CRISPR-CAS COMPONENT SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE
MANIPULATION
Abstract
The invention provides for systems, methods, and compositions
for manipulation of sequences and/or activities of target
sequences. Provided are vectors and vector systems, some of which
encode one or more components of a CRISPR complex, as well as
methods for the design and use of such vectors. Also provided are
methods of directing CRISPR complex formation in eukaryotic cells
and methods for selecting specific cells by introducing precise
mutations utilizing the CRISPR/Cas system.
Inventors: |
Zhang; Feng; (Cambridge,
MA) ; Cox; David Benjamin Turitz; (Cambridge, MA)
; Marraffini; Luciano; (New York, NY) ; Bikard;
David Olivier; (Paris, FR) ; Jiang; Wenyan;
(Whitestone, NY) ; Sanjana; Neville Espi;
(Cambridge, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
THE BROAD INSTITUTE INC.
MASSACHUSETTS INSTITUTE OF TECHNOLOGY
THE ROCKEFELLER UNIVERSITY |
Cambridge
Cambridge
New York |
MA
MA
NY |
US
US
US |
|
|
Family ID: |
49881125 |
Appl. No.: |
14/991083 |
Filed: |
January 8, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14497627 |
Sep 26, 2014 |
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14991083 |
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PCT/US2013/074611 |
Dec 12, 2013 |
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14497627 |
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61768959 |
Feb 25, 2013 |
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61791409 |
Mar 15, 2013 |
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61835931 |
Jun 17, 2013 |
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61736527 |
Dec 12, 2012 |
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61757972 |
Jan 29, 2013 |
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61748427 |
Jan 2, 2013 |
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Current U.S.
Class: |
514/44R |
Current CPC
Class: |
C12N 15/70 20130101;
C12N 9/22 20130101; C12N 15/907 20130101; C12N 15/746 20130101;
C12N 15/113 20130101; C12N 2310/3519 20130101; C12N 15/1082
20130101; C12N 2800/101 20130101; C12N 15/74 20130101; C12N 15/63
20130101; C12N 15/102 20130101; C12N 15/85 20130101; C12N 15/8509
20130101; C12N 2310/20 20170501; C12N 2310/531 20130101 |
International
Class: |
C12N 15/74 20060101
C12N015/74; C12N 15/70 20060101 C12N015/70 |
Goverment Interests
STATEMENT AS TO FEDERALLY SPONSORED RESEARCH
[0003] This invention was made with government support under the
NIH Pioneer Award DP1MH100706, awarded by the National Institutes
of Health. The government has certain rights in the invention.
Claims
1. A method of inducing cell death of one or more prokaryotic
cell(s) comprising: introducing one or more vectors into the
prokaryotic cell(s); wherein the one or more vectors drive
expression of one or more of: a CRISPR enzyme, a guide sequence
linked to a tracr mate sequence, and a tracr sequence; and all of a
CRISPR enzyme, a guide sequence linked to a tracr mate sequence,
and a tracr sequence, are produced in the prokaryotic cell(s);
wherein the CRISPR complex comprises the CRISPR enzyme complexed
with (1) the guide sequence that is hybridized to a target sequence
within a target polynucleotide, and (2) the tracr mate sequence
that is hybridized to the tracr sequence; wherein binding of the
CRISPR complex to the target polynucleotide results in
Cas9-directed cleavage at a targeted site in the prokaryote(s) and
induces cell death.
2. The method of claim 1, wherein the CRISPR enzyme is a type II
CRISPR system enzyme.
3. The method of claim 1, wherein the CRISPR enzyme is a Cas9.
4. The method of claim 3, wherein the Cas9 is S. pyogenes Cas9.
5. The method of claim 1, wherein the CRISPR enzyme is not
endogenous to the prokaryote(s).
6. The method of claim 1 wherein the prokaryote(s) is S. pneumoniae
or E. coli.
7. The method of claim 1 wherein the one or more vectors are
plasmids.
Description
RELATED APPLICATIONS AND INCORPORATION BY REFERENCE
[0001] This application is a divisional of U.S. application Ser.
No. 14/497,627 filed Sep. 26, 2014, which is a continuation in part
of international patent application serial no. PCT/US2013/074611
filed Dec. 12, 2013 which claims priority to U.S. provisional
patent applications 61/736,527, 61/748,427, 61/757,972, 61/768,959,
61/791,409 and 61/835,931 having Broad reference BI-2011/008/WSGR
Docket No. 44063-701.101, BI-2011/008/WSGR Docket No.
44063-701.102, Broad reference BI-2011/008/VP Docket No.
44790.01.2003, BI-2011/008/VP Docket No. 44790.02.2003 and
BI-2011/008/VP Docket No. 44790.03.2003 respectively, all entitled
SYSTEMS METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION filed on
Dec. 12, 2012, Jan. 2, 2013, Jan. 29, 2013, Feb. 25, 2013, Mar. 15,
2013 and Jun. 17, 2013, respectively.
[0002] Reference is made to U.S. provisional patent applications
61/758,468; 61/769,046; 61/802,174; 61/806,375; 61/814,263;
61/819,803 and 61/828,130, each entitled ENGINEERING AND
OPTIMIZATION OF SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE
MANIPULATION, filed on Jan. 30, 2013; Feb. 25, 2013; Mar. 15, 2013;
Mar. 28, 2013; Apr. 20, 2013; May 6, 2013 and May 28, 2013
respectively. Reference is also made to U.S. provisional patent
applications 61/835,936, 61/836,127, 61/836,101, 61/836,080,
61/836,123 and 61/835,973 each filed Jun. 17, 2013. Reference is
also made to U.S. provisional patent application 61/842,322 and
U.S. patent application Ser. No. 14/054,414, each having Broad
reference BI-2011/008A, entitled CRISPR-CAS SYSTEMS AND METHODS FOR
ALTERING EXPRESSION OF GENE PRODUCTS filed on Jul. 2, 2013 and Oct.
15, 2013 respectively.
[0004] The foregoing applications, and all documents cited therein
or during their prosecution ("appln cited documents") and all
documents cited or referenced in the appln cited documents, and all
documents cited or referenced herein ("herein cited documents"),
and all documents cited or referenced in herein cited documents,
together with any manufacturer's instructions, descriptions,
product specifications, and product sheets for any products
mentioned herein or in any document incorporated by reference
herein, are hereby incorporated herein by reference, and may be
employed in the practice of the invention. More specifically, all
referenced documents are incorporated by reference to the same
extent as if each individual document was specifically and
individually indicated to be incorporated by reference.
FIELD OF THE INVENTION
[0005] The present invention generally relates to systems, methods
and compositions used for the control of gene expression involving
sequence targeting, such as genome perturbation or gene-editing,
that may use vector systems related to Clustered Regularly
Interspaced Short Palindromic Repeats (CRISPR) and components
thereof.
SEQUENCE LISTING
[0006] The instant application contains a Sequence Listing which
has been submitted electronically in ASCII format and is hereby
incorporated by reference in its entirety. Said ASCII copy, created
on Mar. 31, 2015, is named 44790.14.2003_SL.txt and is 308,602
bytes in size.
BACKGROUND OF THE INVENTION
[0007] Recent advances in genome sequencing techniques and analysis
methods have significantly accelerated the ability to catalog and
map genetic factors associated with a diverse range of biological
functions and diseases. Precise genome targeting technologies are
needed to enable systematic reverse engineering of causal genetic
variations by allowing selective perturbation of individual genetic
elements, as well as to advance synthetic biology,
biotechnological, and medical applications. Although genome-editing
techniques such as designer zinc fingers, transcription
activator-like effectors (TALEs), or homing meganucleases are
available for producing targeted genome perturbations, there
remains a need for new genome engineering technologies that are
affordable, easy to set up, scalable, and amenable to targeting
multiple positions within the eukaryotic genome.
SUMMARY OF THE INVENTION
[0008] There exists a pressing need for alternative and robust
systems and techniques for sequence targeting with a wide array of
applications. This invention addresses this need and provides
related advantages. The CRISPR/Cas or the CRISPR-Cas system (both
terms are used interchangeably throughout this application) does
not require the generation of customized proteins to target
specific sequences but rather a single Cas enzyme can be programmed
by a short RNA molecule to recognize a specific DNA target, in
other words the Cas enzyme can be recruited to a specific DNA
target using said short RNA molecule. Adding the CRISPR-Cas system
to the repertoire of genome sequencing techniques and analysis
methods may significantly simplify the methodology and accelerate
the ability to catalog and map genetic factors associated with a
diverse range of biological functions and diseases. To utilize the
CRISPR-Cas system effectively for genome editing without
deleterious effects, it is critical to understand aspects of
engineering and optimization of these genome engineering tools,
which are aspects of the claimed invention.
[0009] In one aspect, the invention provides a vector system
comprising one or more vectors. In some embodiments, the system
comprises: (a) a first regulatory element operably linked to a
tracr mate sequence and one or more insertion sites for inserting
one or more guide sequences upstream of the tracr mate sequence,
wherein when expressed, the guide sequence directs
sequence-specific binding of a CRISPR complex to a target sequence
in a eukaryotic cell, wherein the CRISPR complex comprises a CRISPR
enzyme complexed with (1) the guide sequence that is hybridized to
the target sequence, and (2) the tracr mate sequence that is
hybridized to the tracr sequence; and (b) a second regulatory
element operably linked to an enzyme-coding sequence encoding said
CRISPR enzyme comprising a nuclear localization sequence; wherein
components (a) and (b) are located on the same or different vectors
of the system. In some embodiments, component (a) further comprises
the tracr sequence downstream of the tracr mate sequence under the
control of the first regulatory element. In some embodiments,
component (a) further comprises two or more guide sequences
operably linked to the first regulatory element, wherein when
expressed, each of the two or more guide sequences direct sequence
specific binding of a CRISPR complex to a different target sequence
in a eukaryotic cell. In some embodiments, the system comprises the
tracr sequence under the control of a third regulatory element,
such as a polymerase III promoter. In some embodiments, the tracr
sequence exhibits at least 50%, 60%, 70%, 80%0, 90%, 95%, or 99% of
sequence complementarity along the length of the tracr mate
sequence when optimally aligned. Determining optimal alignment is
within the purview of one of skill in the art. For example, there
are publically and commercially available alignment algorithms and
programs such as, but not limited to, ClustalW, Smith-Waterman in
matlab, Bowtie, Geneious, Biopython and SeqMan. In some
embodiments, the CRISPR complex comprises one or more nuclear
localization sequences of sufficient strength to drive accumulation
of said CRISPR complex in a detectable amount in the nucleus of a
eukaryotic cell. Without wishing to be bound by theory, it is
believed that a nuclear localization sequence is not necessary for
CRISPR complex activity in eukaryotes, but that including such
sequences enhances activity of the system, especially as to
targeting nucleic acid molecules in the nucleus. In some
embodiments, the CRISPR enzyme is a type II CRISPR system enzyme.
In some embodiments, the CRISPR enzyme is a Cas9 enzyme. In some
embodiments, the Cas9 enzyme is S. pneumoniae. S. pyogenes, or S.
thermophilus Cas9, and may include mutated Cas9 derived from these
organisms. The enzyme may be a Cas9 homolog or ortholog. In some
embodiments, the CRISPR enzyme is codon-optimized for expression in
a eukaryotic cell. In some embodiments, the CRISPR enzyme directs
cleavage of one or two strands at the location of the target
sequence. In some embodiments, the CRISPR enzyme lacks DNA strand
cleavage activity. In some embodiments, the first regulatory
element is a polymerase III promoter. In some embodiments, the
second regulatory element is a polymerase II promoter. In some
embodiments, the guide sequence is at least 15, 16, 17, 18, 19, 20,
25 nucleotides, or between 10-30, or between 15-25, or between
15-20 nucleotides in length. In general, and throughout this
specification, the term "vector" refers to a nucleic acid molecule
capable of transporting another nucleic acid to which it has been
linked. Vectors include, but are not limited to, nucleic acid
molecules that are single-stranded, double-stranded, or partially
double-stranded; nucleic acid molecules that comprise one or more
free ends, no free ends (e.g. circular); nucleic acid molecules
that comprise DNA, RNA, or both; and other varieties of
polynucleotides known in the art. One type of vector is a
"plasmid," which refers to a circular double stranded DNA loop into
which additional DNA segments can be inserted, such as by standard
molecular cloning techniques. Another type of vector is a viral
vector, wherein virally-derived DNA or RNA sequences are present in
the vector for packaging into a virus (e.g. retroviruses,
replication defective retroviruses, adenoviruses, replication
defective adenoviruses, and adeno-associated viruses). Viral
vectors also include polynucleotides carried by a virus for
transfection into a host cell. Certain vectors are capable of
autonomous replication in a host cell into which they are
introduced (e.g. bacterial vectors having a bacterial origin of
replication and episomal mammalian vectors). Other vectors (e.g.,
non-episomal mammalian vectors) are integrated into the genome of a
host cell upon introduction into the host cell, and thereby are
replicated along with the host genome. Moreover, certain vectors
are capable of directing the expression of genes to which they are
operatively-linked. Such vectors are referred to herein as
"expression vectors." Common expression vectors of utility in
recombinant DNA techniques are often in the form of plasmids.
[0010] Recombinant expression vectors can comprise a nucleic acid
of the invention in a form suitable for expression of the nucleic
acid in a host cell, which means that the recombinant expression
vectors include one or more regulatory elements, which may be
selected on the basis of the host cells to be used for expression,
that is operatively-linked to the nucleic acid sequence to be
expressed. Within a recombinant expression vector, "operably
linked" is intended to mean that the nucleotide sequence of
interest is linked to the regulatory element(s) in a manner that
allows for expression of the nucleotide sequence (e.g. in an in
vitro transcription/translation system or in a host cell when the
vector is introduced into the host cell).
[0011] The term "regulatory element" is intended to include
promoters, enhancers, internal ribosomal entry sites (IRES), and
other expression control elements (e.g. transcription termination
signals, such as polyadenylation signals and poly-U sequences).
Such regulatory elements are described, for example, in Goeddel,
GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic
Press, San Diego, Calif. (1990). Regulatory elements include those
that direct constitutive expression of a nucleotide sequence in
many types of host cell and those that direct expression of the
nucleotide sequence only in certain host cells (e.g.,
tissue-specific regulatory sequences). A tissue-specific promoter
may direct expression primarily in a desired tissue of interest,
such as muscle, neuron, bone, skin, blood, specific organs (e.g.
liver, pancreas), or particular cell types (e.g. lymphocytes).
Regulatory elements may also direct expression in a
temporal-dependent manner, such as in a cell-cycle dependent or
developmental stage-dependent manner, which may or may not also be
tissue or cell-type specific. In some embodiments, a vector
comprises one or more pol III promoter (e.g. 1, 2, 3, 4, 5, or more
pol Ill promoters), one or more pol II promoters (e.g. 1, 2, 3, 4,
5, or more pol II promoters), one or more pol I promoters (e.g. 1,
2, 3, 4, 5, or more pol I promoters), or combinations thereof.
Examples of pol III promoters include, but are not limited to, U6
and H1 promoters. Examples of pol II promoters include, but are not
limited to, the retroviral Rous sarcoma virus (RSV) LTR promoter
(optionally with the RSV enhancer), the cytomegalovirus (CMV)
promoter (optionally with the CMV enhancer) [see, e.g., Boshart et
al, Cell, 41:521-530 (1985)], the SV40 promoter, the dihydrofolate
reductase promoter, the .beta.-actin promoter, the phosphoglycerol
kinase (PGK) promoter, and the EF1.alpha. promoter. Also
encompassed by the term "regulatory element" are enhancer elements,
such as WPRE; CMV enhancers; the R-U5' segment in LTR of HTLV-I
(Mol. Cell. Biol., Vol. 8(1), p. 466-472, 1988); SV40 enhancer; and
the intron sequence between exons 2 and 3 of rabbit .beta.-globin
(Proc. Natl. Acad. Sci. USA., Vol. 78(3), p. 1527-31, 1981). It
will be appreciated by those skilled in the art that the design of
the expression vector can depend on such factors as the choice of
the host cell to be transformed, the level of expression desired,
etc. A vector can be introduced into host cells to thereby produce
transcripts, proteins, or peptides, including fusion proteins or
peptides, encoded by nucleic acids as described herein (e.g.,
clustered regularly interspersed short palindromic repeats (CRISPR)
transcripts, proteins, enzymes, mutant forms thereof, fusion
proteins thereof, etc.).
[0012] Advantageous vectors include lentiviruses and
adeno-associated viruses, and types of such vectors can also be
selected for targeting particular types of cells.
[0013] In one aspect, the invention provides a vector comprising a
regulatory element operably linked to an enzyme-coding sequence
encoding a CRISPR enzyme comprising one or more nuclear
localization sequences. In some embodiments, said regulatory
element drives transcription of the CRISPR enzyme in a eukaryotic
cell such that said CRISPR enzyme accumulates in a detectable
amount in the nucleus of the eukaryotic cell. In some embodiments,
the regulatory element is a polymerase II promoter. In some
embodiments, the CRISPR enzyme is a type II CRISPR system enzyme.
In some embodiments, the CRISPR enzyme is a Cas9 enzyme. In some
embodiments, the Cas9 enzyme is S. pneumoniae, S. pyogenes or S.
thermophilus Cas9, and may include mutated Cas9 derived from these
organisms. In some embodiments, the CRISPR enzyme is
codon-optimized for expression in a eukaryotic cell. In some
embodiments, the CRISPR enzyme directs cleavage of one or two
strands at the location of the target sequence. In some
embodiments, the CRISPR enzyme lacks DNA strand cleavage
activity.
[0014] In one aspect, the invention provides a CRISPR enzyme
comprising one or more nuclear localization sequences of sufficient
strength to drive accumulation of said CRISPR enzyme in a
detectable amount in the nucleus of a eukaryotic cell. In some
embodiments, the CRISPR enzyme is a type II CRISPR system enzyme.
In some embodiments, the CRISPR enzyme is a Cas9 enzyme. In some
embodiments, the Cas9 enzyme is S. pneumoniae, S. pyogenes or S.
thermophilus Cas9, and may include mutated Cas9 derived from these
organisms. The enzyme may be a Cas9 homolog or ortholog. In some
embodiments, the CRISPR enzyme lacks the ability to cleave one or
more strands of a target sequence to which it binds.
[0015] In one aspect, the invention provides a eukaryotic host cell
comprising (a) a first regulatory element operably linked to a
tracr mate sequence and one or more insertion sites for inserting
one or more guide sequences upstream of the tracr mate sequence,
wherein when expressed, the guide sequence directs
sequence-specific binding of a CRISPR complex to a target sequence
in a eukaryotic cell, wherein the CRISPR complex comprises a CRISPR
enzyme complexed with (1) the guide sequence that is hybridized to
the target sequence, and (2) the tracr mate sequence that is
hybridized to the tracr sequence; and/or (b) a second regulatory
element operably linked to an enzyme-coding sequence encoding said
CRISPR enzyme comprising a nuclear localization sequence. In some
embodiments, the host cell comprises components (a) and (b). In
some embodiments, component (a), component (b), or components (a)
and (b) are stably integrated into a genome of the host eukaryotic
cell. In some embodiments, component (a) further comprises the
tracr sequence downstream of the tracr mate sequence under the
control of the first regulatory element. In some embodiments,
component (a) further comprises two or more guide sequences
operably linked to the first regulatory element, wherein when
expressed, each of the two or more guide sequences direct sequence
specific binding of a CRISPR complex to a different target sequence
in a eukaryotic cell. In some embodiments, the eukaryotic host cell
further comprises a third regulatory element, such as a polymerase
III promoter, operably linked to said tracr sequence. In some
embodiments, the tracr sequence exhibits at least 50%, 60%, 70%,
80%, 90%, 95%, or 99% of sequence complementarity along the length
of the tracr mate sequence when optimally aligned. In some
embodiments, the CRISPR enzyme comprises one or more nuclear
localization sequences of sufficient strength to drive accumulation
of said CRISPR enzyme in a detectable amount in the nucleus of a
eukaryotic cell. In some embodiments, the CRISPR enzyme is a type
II CRISPR system enzyme. In some embodiments, the CRISPR enzyme is
a Cas9 enzyme. In some embodiments, the Cas9 enzyme is S.
pneumoniae, S. pyogenes or S. thermophilus Cas9, and may include
mutated Cas9 derived from these organisms. The enzyme may be a Cas9
homolog or ortholog. In some embodiments, the CRISPR enzyme is
codon-optimized for expression in a eukaryotic cell. In some
embodiments, the CRISPR enzyme directs cleavage of one or two
strands at the location of the target sequence. In some
embodiments, the CRISPR enzyme lacks DNA strand cleavage activity.
In some embodiments, the first regulatory element is a polymerase
III promoter. In some embodiments, the second regulatory element is
a polymerase II promoter. In some embodiments, the guide sequence
is at least 15, 16, 17, 18, 19, 20, 25 nucleotides, or between
10-30, or between 15-25, or between 15-20 nucleotides in length. In
an aspect, the invention provides a non-human eukaryotic organism;
preferably a multicellular eukaryotic organism, comprising a
eukaryotic host cell according to any of the described embodiments.
In other aspects, the invention provides a eukaryotic organism;
preferably a multicellular eukaryotic organism, comprising a
eukaryotic host cell according to any of the described embodiments.
The organism in some embodiments of these aspects may be an animal;
for example a mammal. Also, the organism may be an arthropod such
as an insect. The organism also may be a plant. Further, the
organism may be a fungus.
[0016] In one aspect, the invention provides a kit comprising one
or more of the components described herein. In some embodiments,
the kit comprises a vector system and instructions for using the
kit. In some embodiments, the vector system comprises (a) a first
regulatory element operably linked to a tracr mate sequence and one
or more insertion sites for inserting one or more guide sequences
upstream of the tracr mate sequence, wherein when expressed, the
guide sequence directs sequence-specific binding of a CRISPR
complex to a target sequence in a eukaryotic cell, wherein the
CRISPR complex comprises a CRISPR enzyme complexed with (1) the
guide sequence that is hybridized to the target sequence, and (2)
the tracr mate sequence that is hybridized to the tracr sequence;
and/or (b) a second regulatory element operably linked to an
enzyme-coding sequence encoding said CRISPR enzyme comprising a
nuclear localization sequence. In some embodiments, the kit
comprises components (a) and (b) located on the same or different
vectors of the system. In some embodiments, component (a) further
comprises the tracr sequence downstream of the tracr mate sequence
under the control of the first regulatory element. In some
embodiments, component (a) further comprises two or more guide
sequences operably linked to the first regulatory element, wherein
when expressed, each of the two or more guide sequences direct
sequence specific binding of a CRISPR complex to a different target
sequence in a eukaryotic cell. In some embodiments, the system
further comprises a third regulatory element, such as a polymerase
III promoter, operably linked to said tracr sequence. In some
embodiments, the tracr sequence exhibits at least 50%, 60%, 70%,
80%, 90%, 95%, or 99%/0 of sequence complementarity along the
length of the tracr mate sequence when optimally aligned. In some
embodiments, the CRISPR enzyme comprises one or more nuclear
localization sequences of sufficient strength to drive accumulation
of said CRISPR enzyme in a detectable amount in the nucleus of a
eukaryotic cell. In some embodiments, the CRISPR enzyme is a type
II CRISPR system enzyme. In some embodiments, the CRISPR enzyme is
a Cas9 enzyme. In some embodiments, the Cas9 enzyme is S.
pneumoniae, S. pyogenes or S. thermophilus Cas9, and may include
mutated Cas9 derived from these organisms. The enzyme may be a Cas9
homolog or ortholog. In some embodiments, the CRISPR enzyme is
codon-optimized for expression in a eukaryotic cell. In some
embodiments, the CRISPR enzyme directs cleavage of one or two
strands at the location of the target sequence. In some
embodiments, the CRISPR enzyme lacks DNA strand cleavage activity.
In some embodiments, the first regulatory element is a polymerase
III promoter. In some embodiments, the second regulatory element is
a polymerase II promoter. In some embodiments, the guide sequence
is at least 15, 16, 17, 18, 19, 20, 25 nucleotides, or between
10-30, or between 15-25, or between 15-20 nucleotides in
length.
[0017] In one aspect, the invention provides a method of modifying
a target polynucleotide in a eukaryotic cell. In some embodiments,
the method comprises allowing a CRISPR complex to bind to the
target polynucleotide to effect cleavage of said target
polynucleotide thereby modifying the target polynucleotide, wherein
the CRISPR complex comprises a CRISPR enzyme complexed with a guide
sequence hybridized to a target sequence within said target
polynucleotide, wherein said guide sequence is linked to a tracr
mate sequence which in turn hybridizes to a tracr sequence. In some
embodiments, said cleavage comprises cleaving one or two strands at
the location of the target sequence by said CRISPR enzyme. In some
embodiments, said cleavage results in decreased transcription of a
target gene. In some embodiments, the method further comprises
repairing said cleaved target polynucleotide by homologous
recombination with an exogenous template polynucleotide, wherein
said repair results in a mutation comprising an insertion,
deletion, or substitution of one or more nucleotides of said target
polynucleotide. In some embodiments, said mutation results in one
or more amino acid changes in a protein expressed from a gene
comprising the target sequence. In some embodiments, the method
further comprises delivering one or more vectors to said eukaryotic
cell, wherein the one or more vectors drive expression of one or
more of: the CRISPR enzyme, the guide sequence linked to the tracr
mate sequence, and the tracr sequence. In some embodiments, said
vectors are delivered to the eukaryotic cell in a subject. In some
embodiments, said modifying takes place in said eukaryotic cell in
a cell culture. In some embodiments, the method further comprises
isolating said eukaryotic cell from a subject prior to said
modifying. In some embodiments, the method further comprises
returning said eukaryotic cell and/or cells derived therefrom to
said subject.
[0018] In one aspect, the invention provides a method of modifying
expression of a polynucleotide in a eukaryotic cell. In some
embodiments, the method comprises allowing a CRISPR complex to bind
to the polynucleotide such that said binding results in increased
or decreased expression of said polynucleotide; wherein the CRISPR
complex comprises a CRISPR enzyme complexed with a guide sequence
hybridized to a target sequence within said polynucleotide, wherein
said guide sequence is linked to a tracr mate sequence which in
turn hybridizes to a tracr sequence. In some embodiments, the
method further comprises delivering one or more vectors to said
eukaryotic cells, wherein the one or more vectors drive expression
of one or more of: the CRISPR enzyme, the guide sequence linked to
the tracr mate sequence, and the tracr sequence.
[0019] In one aspect, the invention provides a method of generating
a model eukaryotic cell comprising a mutated disease gene. In some
embodiments, a disease gene is any gene associated an increase in
the risk of having or developing a disease. In some embodiments,
the method comprises (a) introducing one or more vectors into a
eukaryotic cell, wherein the one or more vectors drive expression
of one or more of: a CRISPR enzyme, a guide sequence linked to a
tracr mate sequence, and a tracr sequence, and (b) allowing a
CRISPR complex to bind to a target polynucleotide to effect
cleavage of the target polynucleotide within said disease gene,
wherein the CRISPR complex comprises the CRISPR enzyme complexed
with (1) the guide sequence that is hybridized to the target
sequence within the target polynucleotide, and (2) the tracr mate
sequence that is hybridized to the tracr sequence, thereby
generating a model eukaryotic cell comprising a mutated disease
gene. In some embodiments, said cleavage comprises cleaving one or
two strands at the location of the target sequence by said CRISPR
enzyme. In some embodiments, said cleavage results in decreased
transcription of a target gene. In some embodiments, the method
further comprises repairing said cleaved target polynucleotide by
homologous recombination with an exogenous template polynucleotide,
wherein said repair results in a mutation comprising an insertion,
deletion, or substitution of one or more nucleotides of said target
polynucleotide. In some embodiments, said mutation results in one
or more amino acid changes in a protein expression from a gene
comprising the target sequence.
[0020] In one aspect, the invention provides a method for
developing a biologically active agent that modulates a cell
signaling event associated with a disease gene. In some
embodiments, a disease gene is any gene associated an increase in
the risk of having or developing a disease. In some embodiments,
the method comprises (a) contacting a test compound with a model
cell of any one of the described embodiments; and (b) detecting a
change in a readout that is indicative of a reduction or an
augmentation of a cell signaling event associated with said
mutation in said disease gene, thereby developing said biologically
active agent that modulates said cell signaling event associated
with said disease gene.
[0021] In one aspect, the invention provides a recombinant
polynucleotide comprising a guide sequence upstream of a tracr mate
sequence, wherein the guide sequence when expressed directs
sequence-specific binding of a CRISPR complex to a corresponding
target sequence present in a eukaryotic cell. In some embodiments,
the target sequence is a viral sequence present in a eukaryotic
cell. In some embodiments, the target sequence is a proto-oncogene
or an oncogene.
[0022] In one aspect the invention provides for a method of
selecting one or more prokaryotic cell(s) by introducing one or
more mutations in a gene in the one or more prokaryotic cell (s),
the method comprising: introducing one or more vectors into the
prokaryotic cell (s), wherein the one or more vectors drive
expression of one or more of: a CRISPR enzyme, a guide sequence
linked to a tracr mate sequence, a tracr sequence, and a editing
template; wherein the editing template comprises the one or more
mutations that abolish CRISPR enzyme cleavage; allowing homologous
recombination of the editing template with the target
polynucleotide in the cell(s) to be selected; allowing a CRISPR
complex to bind to a target polynucleotide to effect cleavage of
the target polynucleotide within said gene, wherein the CRISPR
complex comprises the CRISPR enzyme complexed with (1) the guide
sequence that is hybridized to the target sequence within the
target polynucleotide, and (2) the tracr mate sequence that is
hybridized to the tracr sequence, wherein binding of the CRISPR
complex to the target polynucleotide induces cell death, thereby
allowing one or more prokaryotic cell(s) in which one or more
mutations have been introduced to be selected. In a preferred
embodiment, the CRISPR enzyme is Cas9. In another aspect of the
invention the cell to be selected may be a eukaryotic cell. Aspects
of the invention allow for selection of specific cells without
requiring a selection marker or a two-step process that may include
a counter-selection system.
[0023] Accordingly, it is an object of the invention not to
encompass within the invention any previously known product,
process of making the product, or method of using the product such
that Applicants reserve the right and hereby disclose a disclaimer
of any previously known product, process, or method. It is further
noted that the invention does not intend to encompass within the
scope of the invention any product, process, or making of the
product or method of using the product, which does not meet the
written description and enablement requirements of the USPTO (35
U.S.C. .sctn.112, first paragraph) or the EPO (Article 83 of the
EPC), such that Applicants reserve the right and hereby disclose a
disclaimer of any previously described product, process of making
the product, or method of using the product.
[0024] It is noted that in this disclosure and particularly in the
claims and/or paragraphs, terms such as "comprises", "comprised",
"comprising" and the like can have the meaning attributed to it in
U.S. Patent law; e.g., they can mean "includes", "included",
"including", and the like; and that terms such as "consisting
essentially of" and "consists essentially of" have the meaning
ascribed to them in U.S. Patent law, e.g., they allow for elements
not explicitly recited, but exclude elements that are found in the
prior art or that affect a basic or novel characteristic of the
invention. These and other embodiments are disclosed or are obvious
from and encompassed by, the following Detailed Description.
BRIEF DESCRIPTION OF THE DRAWINGS
[0025] The novel features of the invention are set forth with
particularity in the appended claims. A better understanding of the
features and advantages of the present invention will be obtained
by reference to the following detailed description that sets forth
illustrative embodiments, in which the principles of the invention
are utilized, and the accompanying drawings of which:
[0026] FIG. 1 shows a schematic model of the CRISPR system. The
Cas9 nuclease from Streptococcus pyogenes (yellow) is targeted to
genomic DNA by a synthetic guide RNA (sgRNA) consisting of a 20-nt
guide sequence (blue) and a scaffold (red). The guide sequence
base-pairs with the DNA target (blue), directly upstream of a
requisite 5'-NGG protospacer adjacent motif (PAM; magenta), and
Cas9 mediates a double-stranded break (DSB) .about.3 bp upstream of
the PAM (red triangle).
[0027] FIG. 2A-2F shows an exemplary CRISPR system and a possible
mechanism of action (FIG. 2A), an example adaptation for expression
in eukaryotic cells (FIG. 2B) and results of tests assessing
nuclear localization and CRISPR activity (FIG. 2D). FIG. 2C
discloses SEQ ID NOS 279-280, respectively, in order of appearance.
FIG. 2E discloses SEQ ID NOS 281-283, respectively, in order of
appearance, and FIG. 2F discloses SEQ ID NOS 284-288, respectively,
in order of appearance.
[0028] FIG. 3A-3C show an exemplary expression cassette for
expression of CRISPR system elements in eukaryotic cells (FIG. 3A),
predicted structures of example guide sequences (FIG. 3B), and
CRISPR system activity as measured in eukaryotic and prokaryotic
cells (SEQ ID NOS 289-298, respectively, in order of appearance)
(FIG. 3C).
[0029] FIG. 4A-4D shows results of an evaluation of SpCas9
specificity for an example target. FIG. 4A discloses SEQ ID NOS
299, 282 and 300-310, respectively, in order of appearance. FIG. 4C
discloses SEQ ID NO: 299, 282 and 300-310, respectively, in order
of appearance. FIG. 4C discloses SEQ ID NO: 299. FIGS. 4B and 4D
show the results of the evaluation of SpCas9 specificity for the
example target.
[0030] FIG. 5A-5G show an exemplary vector system (FIGS. 5A and 5C)
and results for use in directing homologous recombination in
eukaryotic cells (FIGS. 5B and 5D). FIG. 5E discloses SEQ ID NO:
311. FIG. 5F discloses SEQ ID NOS 312-313, respectively, in order
of appearance. FIG. 5G discloses SEQ ID NOS 314-318, respectively,
in order of appearance.
[0031] FIG. 6 provides a table of protospacer sequences (SEQ ID NOS
33, 32, 31, 322-327, 35, 34 and 330-334, respectively, in order of
appearance) and summarizes modification efficiency results for
protospacer targets designed based on exemplary S. pyogenes and S.
thermophilus CRISPR systems with corresponding PAMs against loci in
human and mouse genomes. Cells were transfected with Cas9 and
either pre-crRNA/tracrRNA or chimeric RNA, and analyzed 72 hours
after transfection. Percent indels are calculated based on Surveyor
assay results from indicated cell lines (N=3 for all protospacer
targets, errors are S.E.M., N.D. indicates not detectable using the
Surveyor assay, and N.T. indicates not tested in this study).
[0032] FIG. 7A-7C shows a comparison of different tracrRNA
transcripts for Cas9-mediated gene targeting (FIGS. 7B-7C). FIG. 7A
discloses SEQ ID NOS 335-336, respectively, in order of
appearance.
[0033] FIG. 8 shows a schematic of a surveyor nuclease assay for
detection of double strand break-induced micro-insertions and
-deletions.
[0034] FIG. 9A-9B shows exemplary bicistronic expression vectors
for expression of CRISPR system elements in eukaryotic cells. FIG.
9A discloses SEQ ID NOS 337-339, respectively, in order of
appearance. FIG. 9B discloses SEQ ID NOS 344-342, respectively, in
order of appearance.
[0035] FIG. 10A-10D shows a bacterial plasmid transformation
interference assay (FIG. 10C), expression cassettes and plasmids
(FIG. 10B) used therein, and transformation efficiencies of cells
used therein (FIG. 10D). FIG. 10A discloses SEQ ID NOS 343-345,
respectively, in order of appearance.
[0036] FIG. 11A-11C shows histograms of distances between adjacent
S. pyogenes SF370 locus 1 PAM (NGG) (FIG. 11A) and S. thermophilus
LMD9 locus 2 PAM (NNAGAAW) (FIG. 11B) in the human genome; and
distances for each PAM by chromosome (Chr) (FIG. 1C).
[0037] FIG. 12A-12C shows an exemplary CRISPR system (FIG. 12A), an
example adaptation for expression in eukaryotic cells (FIG. 12B),
and results of tests assessing CRISPR activity. FIG. 12B discloses
SEQ ID NOS 346-347, respectively, in order of appearance. FIG. 12C
discloses SEQ ID NO: 348.
[0038] FIG. 13A-13C shows exemplary manipulations and results (FIG.
13C) of a CRISPR system for targeting of genomic loci in mammalian
cells. FIG. 13A discloses SEQ ID NO: 349. FIG. 13B discloses SEQ ID
NOS 350-352, respectively, in order of appearance.
[0039] FIG. 14A-14B shows the results of a Northern blot analysis
of crRNA processing in mammalian cells (FIG. 14B). FIG. 14A
discloses SEQ ID NO: 353.
[0040] FIG. 15A-15B shows an exemplary selection of protospacers in
the human PVALB and mouse Th loci. FIG. 15A discloses SEQ ID NO:
354. FIG. 15B discloses SEQ ID NO: 355.
[0041] FIG. 16 shows example protospacer and corresponding PAM
sequence targets of the S. thermophilus CRISPR system in the human
EMX1 locus (SEQ ID NO: 348).
[0042] FIG. 17 provides a table of sequences for primers and probes
(SEQ ID NOS 36-39 and 356-363, respectively, in order of
appearance) used for Surveyor, RFLP, genomic sequencing, and
Northern blot assays.
[0043] FIG. 18A-18C shows exemplary manipulation of a CRISPR system
with chimeric RNAs and results of SURVEYOR assays for system
activity in eukaryotic cells (FIGS. 18B and 18C). FIG. 18A
discloses SEQ ID NO: 364.
[0044] FIG. 19A-19B shows two graphical representations of the
results of SURVEYOR assays for CRISPR system activity in eukaryotic
cells (SEQ ID NOS 365-443, respectively, in order of
appearance).
[0045] FIG. 20 shows an exemplary visualization of some S. pyogenes
Cas9 target sites in the human genome using the UCSC genome
browser.
[0046] FIG. 21 shows predicted secondary structures for exemplary
chimeric RNAs comprising a guide sequence, tracr mate sequence, and
tracr sequence (SEQ ID NOS 444-463, respectively, in order of
appearance).
[0047] FIG. 22 shows exemplary bicistronic expression vectors for
expression of CRISPR system elements in eukaryotic cells (SEQ ID
NOS 464 and 341-342, respectively, in order of appearance).
[0048] FIG. 23A-23B shows that Cas9 nuclease activity against
endogenous targets may be exploited for genome editing. (a) Concept
of genome editing using the CRISPR system. The CRISPR targeting
construct directed cleavage of a chromosomal locus and was
co-transformed with an editing template that recombined with the
target to prevent cleavage. Kanamycin-resistant transformants that
survived CRISPR attack contained modifications introduced by the
editing template. tracr, trans-activating CRISPR RNA; aphA-3,
kanamycin resistance gene. (b) Transformation of crR6M DNA in
R6.sup.82325 cells with no editing template, the R6 wild-type srtA
or the R6370.1 editing templates. Recombination of either R6 srtA
or R6.sup.370.1 prevented cleavage by Cas9. Transformation
efficiency was calculated as colony forming units (cfu) per .mu.g
of crR6M DNA; the mean values with standard deviations from at
least three independent experiments are shown. PCR analysis was
performed on 8 clones in each transformation. "Un." indicates the
unedited srtA locus of strain R6.sup.8232.5; "Ed." shows the
editing template. R6.sup.8232.5 and R6.sup.370.1 targets are
distinguished by restriction with EaeI.
[0049] FIG. 24A-24C shows analysis of PAM and seed sequences that
eliminate Cas9 cleavage. (a) PCR products with randomized PAM
sequences or randomized seed sequences were transformed in crR6
cells (SEQ ID NOS 465-469, respectively, in order of appearance).
These cells expressed Cas9 loaded with a crRNA that targeted a
chromosomal region of R6.sup.8232.5 cells (highlighted in pink)
that is absent from the R6 genome. More than 2.times.105
chloramphenicol-resistant transformants, carrying inactive PAM or
seed sequences, were combined for amplification and deep sequencing
of the target region. (b) Relative proportion of number of reads
after transformation of the random PAM constructs in crR6 cells
(compared to number of reads in R6 transformants). The relative
abundance for each 3-nucleotide PAM sequence is shown. Severely
underrepresented sequences (NGG) are shown in red; partially
underrepresented one in orange (NAG) (c) Relative proportion of
number of reads after transformation of the random seed sequence
constructs in crR6 cells (compared to number of reads in R6
transformants). The relative abundance of each nucleotide for each
position of the first 20 nucleotides of the protospacer sequence is
shown (SEQ ID NO: 470). High abundance indicates lack of cleavage
by Cas9, i.e. a CRISPR inactivating mutation. The grey line shows
the level of the WT sequence. The dotted line represents the level
above which a mutation significantly disrupts cleavage (See section
"Analysis of deep sequencing data" in Example 5)
[0050] FIG. 25A-25F shows introduction of single and multiple
mutations using the CRISPR system in S. pneumoniae. (a) Nucleotide
and amino acid sequences of the wild-type and edited (green
nucleotides; underlined amino acid residues) bgaA. The protospacer,
PAM and restriction sites are shown (SEQ ID NOS 471-475 and 472,
respectively, in order of appearance). (b) Transformation
efficiency of cells transformed with targeting constructs in the
presence of an editing template or control. (c) PCR analysis for 8
transformants of each editing experiment followed by digestion with
BtgZI (R.fwdarw.A) and TseI (NE.fwdarw.AA). Deletion of bgaA was
revealed as a smaller PCR product. (d) Miller assay to measure the
.beta.-galactosidase activity of WT and edited strains. (e) For a
single-step, double deletion the targeting construct contained two
spacers (in this case matching srtA and bgaA) and was
co-transformed with two different editing templates (f) PCR
analysis for 8 transformants to detect deletions in srtA and bgaA
loci. 6/8 transformants contained deletions of both genes.
[0051] FIG. 26A-26D provides mechanisms underlying editing using
the CRISPR system. (a) A stop codon was introduced in the
erythromycin resistance gene ermAM to generate strain JEN53. The
wild-type sequence can be restored by targeting the stop codon with
the CRISPR::ermAM (stop) construct, and using the ermAM wild-type
sequence as an editing template. (b) Mutant and wild-type ermAAM
sequences (SEQ ID NOS 476-479, respectively, in order of
appearance). (c) Fraction of erythromicyn-resistant (erm.sup.R) cfu
calculated from total or kanamycin-resistant (kan.sup.R) cfu. (d)
Fraction of total cells that acquire both the CRISPR construct and
the editing template. Co-transformation of the CRISPR targeting
construct produced more transformants (t-test, p=0.011). In all
cases the values show the mean.+-.s.d. for three independent
experiments.
[0052] FIG. 27A-27D illustrates genome editing with the CRISPR
system in E. coli. (a) A kanamycin-resistant plasmid carrying the
CRISPR array (pCRISPR) targeting the gene to edit may be
transformed in the HME63 recombineering strain containing a
chloramphenicol-resistant plasmid harboring cas9 and tracr (pCas9),
together with an oligonucleotide specifying the mutation. (b) A
K42T mutation conferring streptomycin resistance was introduced in
the rpsL gene (SEQ ID NOS 480-483, respectively, in order of
appearance) (c) Fraction of streptomicyn-resistant (strep.sup.R)
cfu calculated from total or kanamycin-resistant (kan.sup.R) cfu.
(d) Fraction of total cells that acquire both the pCRISPR plasmid
and the editing oligonucleotide. Co-transformation of the pCRISPR
targeting plasmid produced more transformants (t-test,
p=0.00.sup.4). In all cases the values showed the mean.+-.s.d. for
three independent experiments.
[0053] FIG. 28A-28B illustrates the transformation of crR6 genomic
DNA leads to editing of the targeted locus (a) The IS1167 element
of S. pneumoniae R6 was replaced by the CRISPR01 locus of S.
pyogenes SF370 to generate crR6 strain. This locus encodes for the
Cas9 nuclease, a CRISPR array with six spacers, the tracrRNA that
is required for crRNA biogenesis and Cas1, Cas2 and Csn2, proteins
not necessary for targeting. Strain crR6M contains a minimal
functional CRISPR system without cas1, cas2 and csn2. The aphA-3
gene encodes kanamycin resistance. Protospacers from the
streptococcal bacteriophages 8232.5 and 370.1 were fused to a
chloramphenicol resistance gene (cat) and integrated in the srtA
gene of strain R6 to generate strains R68232.5 and R6370.1. (b)
Left panel: Transformation of crR6 and crR6M genomic DNA in
R6.sup.8232.5 and R6370.1. As a control of cell competence a
streptomycin resistant gene was also transformed. Right panel: PCR
analysis of 8 R6.sup.8232.5 transformants with crR6 genomic DNA.
Primers that amplify the srtA locus were used for PCR. 7/8
genotyped colonies replaced the R68232.5 srtA locus by the WT locus
from the crR6 genomic DNA.
[0054] FIG. 29A-29F provides chromatograms of DNA sequences of
edited cells obtained in this study. In all cases the wild-type and
mutant protospacer and PAM sequences (or their reverse complement)
are indicated. When relevant, the amino acid sequence encoded by
the protospacer is provided. For each editing experiment, all
strains for which PCR and restriction analysis corroborated the
introduction of the desired modification were sequenced. A
representative chromatogram is shown. (a) Chromatogram for the
introduction of a PAM mutation into the R6.sup.8232.5 target (FIG.
23d) (SEQ ID NOS 484-485, respectively, in order of appearance).
(b) Chromatograms for the introduction of the R>A and NE>AA
mutations into .beta.-galactosidase (bgaA) (FIG. 25c) (SEQ ID NOS
471-475 and 472, respectively, in order of appearance). (c)
Chromatogram for the introduction of a 6664 bp deletion within bgaA
ORF (FIGS. 25c and 25f). The dotted line indicates the limits of
the deletion (SEQ ID NOS 486-488, respectively, in order of
appearance). (d) Chromatogram for the introduction of a 729 bp
deletion within srtA ORF (FIG. 25f). The dotted line indicates the
limits of the deletion (SEQ ID NOS 489-491, respectively, in order
of appearance). (e) Chromatograms for the generation of a premature
stop codon within ermAM (FIG. 33) (SEQ ID NOS 492-495,
respectively, in order of appearance). (f) rpsL editing in E. coli
(FIG. 27) (SEQ ID NOS 480-483, respectively, in order of
appearance).
[0055] FIG. 30A-30C illustrates CRISPR immunity against random S.
pneumoniae targets containing different PAMs. (a) Position of the
10 random targets on the S. pneumoniae R6 genome. The chosen
targets have different PAMs and are on both strands. (b) Spacers
corresponding to the targets were cloned in a minimal CRISPR array
on plasmid pLZ12 and transformed into strain crR6Rc, which supplies
the processing and targeting machinery in trans. (c) Transformation
efficiency of the different plasmids in strain R6 and crR6Rc. No
colonies were recovered for the transformation of pDB99-108
(T1-T10) in crR6Rc. The dashed line represents limit of detection
of the assay.
[0056] FIG. 31 provides a general scheme for targeted genome
editing. To facilitate targeted genome editing, crR6M was further
engineered to contain tracrRNA, Cas9 and only one repeat of the
CRISPR array followed by kanamycin resistance marker (aphA-3),
generating strain crR6Rk. DNA from this strain is used as a
template for PCR with primers designed to introduce a new spacer
(green box designated with N). The left and right PCRs are
assembled using the Gibson method to create the targeting
construct. Both the targeting and editing constructs are then
transformed into strain crR6Rc, which is a strain equivalent to
crR6Rk but has the kanamycin resistance marker replaced by a
chloramphenicol resistance marker (cat). About 90% of the
kanamycin-resistant transformants contain the desired mutation.
[0057] FIG. 32 illustrates the distribution of distances between
PAMs. NGG and CCN that are considered to be valid PAMs. Data is
shown for the S. pneumoniae R6 genome as well as for a random
sequence of the same length and with the same GC-content (39.7%).
The dotted line represents the average distance (12) between PAMs
in the R6 genome.
[0058] FIG. 33A-33D illustrates CRISPR-mediated editing of the
ermAM locus using genomic DNA as targeting construct. To use
genomic DNA as targeting construct it is necessary to avoid CRISPR
autoimmunity, and therefore a spacer against a sequence not present
in the chromosome must be used (in this case the ermAM erythromycin
resistance gene). (a) Nucleotide and amino acid sequences of the
wild-type and mutated (red letters) ermAM gene. The protospacer and
PAM sequences are shown (SEQ ID NOS 492-495, respectively, in order
of appearance). (b) A schematic for CRISPR-mediated editing of the
ermAM locus using genomic DNA. A construct carrying an
ermAM-targeting spacer (blue box) is made by PCR and Gibson
assembly, and transformed into strain crR6Rc, generating strain
JEN37. The genomic DNA of JEN37 was then used as a targeting
construct, and was co-transformed with the editing template into
JEN38, a strain in which the srtA gene was replaced by a wild-type
copy of ermAM. Kanamycin-resistant transformants contain the edited
genotype (JEN43). (c) Number of kanamycin-resistant cells obtained
after co-transformation of targeting and editing or control
templates. In the presence of the control template
5.4.times.10.sup.3; cfu/ml were obtained, and 4.3.times.10.sup.5
cfu/ml when the editing template was used. This difference
indicates an editing efficiency of about 99%
[(4.3.times.10.sup.5-5.4.times.10)/4.3.times.10]. (d) To check for
the presence of edited cells seven kanamycin-resistant clones and
JEN38 were streaked on agar plates with (erm+) or without (erm-)
erythromycin. Only the positive control displayed resistance to
erythromycin. The ermAM mut genotype of one of these transformants
was also verified by DNA sequencing (FIG. 29e).
[0059] FIG. 34A-34D illustrates sequential introduction of
mutations by CRISPR-mediated genome editing. (a) A schematic for
sequential introduction of mutations by CRISPR-mediated genome
editing. First, R6 is engineered to generate crR6Rk. crR6Rk is
co-transformed with a srtA-targeting construct fused to cat for
chloramphenicol selection of edited cells, along with an editing
construct for a .DELTA.srtA in-frame deletion. Strain crR6
.DELTA.srtA is generated by selection on chlramphenicol.
Subsequently, the .DELTA.srtA strain is co-transformed with a
bgaA-targeting construct fused to aphA-3 for kanamycin selection of
edited cells, and an editing construct containing a .DELTA.bgaA
in-frame deletion. Finally, the engineered CRISPR locus can be
erased from the chromosome by first co-transforming R6 DNA
containing the wild-type IS1167 locus and a plasmid carrying a bgaA
protospacer (pDB97), and selection on spectinomycin. (b) PCR
analysis for 8 chloramphenicol (Cam)-resistant transformants to
detect the deletion in the srtA locus. (c) .beta.-galactosidase
activity as measured by Miller assay. In S. pneumoniae, this enzyme
is anchored to the cell wall by sortase A. Deletion of the srtA
gene results in the release of .beta.-galactosidase into the
supernatant. .DELTA.bgaA mutants show no activity. (d) PCR analysis
for 8 spectinomycin (Spec)-resistant transformants to detect the
replacement of the CRISPR locus by wild-type IS1167.
[0060] FIG. 35A-35C illustrates the background mutation frequency
of CRISPR in S. pneumoniae. (a) Transformation of the CRISPR::O or
CRISPR::erm (stop) targeting constructs in JEN53, with or without
the ermAM editing template. The difference in kan.sup.R CFU between
CRISPR::O and CRISPR::erm (stop) indicates that Cas9 cleavage kills
non-edited cells. Mutants that escape CRISPR interference in the
absence of editing template are observed at a frequency of
3.times.10.sup.-3. (b) PCR analysis of the CRISPR locus of escapers
shows that 7/8 have a spacer deletion. (c) Escaper #2 carries a
point mutation in cas9 (SEQ ID NOS 496-499, respectively, in order
of appearance).
[0061] FIG. 36 illustrates that the essential elements of the S.
pyogenes CRISPR locus 1 are reconstituted in E. coli using pCas9.
The plasmid contained tracrRNA, Cas9, as well as a leader sequence
driving the crRNA array. The pCRISPR plasmids contained the leader
and the array only. Spacers may be inserted into the crRNA array
between BsaI sites using annealed oligonucleotides (SEQ ID NOS 343,
500 and 127, respectively, in order of appearance). Oligonucleotide
design is shown at bottom. pCas9 carried chloramphenicol resistance
(CmR) and is based on the low-copy pACYC184 plasmid backbone.
pCRISPR is based on the high-copy number pZE21 plasmid. Two
plasmids were required because a pCRISPR plasmid containing a
spacer targeting the E. coli chromosome may not be constructed
using this organism as a cloning host if Cas9 is also present (it
will kill the host).
[0062] FIG. 37 illustrates CRISPR-directed editing in E. coli
MG1655. An oligonucleotide (W542) carrying a point mutation that
both confers streptomycin resistance and abolishes CRISPR immunity,
together with a plasmid targeting rpsL (pCRISPR::rpsL) or a control
plasmid (pCRISPR::O) were co-transformed into wild-type E. coli
strain MG1655 containing pCas9. Transformants were selected on
media containing either streptomycin or kanamycin. Dashed line
indicates limit of detection of the transformation assay.
[0063] FIG. 38A-38B illustrates the background mutation frequency
of CRISPR in E. coli HME63. (a) Transformation of the pCRISPR::O or
pCRISPR::rpsL plasmids into HME63 competent cells. Mutants that
escape CRISPR interference were observed at a frequency of
2.6.times.10.sup.-4. (b) Amplification of the CRISPR array of
escapers showed that 8/8 have deleted the spacer.
[0064] FIG. 39A-39D shows a circular depiction of the phylogenetic
analysis revealing five families of Cas9s, including three groups
of large Cas9s (.about.1400 amino acids) and two of small Cas9s
(.about.1100 amino acids).
[0065] FIG. 40A-40F shows the linear depiction of the phylogenetic
analysis revealing five families of Cas9s, including three groups
of large Cas9s (.about.1400 amino acids) and two of small Cas9s
(.about.1100 amino acids).
[0066] FIG. 41A-41M shows sequences where the mutation points are
located within the SpCas9 gene (SEQ ID NOS 501-502, respectively,
in order of appearance).
[0067] FIG. 42 shows a schematic construct in which the
transcriptional activation domain (VP64) is fused to Cas9 with two
mutations in the catalytic domains (D10 and H840).
[0068] FIG. 43A-43D shows genome editing via homologous
recombination. (a) Schematic of SpCas9 nickase, with D10A mutation
in the RuvC 1 catalytic domain. (b) Schematic representing
homologous recombination (HR) at the human EMX1 locus using either
sense or antisense single stranded oligonucleotides as repair
templates. Red arrow above indicates sgRNA cleavage site; PCR
primers for genotyping (Tables J and K) are indicated as arrows in
right panel. (c) Sequence of region modified by HR. d, SURVEYOR
assay for wildtype (wt) and nickase (D10A) SpCas9-mediated indels
at the EMX1 target 1 locus (n=3) (SEQ ID NOS 503-505, 503, 506 and
505, respectively, in order of appearance). Arrows indicate
positions of expected fragment sizes.
[0069] FIG. 44A-44B shows single vector designs for SpCas9. FIG.
44A discloses SEQ ID NOS 320-321 and 328, respectively, in order of
appearance. FIG. 44B discloses SEQ ID NO: 329.
[0070] FIG. 45 shows quantification of cleavage of NLS-Csn1
constructs NLS-Csn1, Csn1, Csn1-NLS, NLS-Csn1-NLS, NLS-Csn1-GFP-NLS
and UnTFN.
[0071] FIG. 46 shows index frequency of NLS-Cas9, Cas9, Cas9-NLS
and NLS-Cas9-NLS.
[0072] FIG. 47 shows a gel demonstrating that SpCas9 with nickase
mutations (individually) do not induce double strand breaks.
[0073] FIG. 48A-48B shows a design of the oligo DNA used as
Homologous Recombination (HR) template in this experiment (FIG.
48A) and a comparison of HR efficiency induced by different
combinations of Cas9 protein and HR template (FIG. 48B).
[0074] FIG. 49A shows the Conditional Cas9, Rosa26 targeting vector
map.
[0075] FIG. 49B shows the Constitutive Cas9, Rosa26 targeting
vector map.
[0076] FIG. 50A-50H show the sequences of each element present in
the vector maps of FIGS. 49A-B (SEQ ID NOS 507-516, respectively,
in order of appearance).
[0077] FIG. 51 shows a schematic of the important elements in the
Constitutive and Conditional Cas9 constructs.
[0078] FIG. 52 shows the functional validation of the expression of
Constitutive and Conditional Cas9 constructs.
[0079] FIG. 53 shows the validation of Cas9 nuclease activity by
Surveyor.
[0080] FIG. 54 shows the quantification of Cas9 nuclease
activity.
[0081] FIG. 55 shows construct design and homologous recombination
(HR) strategy.
[0082] FIG. 56 shows the genomic PCR genotyping results for the
constitutive (Right) and conditional (Left) constructs at two
different gel exposure times (top row for 3 min and bottom row for
1 min).
[0083] FIG. 57 shows Cas9 activation in mESCs.
[0084] FIG. 58 shows a schematic of the strategy used to mediate
gene knockout via NHEJ using a nickase version of Cas9 along with
two guide RNAs.
[0085] FIG. 59 shows how DNA double-strand break (DSB) repair
promotes gene editing. In the error-prone non-homologous end
joining (NHEJ) pathway, the ends of a DSB are processed by
endogenous DNA repair machineries and rejoined together, which can
result in random insertion/deletion (indel) mutations at the site
of junction. Indel mutations occurring within the coding region of
a gene can result in frame-shift and a premature stop codon,
leading to gene knockout. Alternatively, a repair template in the
form of a plasmid or single-stranded oligodeoxynucleotides (ssODN)
can be supplied to leverage the homology-directed repair (HDR)
pathway, which allows high fidelity and precise editing.
[0086] FIG. 60 shows the timeline and overview of experiments.
Steps for reagent design, construction, validation, and cell line
expansion. Custom sgRNAs (light blue bars) for each target, as well
as genotyping primers, are designed in silico via our online design
tool (available at the website genome-engineering.org/tools). sgRNA
expression vectors are then cloned into a plasmid containing Cas9
(PX330) and verified via DNA sequencing. Completed plasmids
(pCRISPRs), and optional repair templates for facilitating homology
directed repair, are then transfected into cells and assayed for
ability to mediate targeted cleavage. Finally, transfected cells
can be clonally expanded to derive isogenic cell lines with defined
mutations.
[0087] FIG. 61A-61C shows Target selection and reagent preparation.
(a) For S. pyogenes Cas9, 20-bp targets (highlighted in blue) must
be followed by 5'-NGG, which can occur in either strand on genomic
DNA. We recommend using the online tool described in this protocol
in aiding target selection (www.genome-engineering.org/tools). (b)
Schematic for co-transfection of Cas9 expression plasmid (PX165)
and PCR-amplified U6-driven sgRNA expression cassette. Using a U6
promoter-containing PCR template and a fixed forward primer (U6
Fwd), sgRNA-encoding DNA can appended onto the U6 reverse primer
(U6 Rev) and synthesized as an extended DNA oligo (Ultramer oligos
from IDT). Note the guide sequence (blue N's) in U6 Rev is the
reverse complement of the 5'-NGG flanking target sequence (SEQ ID
NOS 517 and 517-519, respectively, in order of appearance). (c)
Schematic for scarless cloning of the guide sequence oligos into a
plasmid containing Cas9 and sgRNA scaffold (PX330). The guide
oligos (blue N's) contain overhangs for ligation into the pair of
BbsI sites on PS330, with the top and bottom strand orientations
matching those of the genomic target (i.e. top oligo is the 20-bp
sequence preceding 5'-NGG in genomic DNA). Digestion of PX330 with
BbsI allows the replacement of the Type IIs restriction sites (blue
outline) with direct insertion of annealed oligos. It is worth
noting that an extra G was placed before the first base of the
guide sequence. Applicants have found that an extra G in front of
the guide sequence does not adversely affect targeting efficiency.
In cases when the 20-nt guide sequence of choice does not begin
with guanine, the extra guanine will ensure the sgRNA is
efficiently transcribed by the U6 promoter, which prefers a guanine
in the first base of the transcript (SEQ ID NOS 320-321 and 328,
respectively, in order of appearance).
[0088] FIG. 62A-62D shows the anticipated results for multiplex
NHEJ. (a) Schematic of the SURVEYOR assay used to determine indel
percentage. First, genomic DNA from the heterogeneous population of
Cas9-targeted cells is amplified by PCR. Amplicons are then
reannealed slowly to generate heteroduplexes. The reannealed
heteroduplexes are cleaved by SURVEYOR nuclease, whereas
homoduplexes are left intact. Cas9-mediated cleavage efficiency (%
indel) is calculated based on the fraction of cleaved DNA, as
determined by integrated intensity of gel bands. (b) Two sgRNAs
(orange and blue bars) are designed to target the human GRIN2B and
DYRK1A loci. SURVEYOR gel shows modification at both loci in
transfected cells. Colored arrows indicated expected fragment sizes
for each locus. (c) A pair of sgRNAs (light blue and green bars)
are designed to excise an exon (dark blue) in the human EMX1 locus.
Target sequences and PAMs (red) are shown in respective colors, and
sites of cleavage indicated by red triangle. Predicted junction is
shown below. Individual clones isolated from cell populations
transfected with sgRNA 3, 4, or both are assayed by PCR (OUT Fwd,
OUT Rev), reflecting a deletion of .about.270-bp. Representative
clones with no modification (12/23), mono-allelic (10/23), and
bi-allelic (1/23) modifications are shown. IN Fwd and IN Rev
primers are used to screen for inversion events (FIG. 6d) (SEQ ID
NOS 520-522, respectively, in order of appearance). (d)
Quantification of clonal lines with EMX1 exon deletions. Two pairs
of sgRNAs (3.1, 3.2 left-flanking sgRNAs; 4.1, 4.2, right flanking
sgRNAs) are used to mediate deletions of variable sizes around one
EMX1 exon. Transfected cells are clonally isolated and expanded for
genotyping analysis for deletions and inversion events. Of the 105
clones are screened, 51 (49%) and 11 (10%) carrying heterozygous
and homozygous deletions, respectively. Approximate deletion sizes
are given since junctions may be variable.
[0089] FIG. 63A-63C shows the application of ssODNs and targeting
vectors (FIG. 63A) to mediate HR with both wildtype and nickase
mutant of Cas9 in HEK293FT and HUES9 cells with efficiencies
ranging from 1.0-27% (FIG. 63C). FIG. 63B discloses SEQ ID NOS
503-505, 503, 506 and 505, respectively, in order of
appearance.
[0090] FIG. 64 shows a schematic of a PCR-based method for rapid
and efficient CRISPR targeting in mammalian cells. A plasmid
containing the human RNA polymerase III promoter U6 is
PCR-amplified using a U6-specific forward primer and a reverse
primer carrying the reverse complement of part of the U6 promoter,
the sgRNA (+85) scaffold with guide sequence, and 7 T nucleotides
for transcriptional termination. The resulting PCR product is
purified and co-delivered with a plasmid carrying Cas9 driven by
the CBh promoter (SEQ ID NOS 517, 523, 518 and 524-525,
respectively, in order of appearance).
[0091] FIG. 65 shows SURVEYOR Mutation Detection Kit from
Transgenomics results for each gRNA and respective controls. A
positive SURVEYOR result is one large band corresponding to the
genomic PCR and two smaller bands that are the product of the
SURVEYOR nuclease making a double-strand break at the site of a
mutation. Each gRNA was validated in the mouse cell line,
Neuro-N2a, by liposomal transient co-transfection with hSpCas9. 72
hours post-transfection genomic DNA was purified using QuickExtract
DNA from Epicentre. PCR was performed to amplify the locus of
interest.
[0092] FIG. 66 shows Surveyor results for 38 live pups (lanes 1-38)
1 dead pup (lane 39) and I wild-type pup for comparison (lane 40).
Pups 1-19 were injected with gRNA Chd8.2 and pups 20-38 were
injected with gRNA Chd8.3. Of the 38 live pups, 13 were positive
for a mutation. The one dead pup also had a mutation. There was no
mutation detected in the wild-type sample. Genomic PCR sequencing
was consistent with the SURVEYOR assay findings (SEQ ID NOS
526-528, respectively, in order of appearance).
[0093] FIG. 67 shows a design of different Cas9 NLS constructs. All
Cas9 were the human-codon-optimized version of the Sp Cas9. NLS
sequences are linked to the cas9 gene at either N-terminus or
C-terminus. All Cas9 variants with different NLS designs were
cloned into a backbone vector containing so it is driven by
EF1.alpha. promoter. On the same vector there is a chimeric RNA
targeting human EMX1 locus driven by U6 promoter, together forming
a two-component system.
[0094] FIG. 68 shows the efficiency of genomic cleavage induced by
Cas9 variants bearing different NLS designs. The percentage
indicate the portion of human EMX1 genomic DNA that were cleaved by
each construct. All experiments are from 3 biological replicates.
n=3, error indicates S.E.M.
[0095] FIG. 69A shows a design of the CRISPR-TF (Transcription
Factor) with transcriptional activation activity. The chimeric RNA
is expressed by U6 promoter, while a human-codon-optimized,
double-mutant version of the Cas9 protein (hSpCas9m), operably
linked to triple NLS and a VP64 functional domain is expressed by a
EF1.alpha. promoter. The double mutations, DIOA and H840A, renders
the cas9 protein unable to introduce any cleavage but maintained
its capacity to bind to target DNA when guided by the chimeric
RNA.
[0096] FIG. 69B shows transcriptional activation of the human SOX2
gene with CRISPR-TF system (Chimeric RNA and the Cas9-NLS-VP64
fusion protein). 293FT cells were transfected with plasmids bearing
two components: (1) U6-driven different chimeric RNAs targeting
20-bp sequences within or around the human SOX2 genomic locus, and
(2) EF1a-driven hSpCas9m (double mutant)-NLS-VP64 fusion protein.
96 hours post transfection, 293FT cells were harvested and the
level of activation is measured by the induction of mRNA expression
using a qRT-PCR assay. All expression levels are normalized against
the control group (grey bar), which represents results from cells
transfected with the CRISPR-TF backbone plasmid without chimeric
RNA. The qRT-PCR probes used for detecting the SOX2 mRNA is Taqman
Human Gene Expression Assay (Life Technologies). All experiments
represents data from 3 biological replicates, n=3, error bars show
s.e.m.
[0097] FIG. 70 depicts NLS architecture optimization for
SpCas9.
[0098] FIG. 71 shows a QQ plot for NGGNN sequences.
[0099] FIG. 72 shows a histogram of the data density with fitted
normal distribution (black line) and 0.99 quantile (dotted
line).
[0100] FIG. 73A-73C shows RNA-guided repression of bgaA expression
by dgRNA::cas9**. a. The Cas9 protein binds to the tracrRNA, and to
the precursor CRISPR RNA which is processed by RNAseIII to form the
crRNA. The crRNA directs binding of Cas9 to the bgaA promoter and
represses transcription. b. The targets used to direct Cas9** to
the bgaA promoter are represented (SEQ ID NO: 529). Putative-35,
-10 as well as the bgaA start codon are in bold. c.
Betagalactosidase activity as measure by Miller assay in the
absence of targeting and for the four different targets.
[0101] FIG. 74A-74E shows characterization of Cas9** mediated
repression. a. The gfpmut2 gene and its promoter, including the -35
and -10 signals are represented together with the position of the
different target sites used the study. b. Relative fluorescence
upon targeting of the coding strand. c. Relative fluorescence upon
targeting of the non-coding strand. d. Northern blot with probes
B477 and B478 on RNA extracted from T5, T10, B10 or a control
strain without a target. e. Effect of an increased number of
mutations in the 5' end of the crRNA of B1, T5 and B10.
[0102] The figures herein are for illustrative purposes only and
are not necessarily drawn to scale.
DETAILED DESCRIPTION OF THE INVENTION
[0103] The terms "polynucleotide", "nucleotide", "nucleotide
sequence", "nucleic acid" and "oligonucleotide" are used
interchangeably. They refer to a polymeric form of nucleotides of
any length, either deoxyribonucleotides or ribonucleotides, or
analogs thereof. Polynucleotides may have any three dimensional
structure, and may perform any function, known or unknown. The
following are non-limiting examples of polynucleotides: coding or
non-coding regions of a gene or gene fragment, loci (locus) defined
from linkage analysis, exons, introns, messenger RNA (mRNA),
transfer RNA, ribosomal RNA, short interfering RNA (siRNA),
short-hairpin RNA (shRNA), micro-RNA (miRNA), ribozymes, cDNA,
recombinant polynucleotides, branched polynucleotides, plasmids,
vectors, isolated DNA of any sequence, isolated RNA of any
sequence, nucleic acid probes, and primers. A polynucleotide may
comprise one or more modified nucleotides, such as methylated
nucleotides and nucleotide analogs. If present, modifications to
the nucleotide structure may be imparted before or after assembly
of the polymer. The sequence of nucleotides may be interrupted by
non-nucleotide components. A polynucleotide may be further modified
after polymerization, such as by conjugation with a labeling
component.
[0104] In aspects of the invention the terms "chimeric RNA",
"chimeric guide RNA", "guide RNA", "single guide RNA" and
"synthetic guide RNA" are used interchangeably and refer to the
polynucleotide sequence comprising the guide sequence, the tracr
sequence and the tracr mate sequence. The term "guide sequence"
refers to the about 20 bp sequence within the guide RNA that
specifies the target site and may be used interchangeably with the
terms "guide" or "spacer". The term "tracr mate sequence" may also
be used interchangeably with the term "direct repeat(s)".
[0105] As used herein the term "wild type" is a term of the art
understood by skilled persons and means the typical form of an
organism, strain, gene or characteristic as it occurs in nature as
distinguished from mutant or variant forms.
[0106] As used herein the term "variant" should be taken to mean
the exhibition of qualities that have a pattern that deviates from
what occurs in nature.
[0107] The terms "non-naturally occurring" or "engineered" are used
interchangeably and indicate the involvement of the hand of man.
The terms, when referring to nucleic acid molecules or polypeptides
mean that the nucleic acid molecule or the polypeptide is at least
substantially free from at least one other component with which
they are naturally associated in nature and as found in nature.
[0108] "Complementarity" refers to the ability of a nucleic acid to
form hydrogen bond(s) with another nucleic acid sequence by either
traditional Watson-Crick base pairing or other non-traditional
types. A percent complementarity indicates the percentage of
residues in a nucleic acid molecule which can form hydrogen bonds
(e.g., Watson-Crick base pairing) with a second nucleic acid
sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%,
80%, 90%, and 100% complementary). "Perfectly complementary" means
that all the contiguous residues of a nucleic acid sequence will
hydrogen bond with the same number of contiguous residues in a
second nucleic acid sequence. "Substantially complementary" as used
herein refers to a degree of complementarity that is at least 60%,
65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% over a
region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 30, 35, 40, 45, 50, or more nucleotides, or refers to
two nucleic acids that hybridize under stringent conditions.
[0109] As used herein, "stringent conditions" for hybridization
refer to conditions under which a nucleic acid having
complementarity to a target sequence predominantly hybridizes with
the target sequence, and substantially does not hybridize to
non-target sequences. Stringent conditions are generally
sequence-dependent, and vary depending on a number of factors. In
general, the longer the sequence, the higher the temperature at
which the sequence specifically hybridizes to its target sequence.
Non-limiting examples of stringent conditions are described in
detail in Tijssen (1993), Laboratory Techniques In Biochemistry And
Molecular Biology-Hybridization With Nucleic Acid Probes Part 1,
Second Chapter "Overview of principles of hybridization and the
strategy of nucleic acid probe assay", Elsevier, N.Y.
[0110] "Hybridization" refers to a reaction in which one or more
polynucleotides react to form a complex that is stabilized via
hydrogen bonding between the bases of the nucleotide residues. The
hydrogen bonding may occur by Watson Crick base pairing, Hoogstein
binding, or in any other sequence specific manner. The complex may
comprise two strands forming a duplex structure, three or more
strands forming a multi stranded complex, a single self hybridizing
strand, or any combination of these. A hybridization reaction may
constitute a step in a more extensive process, such as the
initiation of PCR, or the cleavage of a polynucleotide by an
enzyme. A sequence capable of hybridizing with a given sequence is
referred to as the "complement" of the given sequence.
[0111] As used herein, "expression" refers to the process by which
a polynucleotide is transcribed from a DNA template (such as into
and mRNA or other RNA transcript) and/or the process by which a
transcribed mRNA is subsequently translated into peptides,
polypeptides, or proteins. Transcripts and encoded polypeptides may
be collectively referred to as "gene product." If the
polynucleotide is derived from genomic DNA, expression may include
splicing of the mRNA in a eukaryotic cell.
[0112] The terms "polypeptide", "peptide" and "protein" are used
interchangeably herein to refer to polymers of amino acids of any
length. The polymer may be linear or branched, it may comprise
modified amino acids, and it may be interrupted by non amino acids.
The terms also encompass an amino acid polymer that has been
modified; for example, disulfide bond formation, glycosylation,
lipidation, acetylation, phosphorylation, or any other
manipulation, such as conjugation with a labeling component. As
used herein the term "amino acid" includes natural and/or unnatural
or synthetic amino acids, including glycine and both the D or L
optical isomers, and amino acid analogs and peptidomimetics.
[0113] The terms "subject," "individual," and "patient" are used
interchangeably herein to refer to a vertebrate, preferably a
mammal, more preferably a human. Mammals include, but are not
limited to, murines, simians, humans, farm animals, sport animals,
and pets. Tissues, cells and their progeny of a biological entity
obtained in vivo or cultured in vitro are also encompassed.
[0114] The terms "therapeutic agent", "therapeutic capable agent"
or "treatment agent" are used interchangeably and refer to a
molecule or compound that confers some beneficial effect upon
administration to a subject. The beneficial effect includes
enablement of diagnostic determinations; amelioration of a disease,
symptom, disorder, or pathological condition; reducing or
preventing the onset of a disease, symptom, disorder or condition;
and generally counteracting a disease, symptom, disorder or
pathological condition.
[0115] As used herein, "treatment" or "treating," or "palliating"
or "ameliorating" are used interchangeably. These terms refer to an
approach for obtaining beneficial or desired results including but
not limited to a therapeutic benefit and/or a prophylactic benefit.
By therapeutic benefit is meant any therapeutically relevant
improvement in or effect on one or more diseases, conditions, or
symptoms under treatment. For prophylactic benefit, the
compositions may be administered to a subject at risk of developing
a particular disease, condition, or symptom, or to a subject
reporting one or more of the physiological symptoms of a disease,
even though the disease, condition, or symptom may not have yet
been manifested.
[0116] The term "effective amount" or "therapeutically effective
amount" refers to the amount of an agent that is sufficient to
effect beneficial or desired results. The therapeutically effective
amount may vary depending upon one or more of: the subject and
disease condition being treated, the weight and age of the subject,
the severity of the disease condition, the manner of administration
and the like, which can readily be determined by one of ordinary
skill in the art. The term also applies to a dose that will provide
an image for detection by any one of the imaging methods described
herein. The specific dose may vary depending on one or more of: the
particular agent chosen, the dosing regimen to be followed, whether
it is administered in combination with other compounds, timing of
administration, the tissue to be imaged, and the physical delivery
system in which it is carried.
[0117] The practice of the present invention employs, unless
otherwise indicated, conventional techniques of immunology,
biochemistry, chemistry, molecular biology, microbiology, cell
biology, genomics and recombinant DNA, which are within the skill
of the art. See Sambrook, Fritsch and Maniatis, MOLECULAR CLONING:
A LABORATORY MANUAL, 2nd edition (1989); CURRENT PROTOCOLS IN
MOLECULAR BIOLOGY (F. M. Ausubel, et al. eds., (1987)); the series
METHODS IN ENZYMOLOGY (Academic Press, Inc.): PCR 2: A PRACTICAL
APPROACH (M. J. MacPherson, B. D. Hames and G. R. Taylor eds.
(1995)), Harlow and Lane, eds. (1988) ANTIBODIES, A LABORATORY
MANUAL, and ANIMAL CELL CULTURE (R. I. Freshney, ed. (1987)).
[0118] Several aspects of the invention relate to vector systems
comprising one or more vectors, or vectors as such. Vectors can be
designed for expression of CRISPR transcripts (e.g. nucleic acid
transcripts, proteins, or enzymes) in prokaryotic or eukaryotic
cells. For example, CRISPR transcripts can be expressed in
bacterial cells such as Escherichia coli, insect cells (using
baculovirus expression vectors), yeast cells, or mammalian cells.
Suitable host cells are discussed further in Goeddel, GENE
EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press,
San Diego, Calif. (1990). Alternatively, the recombinant expression
vector can be transcribed and translated in vitro, for example
using T7 promoter regulatory sequences and T7 polymerase.
[0119] Vectors may be introduced and propagated in a prokaryote. In
some embodiments, a prokaryote is used to amplify copies of a
vector to be introduced into a eukaryotic cell or as an
intermediate vector in the production of a vector to be introduced
into a eukaryotic cell (e.g. amplifying a plasmid as part of a
viral vector packaging system). In some embodiments, a prokaryote
is used to amplify copies of a vector and express one or more
nucleic acids, such as to provide a source of one or more proteins
for delivery to a host cell or host organism. Expression of
proteins in prokaryotes is most often carried out in Escherichia
coli with vectors containing constitutive or inducible promoters
directing the expression of either fusion or non-fusion proteins.
Fusion vectors add a number of amino acids to a protein encoded
therein, such as to the amino terminus of the recombinant protein.
Such fusion vectors may serve one or more purposes, such as: (i) to
increase expression of recombinant protein; (ii) to increase the
solubility of the recombinant protein; and (iii) to aid in the
purification of the recombinant protein by acting as a ligand in
affinity purification. Often, in fusion expression vectors, a
proteolytic cleavage site is introduced at the junction of the
fusion moiety and the recombinant protein to enable separation of
the recombinant protein from the fusion moiety subsequent to
purification of the fusion protein. Such enzymes, and their cognate
recognition sequences, include Factor Xa, thrombin and
enterokinase. Example fusion expression vectors include pGEX
(Pharmacia Biotech Inc; Smith and Johnson, 1988. Gene 67: 31-40),
pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia,
Piscataway, N.J.) that fuse glutathione S-transferase (GST),
maltose E binding protein, or protein A, respectively, to the
target recombinant protein.
[0120] Examples of suitable inducible non-fusion E. coli expression
vectors include pTrc (Amrann et al., (1988) Gene 69:301-315) and
pET lid (Studier et al., GENE EXPRESSION TECHNOLOGY: METHODS IN
ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990)
60-89).
[0121] In some embodiments, a vector is a yeast expression vector.
Examples of vectors for expression in yeast Saccharomyces cerivisae
include pYepSecl (Baldari, et al., 1987. EMBO J. 6: 229-234), pMFa
(Kuijan and Herskowitz, 1982. Cell 30: 933-943), pJRY88 (Schultz et
al., 1987. Gene 54: 113-123), pYES2 (Invitrogen Corporation, San
Diego, Calif.), and picZ (InVitrogen Corp, San Diego, Calif.).
[0122] In some embodiments, a vector drives protein expression in
insect cells using baculovirus expression vectors. Baculovirus
vectors available for expression of proteins in cultured insect
cells (e.g., SF9 cells) include the pAc series (Smith, et al.,
1983. Mol. Cell. Biol. 3: 2156-2165) and the pVL series (Lucklow
and Summers, 1989. Virology 170: 31-39).
[0123] In some embodiments, a vector is capable of driving
expression of one or more sequences in mammalian cells using a
mammalian expression vector. Examples of mammalian expression
vectors include pCDM8 (Seed, 1987. Nature 329: 840) and pMT2PC
(Kaufman, et al., 1987. EMBO J. 6: 187-195). When used in mammalian
cells, the expression vector's control functions are typically
provided by one or more regulatory elements. For example, commonly
used promoters are derived from polyoma, adenovirus 2,
cytomegalovirus, simian virus 40, and others disclosed herein and
known in the art. For other suitable expression systems for both
prokaryotic and eukaryotic cells see, e.g., Chapters 16 and 17 of
Sambrook, et al., MOLECULAR CLONING: A LABORATORY MANUAL. 2nd ed.,
Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press,
Cold Spring Harbor, N. Y., 1989.
[0124] In some embodiments, the recombinant mammalian expression
vector is capable of directing expression of the nucleic acid
preferentially in a particular cell type (e.g., tissue-specific
regulatory elements are used to express the nucleic acid).
Tissue-specific regulatory elements are known in the art.
Non-limiting examples of suitable tissue-specific promoters include
the albumin promoter (liver-specific; Pinkert, et al., 1987. Genes
Dev. 1: 268-277), lymphoid-specific promoters (Calame and Eaton,
1988. Adv. Immunol. 43: 235-275), in particular promoters of T cell
receptors (Winoto and Baltimore, 1989. EMBO J. 8: 729-733) and
immunoglobulins (Baneiji, et al., 1983. Cell 33: 729-740; Queen and
Baltimore, 1983. Cell 33: 741-748), neuron-specific promoters
(e.g., the neurofilament promoter; Byrne and Ruddle, 1989. Proc.
Natl. Acad. Sci. USA 86: 5473-5477), pancreas-specific promoters
(Edlund, et al., 1985. Science 230: 912-916), and mammary
gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No.
4,873,316 and European Application Publication No. 264,166).
Developmentally-regulated promoters are also encompassed, e.g., the
murine hox promoters (Kessel and Gruss, 1990. Science 249: 374-379)
and the a-fetoprotein promoter (Campes and Tilghman, 1989. Genes
Dev. 3: 537-546).
[0125] In some embodiments, a regulatory element is operably linked
to one or more elements of a CRISPR system so as to drive
expression of the one or more elements of the CRISPR system. In
general, CRISPRs (Clustered Regularly Interspaced Short Palindromic
Repeats), also known as SPIDRs (SPacer Interspersed Direct
Repeats), constitute a family of DNA loci that are usually specific
to a particular bacterial species. The CRISPR locus comprises a
distinct class of interspersed short sequence repeats (SSRs) that
were recognized in E. coli (Ishino et al., J. Bacteriol.,
169:5429-5433 [1987]; and Nakata et al., J. Bacteriol.,
171:3553-3556 [1989]), and associated genes. Similar interspersed
SSRs have been identified in Haloferax mediterranei, Streptococcus
pyogenes, Anabaena, and Mycobacterium tuberculosis (See, Groenen et
al., Mol. Microbiol., 10:1057-1065 [1993]; Hoe et al., Emerg.
Infect. Dis., 5:254-263 [1999]; Masepohl et al., Biochim. Biophys.
Acta 1307:26-30 [1996]; and Mojica et al., Mol. Microbiol.,
17:85-93 [1995]). The CRISPR loci typically differ from other SSRs
by the structure of the repeats, which have been termed short
regularly spaced repeats (SRSRs) (Janssen et al., OMICS J. Integ.
Biol., 6:23-33 [2002]; and Mojica et al., Mol. Microbiol.,
36:244-246 [2000]). In general, the repeats are short elements that
occur in clusters that are regularly spaced by unique intervening
sequences with a substantially constant length (Mojica et al.,
[2000], supra). Although the repeat sequences are highly conserved
between strains, the number of interspersed repeats and the
sequences of the spacer regions typically differ from strain to
strain (van Embden et al., J. Bacteriol., 182:2393-2401 [2000]).
CRISPR loci have been identified in more than 40 prokaryotes (See
e.g., Jansen et al., Mol. Microbiol., 43:1565-1575 [2002]; and
Mojica et al., [2005]) including, but not limited to Aeropyrum,
Pyrobaculum, Sulfolobus, Archaeoglobus, Halocarcula,
Methanobacterium, Methanococcus, Methanosarcina, Methanopyrus,
Pyrococcus, Picrophilus, Thermoplasma, Corynebacterium,
Myvcobacterium, Streptomyces. Aquifex. Porphyromonas, Chlorobium,
Thermus, Bacillus, Listeria, Staphylococcus, Clostridium,
Thermoanaerobacter, Mycoplasma, Fusobacterium, Azarcus,
Chromobacterium, Neisseria, Nitrosomonas, Desulfovibrio, Geobacter,
Myrcoccus, Campylobacter, Wolinella, Acinetobacter. Erwinia,
Escherichia. Legionella, Methylococcus, Pasteurella,
Photobacterium, Salmonella, Xanthomonas, Yersinia, Treponema, and
Thermotoga.
[0126] In general, "CRISPR system" refers collectively to
transcripts and other elements involved in the expression of or
directing the activity of CRISPR-associated ("Cas") genes,
including sequences encoding a Cas gene, a tracr (trans-activating
CRISPR) sequence (e.g. tracrRNA or an active partial tracrRNA), a
tracr-mate sequence (encompassing a "direct repeat" and a
tracrRNA-processed partial direct repeat in the context of an
endogenous CRISPR system), a guide sequence (also referred to as a
"spacer" in the context of an endogenous CRISPR system), or other
sequences and transcripts from a CRISPR locus. In some embodiments,
one or more elements of a CRISPR system is derived from a type I,
type II, or type III CRISPR system. In some embodiments, one or
more elements of a CRISPR system is derived from a particular
organism comprising an endogenous CRISPR system, such as
Streptococcus pyogenes. In general, a CRISPR system is
characterized by elements that promote the formation of a CRISPR
complex at the site of a target sequence (also referred to as a
protospacer in the context of an endogenous CRISPR system). In the
context of formation of a CRISPR complex, "target sequence" refers
to a sequence to which a guide sequence is designed to have
complementarity, where hybridization between a target sequence and
a guide sequence promotes the formation of a CRISPR complex. Full
complementarity is not necessarily required, provided there is
sufficient complementarity to cause hybridization and promote
formation of a CRISPR complex. A target sequence may comprise any
polynucleotide, such as DNA or RNA polynucleotides. In some
embodiments, a target sequence is located in the nucleus or
cytoplasm of a cell. In some embodiments, the target sequence may
be within an organelle of a eukaryotic cell, for example,
mitochondrion or chloroplast. A sequence or template that may be
used for recombination into the targeted locus comprising the
target sequences is referred to as an "editing template" or
"editing polynucleotide" or "editing sequence". In aspects of the
invention, an exogenous template polynucleotide may be referred to
as an editing template. In an aspect of the invention the
recombination is homologous recombination.
[0127] Typically, in the context of an endogenous CRISPR system,
formation of a CRISPR complex (comprising a guide sequence
hybridized to a target sequence and complexed with one or more Cas
proteins) results in cleavage of one or both strands in or near
(e.g. within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or more base
pairs from) the target sequence. Without wishing to be bound by
theory, the tracr sequence, which may comprise or consist of all or
a portion of a wild-type tracr sequence (e.g. about or more than
about 20, 26, 32, 45, 48, 54, 63, 67, 85, or more nucleotides of a
wild-type tracr sequence), may also form part of a CRISPR complex,
such as by hybridization along at least a portion of the tracr
sequence to all or a portion of a tracr mate sequence that is
operably linked to the guide sequence. In some embodiments, the
tracr sequence has sufficient complementarity to a tracr mate
sequence to hybridize and participate in formation of a CRISPR
complex. As with the target sequence, it is believed that complete
complementarity is not needed, provided there is sufficient to be
functional. In some embodiments, the tracr sequence has at least
50%, 60%0, 70%, 80.degree. %., 90%, 95% or 99% of sequence
complementarity along the length of the tracr mate sequence when
optimally aligned. In some embodiments, one or more vectors driving
expression of one or more elements of a CRISPR system are
introduced into a host cell such that expression of the elements of
the CRISPR system direct formation of a CRISPR complex at one or
more target sites. For example, a Cas enzyme, a guide sequence
linked to a tracr-mate sequence, and a tracr sequence could each be
operably linked to separate regulatory elements on separate
vectors. Alternatively, two or more of the elements expressed from
the same or different regulatory elements, may be combined in a
single vector, with one or more additional vectors providing any
components of the CRISPR system not included in the first vector.
CRISPR system elements that are combined in a single vector may be
arranged in any suitable orientation, such as one element located
5' with respect to ("upstream" of) or 3' with respect to
("downstream" of) a second element. The coding sequence of one
element may be located on the same or opposite strand of the coding
sequence of a second element, and oriented in the same or opposite
direction. In some embodiments, a single promoter drives expression
of a transcript encoding a CRISPR enzyme and one or more of the
guide sequence, tracr mate sequence (optionally operably linked to
the guide sequence), and a tracr sequence embedded within one or
more intron sequences (e.g. each in a different intron, two or more
in at least one intron, or all in a single intron). In some
embodiments, the CRISPR enzyme, guide sequence, tracr mate
sequence, and tracr sequence are operably linked to and expressed
from the same promoter.
[0128] In some embodiments, a vector comprises one or more
insertion sites, such as a restriction endonuclease recognition
sequence (also referred to as a "cloning site"). In some
embodiments, one or more insertion sites (e.g. about or more than
about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more insertion sites) are
located upstream and/or downstream of one or more sequence elements
of one or more vectors. In some embodiments, a vector comprises an
insertion site upstream of a tracr mate sequence, and optionally
downstream of a regulatory element operably linked to the tracr
mate sequence, such that following insertion of a guide sequence
into the insertion site and upon expression the guide sequence
directs sequence-specific binding of a CRISPR complex to a target
sequence in a eukaryotic cell. In some embodiments, a vector
comprises two or more insertion sites, each insertion site being
located between two tracr mate sequences so as to allow insertion
of a guide sequence at each site. In such an arrangement, the two
or more guide sequences may comprise two or more copies of a single
guide sequence, two or more different guide sequences, or
combinations of these. When multiple different guide sequences are
used, a single expression construct may be used to target CRISPR
activity to multiple different, corresponding target sequences
within a cell. For example, a single vector may comprise about or
more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more
guide sequences. In some embodiments, about or more than about 1,
2, 3, 4, 5, 6, 7, 8, 9, 10, or more such guide-sequence-containing
vectors may be provided, and optionally delivered to a cell.
[0129] In some embodiments, a vector comprises a regulatory element
operably linked to an enzyme-coding sequence encoding a CRISPR
enzyme, such as a Cas protein. Non-limiting examples of Cas
proteins include Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7,
Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3,
Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6,
Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14,
Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4,
homologs thereof, or modified versions thereof. These enzymes are
known; for example, the amino acid sequence of S. pyogenes Cas9
protein may be found in the SwissProt database under accession
number Q99ZW2. In some embodiments, the unmodified CRISPR enzyme
has DNA cleavage activity, such as Cas9. In some embodiments the
CRISPR enzyme is Cas9, and may be Cas9 from S. pyogenes or S.
pneumoniae. In some embodiments, the CRISPR enzyme directs cleavage
of one or both strands at the location of a target sequence, such
as within the target sequence and/or within the complement of the
target sequence. In some embodiments, the CRISPR enzyme directs
cleavage of one or both strands within about 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from
the first or last nucleotide of a target sequence. In some
embodiments, a vector encodes a CRISPR enzyme that is mutated to
with respect to a corresponding wild-type enzyme such that the
mutated CRISPR enzyme lacks the ability to cleave one or both
strands of a target polynucleotide containing a target sequence.
For example, an aspartate-to-alanine substitution (D10A) in the
RuvC 1 catalytic domain of Cas9 from S. pyogenes converts Cas9 from
a nuclease that cleaves both strands to a nickase (cleaves a single
strand). Other examples of mutations that render Cas9 a nickase
include, without limitation, H840A, N854A, and N863A. In some
embodiments, a Cas9 nickase may be used in combination with guide
sequenc(es), e.g., two guide sequences, which target respectively
sense and antisense strands of the DNA target. This combination
allows both strands to be nicked and used to induce NHEJ.
Applicants have demonstrated (data not shown) the efficacy of two
nickase targets (i.e., sgRNAs targeted at the same location but to
different strands of DNA) in inducing mutagenic NHEJ. A single
nickase (Cas9-D10A with a single sgRNA) is unable to induce NHEJ
and create indels but Applicants have shown that double nickase
(Cas9-D10A and two sgRNAs targeted to different strands at the same
location) can do so in human embryonic stem cells (hESCs). The
efficiency is about 50% of nuclease (i.e., regular Cas9 without D10
mutation) in hESCs.
[0130] As a further example, two or more catalytic domains of Cas9
(RuvC 1, RuvC II, and RuvC III) may be mutated to produce a mutated
Cas9 substantially lacking all DNA cleavage activity. In some
embodiments, a D10A mutation is combined with one or more of H840A,
N854A, or N863A mutations to produce a Cas9 enzyme substantially
lacking all DNA cleavage activity. In some embodiments, a CRISPR
enzyme is considered to substantially lack all DNA cleavage
activity when the DNA cleavage activity of the mutated enzyme is
less than about 25%, 10%, 5%, 1%, 0.1%, 0.01%, or lower with
respect to its non-mutated form. Other mutations may be useful;
where the Cas9 or other CRISPR enzyme is from a species other than
S. pyogenes, mutations in corresponding amino acids may be made to
achieve similar effects.
[0131] In some embodiments, an enzyme coding sequence encoding a
CRISPR enzyme is codon optimized for expression in particular
cells, such as eukaryotic cells. The eukaryotic cells may be those
of or derived from a particular organism, such as a mammal,
including but not limited to human, mouse, rat, rabbit, dog, or
non-human primate. In general, codon optimization refers to a
process of modifying a nucleic acid sequence for enhanced
expression in the host cells of interest by replacing at least one
codon (e.g. about or more than about 1, 2, 3, 4, 5, 10, 15, 20, 25,
50, or more codons) of the native sequence with codons that are
more frequently or most frequently used in the genes of that host
cell while maintaining the native amino acid sequence. Various
species exhibit particular bias for certain codons of a particular
amino acid. Codon bias (differences in codon usage between
organisms) often correlates with the efficiency of translation of
messenger RNA (mRNA), which is in turn believed to be dependent on,
among other things, the properties of the codons being translated
and the availability of particular transfer RNA (tRNA) molecules.
The predominance of selected tRNAs in a cell is generally a
reflection of the codons used most frequently in peptide synthesis.
Accordingly, genes can be tailored for optimal gene expression in a
given organism based on codon optimization. Codon usage tables are
readily available, for example, at the "Codon Usage Database", and
these tables can be adapted in a number of ways. See Nakamura, Y.,
et al. "Codon usage tabulated from the international DNA sequence
databases: status for the year 2000" Nucl. Acids Res. 28:292
(2000). Computer algorithms for codon optimizing a particular
sequence for expression in a particular host cell are also
available, such as Gene Forge (Aptagen; Jacobus, P A), are also
available. In some embodiments, one or more codons (e.g. 1, 2, 3,
4, 5, 10, 15, 20, 25, 50, or more, or all codons) in a sequence
encoding a CRISPR enzyme correspond to the most frequently used
codon for a particular amino acid.
[0132] In some embodiments, a vector encodes a CRISPR enzyme
comprising one or more nuclear localization sequences (NLSs), such
as about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more
NLSs. In some embodiments, the CRISPR enzyme comprises about or
more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or
near the amino-terminus, about or more than about 1, 2, 3, 4, 5, 6,
7, 8, 9, 10, or more NLSs at or near the carboxy-terminus, or a
combination of these (e.g. one or more NLS at the amino-terminus
and one or more NLS at the carboxy terminus). When more than one
NLS is present, each may be selected independently of the others,
such that a single NLS may be present in more than one copy and/or
in combination with one or more other NLSs present in one or more
copies. In a preferred embodiment of the invention, the CRISPR
enzyme comprises at most 6 NLSs. In some embodiments, an NLS is
considered near the N- or C-terminus when the nearest amino acid of
the NLS is within about 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50,
or more amino acids along the polypeptide chain from the N- or
C-terminus. Typically, an NLS consists of one or more short
sequences of positively charged lysines or arginines exposed on the
protein surface, but other types of NLS are known. Non-limiting
examples of NLSs include an NLS sequence derived from: the NLS of
the SV40 virus large T-antigen, having the amino acid sequence
PKKKRKV (SEQ ID NO: 1); the NLS from nucleoplasmin (e.g. the
nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ
ID NO: 2)); the c-myc NLS having the amino acid sequence PAAKRVKLD
(SEQ ID NO: 3) or RQRRNELKRSP (SEQ ID NO: 4); the hRNPAI M9 NLS
having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID
NO: 5); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV
(SEQ ID NO: 6) of the IBB domain from importin-alpha; the sequences
VSRKRPRP (SEQ ID NO: 7) and PPKKARED (SEQ ID NO: 8) of the myoma T
protein; the sequence PQPKKKPL (SEQ ID NO: 9) of human p53; the
sequence SALIKKKKKMAP (SEQ ID NO: 10) of mouse c-abl IV; the
sequences DRLRR (SEQ ID NO: 11) and PKQKKRK (SEQ ID NO: 12) of the
influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO: 13) of the
Hepatitis virus delta antigen; the sequence REKKKFLKRR (SEQ ID NO:
14) of the mouse Mxl protein; the sequence KRKGDEVDGVDEVAKKKSKK
(SEQ ID NO: 15) of the human poly(ADP-ribose) polymerase; and the
sequence RKCLQAGMNLEARKTKK (SEQ ID NO: 16) of the steroid hormone
receptors (human) glucocorticoid.
[0133] In general, the one or more NLSs are of sufficient strength
to drive accumulation of the CRISPR enzyme in a detectable amount
in the nucleus of a eukaryotic cell. In general, strength of
nuclear localization activity may derive from the number of NLSs in
the CRISPR enzyme, the particular NLS(s) used, or a combination of
these factors. Detection of accumulation in the nucleus may be
performed by any suitable technique. For example, a detectable
marker may be fused to the CRISPR enzyme, such that location within
a cell may be visualized, such as in combination with a means for
detecting the location of the nucleus (e.g. a stain specific for
the nucleus such as DAPI). Examples of detectable markers include
fluorescent proteins (such as Green fluorescent proteins, or GFP;
RFP; CFP), and epitope tags (HA tag. flag tag, SNAP tag). Cell
nuclei may also be isolated from cells, the contents of which may
then be analyzed by any suitable process for detecting protein,
such as immunohistochemistry, Western blot, or enzyme activity
assay. Accumulation in the nucleus may also be determined
indirectly, such as by an assay for the effect of CRISPR complex
formation (e.g. assay for DNA cleavage or mutation at the target
sequence, or assay for altered gene expression activity affected by
CRISPR complex formation and/or CRISPR enzyme activity), as
compared to a control no exposed to the CRISPR enzyme or complex,
or exposed to a CRISPR enzyme lacking the one or more NLSs.
[0134] In general, a guide sequence is any polynucleotide sequence
having sufficient complementarity with a target polynucleotide
sequence to hybridize with the target sequence and direct
sequence-specific binding of a CRISPR complex to the target
sequence. In some embodiments, the degree of complementarity
between a guide sequence and its corresponding target sequence,
when optimally aligned using a suitable alignment algorithm, is
about or more than about 50%, 60%, 75%, 80%, 85%, 90%0/6, 95%,
97.5%, 99%, or more. Optimal alignment may be determined with the
use of any suitable algorithm for aligning sequences, non-limiting
example of which include the Smith-Waterman algorithm, the
Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler
Transform (e.g. the Burrows Wheeler Aligner), ClustalW, Clustal X,
BLAT, Novoalign (Novocraft Technologies, ELAND (Illumina, San
Diego, Calif.), SOAP (available at soap.genomics.org.cn), and Maq
(available at maq.sourceforge.net). In some embodiments, a guide
sequence is about or more than about 5, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45,
50, 75, or more nucleotides in length. In some embodiments, a guide
sequence is less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12,
or fewer nucleotides in length. The ability of a guide sequence to
direct sequence-specific binding of a CRISPR complex to a target
sequence may be assessed by any suitable assay. For example, the
components of a CRISPR system sufficient to form a CRISPR complex,
including the guide sequence to be tested, may be provided to a
host cell having the corresponding target sequence, such as by
transfection with vectors encoding the components of the CRISPR
sequence, followed by an assessment of preferential cleavage within
the target sequence, such as by Surveyor assay as described herein.
Similarly, cleavage of a target polynucleotide sequence may be
evaluated in a test tube by providing the target sequence,
components of a CRISPR complex, including the guide sequence to be
tested and a control guide sequence different from the test guide
sequence, and comparing binding or rate of cleavage at the target
sequence between the test and control guide sequence reactions.
Other assays are possible, and will occur to those skilled in the
art.
[0135] A guide sequence may be selected to target any target
sequence. In some embodiments, the target sequence is a sequence
within a genome of a cell. Exemplary target sequences include those
that are unique in the target genome. For example, for the S.
pyogenes Cas9, a unique target sequence in a genome may include a
Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXGG (SEQ ID NO:
530) where NNNNNNNNNNNNXGG (SEQ ID NO: 531) (N is A, G, T, or C;
and X can be anything) has a single occurrence in the genome. A
unique target sequence in a genome may include an S. pyogenes Cas9
target site of the form MMMMMMMMMNNNNNNNNNNNXGG (SEQ ID NO: 532)
where NNNNNNNNNNNXGG (SEQ ID NO: 533) (N is A, G, T, or C; and X
can be anything) has a single occurrence in the genome. For the S.
thermophilus CRISPR1 Cas9, a unique target sequence in a genome may
include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXXAGAAW
(SEQ ID NO: 17) where NNNNNNNNNNNNXXAGAAW (SEQ ID NO: 18) (N is A,
G. T, or C; X can be anything; and W is A or T) has a single
occurrence in the genome. A unique target sequence in a genome may
include an S. thermophilus CRISPR1 Cas9 target site of the form
MMMMMMMMNNNNNNNNNNNXXAGAAW (SEQ ID NO: 19) where NNNNNNNNNNNXXAGAAW
(SEQ ID NO: 20) (N is A, G, T, or C; X can be anything; and W is A
or T) has a single occurrence in the genome. For the S. pyogenes
Cas9, a unique target sequence in a genome may include a Cas9
target site of the form MMMMMMMMXGGXG (SEQ ID NO: 534) where
NNNNNNNNNNNNXGGXG (SEQ ID NO: 535) (N is A, G, T, or C; and X can
be anything) has a single occurrence in the genome. A unique target
sequence in a genome may include an S. pyogenes Cas9 target site of
the form MMMMMMMMMNNNNNNNNNNNXGGXG (SEQ ID NO: 536) where
NNNNNNNNNNNXGGXG (SEQ ID NO: 537) (N is A, G, T, or C; and X can be
anything) has a single occurrence in the genome. In each of these
sequences "M" may be A, G, T, or C, and need not be considered in
identifying a sequence as unique.
[0136] In some embodiments, a guide sequence is selected to reduce
the degree of secondary structure within the guide sequence.
Secondary structure may be determined by any suitable
polynucleotide folding algorithm. Some programs are based on
calculating the minimal Gibbs free energy. An example of one such
algorithm is mFold, as described by Zuker and Stiegler (Nucleic
Acids Res. 9 (1981), 133-148). Another example folding algorithm is
the online webserver RNAfold, developed at Institute for
Theoretical Chemistry at the University of Vienna, using the
centroid structure prediction algorithm (see e.g. A. R. Gruber et
al., 2008, Cell 106(1): 23-24; and PA Carr and GM Church, 2009,
Nature Biotechnology 27(12): 1151-62). Further algorithms may be
found in U.S. application Ser. No. TBA (attorney docket
44790.11.2022; Broad Reference BI-2013/004A); incorporated herein
by reference.
[0137] In general, a tracr mate sequence includes any sequence that
has sufficient complementarity with a tracr sequence to promote one
or more of: (1) excision of a guide sequence flanked by tracr mate
sequences in a cell containing the corresponding tracr sequence;
and (2) formation of a CRISPR complex at a target sequence, wherein
the CRISPR complex comprises the tracr mate sequence hybridized to
the tracr sequence. In general, degree of complementarity is with
reference to the optimal alignment of the tracr mate sequence and
tracr sequence, along the length of the shorter of the two
sequences. Optimal alignment may be determined by any suitable
alignment algorithm, and may further account for secondary
structures, such as self-complementarity within either the tracr
sequence or tracr mate sequence. In some embodiments, the degree of
complementarity between the tracr sequence and tracr mate sequence
along the length of the shorter of the two when optimally aligned
is about or more than about 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%,
95%, 97.5%, 99%, or higher. Example illustrations of optimal
alignment between a tracr sequence and a tracr mate sequence are
provided in FIGS. 12B and 13B. In some embodiments, the tracr
sequence is about or more than about 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or more nucleotides in
length. In some embodiments, the tracr sequence and tracr mate
sequence are contained within a single transcript, such that
hybridization between the two produces a transcript having a
secondary structure, such as a hairpin. Preferred loop forming
sequences for use in hairpin structures are four nucleotides in
length, and most preferably have the sequence GAAA. However, longer
or shorter loop sequences may be used, as may alternative
sequences. The sequences preferably include a nucleotide triplet
(for example, AAA), and an additional nucleotide (for example C or
G). Examples of loop forming sequences include CAAA and AAAG. In an
embodiment of the invention, the transcript or transcribed
polynucleotide sequence has at least two or more hairpins. In
preferred embodiments, the transcript has two, three, four or five
hairpins. In a further embodiment of the invention, the transcript
has at most five hairpins. In some embodiments, the single
transcript further includes a transcription termination sequence;
preferably this is a polyT sequence, for example six T nucleotides.
An example illustration of such a hairpin structure is provided in
the lower portion of FIG. 13B, where the portion of the sequence 5'
of the final "N" and upstream of the loop corresponds to the tracr
mate sequence, and the portion of the sequence 3' of the loop
corresponds to the tracr sequence. Further non-limiting examples of
single polynucleotides comprising a guide sequence, a tracr mate
sequence, and a tracr sequence are as follows (listed 5' to 3'),
where "N" represents a base of a guide sequence, the first block of
lower case letters represent the tracr mate sequence, and the
second block of lower case letters represent the tracr sequence,
and the final poly-T sequence represents the transcription
terminator: (1)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaagatttaGAAAtaaatcttgcagaagctacaaagataa-
ggctt catgccgaaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTT
(SEQ ID NO: 21); (2)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaa-
atca acaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (SEQ ID NO:
22); (3)
NNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaaatca
acaccctgtcattttatggcagggtgtTTTTTT (SEQ ID NO: 23); (4)
NNNNNNNNNNNNNNgttttagagctaGAAAtagcaagttaaaataaggctagtccgttatcaacttgaaaa
agtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 24); (5)
NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAATAGcaagttaaaataaggctagtccgttatcaacttg-
aa aaagtgTTTTTTT (SEQ ID NO: 25); and (6)
gNNNNNNNNtNNNNNNNNNNNtttagagctagAAATAGcaagttaaaataaggctagtccgttatcaTTTTT
TTT (SEQ ID NO: 26). In some embodiments, sequences (1) to (3) are
used in combination with Cas9 from S. thermophilus CRISPR1. In some
embodiments, sequences (4) to (6) are used in combination with Cas9
from S. pyogenes. In some embodiments, the tracr sequence is a
separate transcript from a transcript comprising the tracr mate
sequence (such as illustrated in the top portion of FIG. 13B).
[0138] In some embodiments, a recombination template is also
provided. A recombination template may be a component of another
vector as described herein, contained in a separate vector, or
provided as a separate polynucleotide. In some embodiments, a
recombination template is designed to serve as a template in
homologous recombination, such as within or near a target sequence
nicked or cleaved by a CRISPR enzyme as a part of a CRISPR complex.
A template polynucleotide may be of any suitable length, such as
about or more than about 10, 15, 20, 25, 50, 75, 100, 150, 200,
500, 1000, or more nucleotides in length. In some embodiments, the
template polynucleotide is complementary to a portion of a
polynucleotide comprising the target sequence. When optimally
aligned, a template polynucleotide might overlap with one or more
nucleotides of a target sequences (e.g. about or more than about 1,
5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100 or more
nucleotides). In some embodiments, when a template sequence and a
polynucleotide comprising a target sequence are optimally aligned,
the nearest nucleotide of the template polynucleotide is within
about 1, 5, 10, 15, 20, 25, 50, 75, 100, 200, 300, 400, 500, 1000,
5000, 10000, or more nucleotides from the target sequence.
[0139] In some embodiments, the CRISPR enzyme is part of a fusion
protein comprising one or more heterologous protein domains (e.g.
about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more
domains in addition to the CRISPR enzyme). A CRISPR enzyme fusion
protein may comprise any additional protein sequence, and
optionally a linker sequence between any two domains. Examples of
protein domains that may be fused to a CRISPR enzyme include,
without limitation, epitope tags, reporter gene sequences, and
protein domains having one or more of the following activities:
methylase activity, demethylase activity, transcription activation
activity, transcription repression activity, transcription release
factor activity, histone modification activity, RNA cleavage
activity and nucleic acid binding activity. Non-limiting examples
of epitope tags include histidine (His) tags, V5 tags, FLAG tags,
influenza hemagglutinin (HA) tags, Myc tags, VSV-G tags, and
thioredoxin (Trx) tags. Examples of reporter genes include, but are
not limited to, glutathione-S-transferase (GST), horseradish
peroxidase (HRP), chloramphenicol acetyltransferase (CAT)
beta-galactosidase, beta-glucuronidase, luciferase, green
fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein
(CFP), yellow fluorescent protein (YFP), and autofluorescent
proteins including blue fluorescent protein (BFP). A CRISPR enzyme
may be fused to a gene sequence encoding a protein or a fragment of
a protein that bind DNA molecules or bind other cellular molecules,
including but not limited to maltose binding protein (MBP), S-tag,
Lex A DNA binding domain (DBD) fusions, GALA DNA binding domain
fusions, and herpes simplex virus (HSV) BP16 protein fusions.
Additional domains that may form part of a fusion protein
comprising a CRISPR enzyme are described in US20110059502,
incorporated herein by reference. In some embodiments, a tagged
CRISPR enzyme is used to identify the location of a target
sequence.
[0140] In some aspects, the invention provides methods comprising
delivering one or more polynucleotides, such as or one or more
vectors as described herein, one or more transcripts thereof,
and/or one or proteins transcribed therefrom, to a host cell. In
some aspects, the invention further provides cells produced by such
methods, and organisms (such as animals, plants, or fungi)
comprising or produced from such cells. In some embodiments, a
CRISPR enzyme in combination with (and optionally complexed with) a
guide sequence is delivered to a cell. Conventional viral and
non-viral based gene transfer methods can be used to introduce
nucleic acids in mammalian cells or target tissues. Such methods
can be used to administer nucleic acids encoding components of a
CRISPR system to cells in culture, or in a host organism. Non-viral
vector delivery systems include DNA plasmids, RNA (e.g. a
transcript of a vector described herein), naked nucleic acid, and
nucleic acid complexed with a delivery vehicle, such as a liposome.
Viral vector delivery systems include DNA and RNA viruses, which
have either episomal or integrated genomes after delivery to the
cell. For a review of gene therapy procedures, see Anderson,
Science 256:808-813 (1992); Nabel & Felgner, TIBTECH 11:211-217
(1993); Mitani & Caskey, TIBTECH 11:162-166 (1993); Dillon,
TIBTECH 11:167-175 (1993); Miller, Nature 357:455-460 (1992); Van
Brunt, Biotechnology 6(10):1149-1154 (1988); Vigne, Restorative
Neurology and Neuroscience 8:35-36 (1995); Kremer &
Perricaudet, British Medical Bulletin 51(1):31-44 (1995); Haddada
et al., in Current Topics in Microbiology and Immunology, Doerfler
and Bohm (eds) (1995); and Yu et al., Gene Therapy 1:13-26
(1994).
[0141] Methods of non-viral delivery of nucleic acids include
lipofection, nucleofection, microinjection, biolistics, virosomes,
liposomes, immunoliposomes, polycation or lipid:nucleic acid
conjugates, naked DNA, artificial virions, and agent-enhanced
uptake of DNA. Lipofection is described in e.g., U.S. Pat. Nos.
5,049,386, 4,946,787; and 4,897,355) and lipofection reagents are
sold commercially (e.g., Transfectam.TM. and Lipofectin.sup.TM).
Cationic and neutral lipids that are suitable for efficient
receptor-recognition lipofection of polynucleotides include those
of Felgner, WO 91/17424; WO 91/16024. Delivery can be to cells
(e.g. in vitro or ex vivo administration) or target tissues (e.g.
in vivo administration).
[0142] The preparation of lipid:nucleic acid complexes, including
targeted liposomes such as immunolipid complexes, is well known to
one of skill in the art (see, e.g., Crystal, Science 270:404-410
(1995); Blaese et al., Cancer Gene Ther. 2:291-297 (1995); Behr et
al., Bioconjugate Chem. 5:382-389 (1994); Remy et al., Bioconjugate
Chem. 5:647-654 (1994); Gao et al., Gene Therapy 2:710-722 (1995);
Ahmad et al., Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos.
4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728,
4,774,085, 4,837,028, and 4,946,787).
[0143] The use of RNA or DNA viral based systems for the delivery
of nucleic acids takes advantage of highly evolved processes for
targeting a virus to specific cells in the body and trafficking the
viral payload to the nucleus. Viral vectors can be administered
directly to patients (in vivo) or they can be used to treat cells
in vitro, and the modified cells may optionally be administered to
patients (ex vivo). Conventional viral based systems could include
retroviral, lentivirus, adenoviral, adeno-associated and herpes
simplex virus vectors for gene transfer. Integration in the host
genome is possible with the retrovirus, lentivirus, and
adeno-associated virus gene transfer methods, often resulting in
long term expression of the inserted transgene. Additionally, high
transduction efficiencies have been observed in many different cell
types and target tissues.
[0144] The tropism of a retrovirus can be altered by incorporating
foreign envelope proteins, expanding the potential target
population of target cells. Lentiviral vectors are retroviral
vectors that are able to transduce or infect non-dividing cells and
typically produce high viral titers. Selection of a retroviral gene
transfer system would therefore depend on the target tissue.
Retroviral vectors are comprised of cis-acting long terminal
repeats with packaging capacity for up to 6-10 kb of foreign
sequence. The minimum cis-acting LTRs are sufficient for
replication and packaging of the vectors, which are then used to
integrate the therapeutic gene into the target cell to provide
permanent transgene expression. Widely used retroviral vectors
include those based upon murine leukemia virus (MuLV), gibbon ape
leukemia virus (GaLV), Simian Immuno deficiency virus (SIV), human
immuno deficiency virus (HIV), and combinations thereof (see, e.g.,
Buchscher et al., J. Virol. 66:2731-2739 (1992); Johann et al., J.
Virol. 66:1635-1640 (1992); Sommnerfelt et al., Virol. 176:58-59
(1990); Wilson et al., J. Virol. 63:2374-2378 (1989); Miller et
al., J. Virol. 65:2220-2224 (1991); PCT/US94/05700).In applications
where transient expression is preferred, adenoviral based systems
may be used. Adenoviral based vectors are capable of very high
transduction efficiency in many cell types and do not require cell
division. With such vectors, high titer and levels of expression
have been obtained. This vector can be produced in large quantities
in a relatively simple system. Adeno-associated virus ("AAV")
vectors may also be used to transduce cells with target nucleic
acids, e.g., in the in vitro production of nucleic acids and
peptides, and for in vivo and ex vivo gene therapy procedures (see,
e.g., West et al., Virology 160:38-47 (1987); U. S. Pat. No.
4,797,368; WO 93/24641; Kotin, Human Gene Therapy 5:793-801 (1994);
Muzyczka, J. Clin. Invest. 94:1351 (1994). Construction of
recombinant AAV vectors are described in a number of publications,
including U.S. Pat. No. 5,173,414; Tratschin et al., Mol. Cell.
Biol. 5:3251-3260 (1985); Tratschin, et al., Mol. Cell. Biol.
4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470
(1984); and Samulski et al., J. Virol. 63:03822-3828 (1989).
[0145] Packaging cells are typically used to form virus particles
that are capable of infecting a host cell. Such cells include 293
cells, which package adenovirus, and w.sup.2 cells or PA317 cells,
which package retrovirus. Viral vectors used in gene therapy are
usually generated by producing a cell line that packages a nucleic
acid vector into a viral particle. The vectors typically contain
the minimal viral sequences required for packaging and subsequent
integration into a host, other viral sequences being replaced by an
expression cassette for the polynucleotide(s) to be expressed. The
missing viral functions are typically supplied in trans by the
packaging cell line. For example, AAV vectors used in gene therapy
typically only possess ITR sequences from the AAV genome which are
required for packaging and integration into the host genome. Viral
DNA is packaged in a cell line, which contains a helper plasmid
encoding the other AAV genes, namely rep and cap, but lacking ITR
sequences. The cell line may also be infected with adenovirus as a
helper. The helper virus promotes replication of the AAV vector and
expression of AAV genes from the helper plasmid. The helper plasmid
is not packaged in significant amounts due to a lack of ITR
sequences. Contamination with adenovirus can be reduced by, e.g.,
heat treatment to which adenovirus is more sensitive than AAV.
Additional methods for the delivery of nucleic acids to cells are
known to those skilled in the art. See, for example, US20030087817,
incorporated herein by reference.
[0146] In some embodiments, a host cell is transiently or
non-transiently transfected with one or more vectors described
herein. In some embodiments, a cell is transfected as it naturally
occurs in a subject. In some embodiments, a cell that is
transfected is taken from a subject. In some embodiments, the cell
is derived from cells taken from a subject, such as a cell line. A
wide variety of cell lines for tissue culture are known in the art.
Examples of cell lines include, but are not limited to, C8161,
CCRF-CEM, MOLT, mIMCD-3, NHDF, HeLa-S3, Huh1, Huh4, Huh7, HUVEC,
HASMC, HEKn, HEKa, MiaPaCell, Panc1, PC-3, TF1, CTLL-2, CIR, Rat6,
CV1, RPTE, A10, T24, J82, A375, ARH-77, Calu1, SW480, SW620, SKOV3,
SK-UT, CaCo2, P388D1, SEM-K2, WEHI-231, HB56, TIB55, Jurkat,
J45.01, LRMB, Bcl-1, BC-3, IC21, DLD2, Raw264.7, NRK, NRK-52E,
MRC5, MEF, Hep G2, HeLa B, HeLa T4, COS, COS-1, COS-6, COS-M6A,
BS-C-1 monkey kidney epithelial, BALB/3T3 mouse embryo fibroblast,
3T3 Swiss, 3T3-L1, 132-d5 human fetal fibroblasts; 10.1 mouse
fibroblasts, 293-T, 3T3, 721, 9L, A2780, A2780ADR, A2780cis, A172,
A20, A253, A431, A-549, ALC, B16, B35, BCP-1 cells, BEAS-2B,
bEnd.3, BHK-21, BR 293, BxPC3, C3H-10T1/2, C6/36, Cal-27, CHO,
CHO-7, CHO-IR, CHO-K1, CHO-K2, CHO-T, CHO Dhfr -/-, COR-L23,
COR-L23/CPR, COR-L23/5010, COR-L23/R23, COS-7, COV-434, CML T1,
CMT, CT26, D17, DH82, DU145, DuCaP, EL4, EM2, EM3, EMT6/ARI,
EMT6/AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, HEK-293, HeLa,
Hepalclc7, HL-60, HMEC, HT-29, Jurkat, JY cells, K562 cells. Ku812,
KCL22, KGI, KYOl, LNCap, Ma-Mel 1-48, MC-38, MCF-7, MCF-10A,
MDA-MB-231, MDA-MB-468, MDA-MB-435, MDCK II, MDCK II, MOR/0.2R,
MONO-MAC 6. MTD-1A, MyEnd, NCI-H69/CPR, NCI-H69/LX10, NCI-H69/LX20,
NCI-H69/LX4, NIH-3T3, NALM-1, NW-145, OPCN/OPCT cell lines, Peer,
PNT-1A/PNT 2, RenCa, RIN-5F, RMA/RMAS, Saos-2 cells, Sf-9, SkBr3,
T2, T-47D, T84, THP1 cell line, U373, U87, U937, VCaP, Vero cells,
WM39, WT-49, X63, YAC-1, YAR, and transgenic varieties thereof.
Cell lines are available from a variety of sources known to those
with skill in the art (see. e.g., the American Type Culture
Collection (ATCC) (Manassas, Va.)). In some embodiments, a cell
transfected with one or more vectors described herein is used to
establish a new cell line comprising one or more vector-derived
sequences. In some embodiments, a cell transiently transfected with
the components of a CRISPR system as described herein (such as by
transient transfection of one or more vectors, or transfection with
RNA), and modified through the activity of a CRISPR complex, is
used to establish a new cell line comprising cells containing the
modification but lacking any other exogenous sequence. In some
embodiments, cells transiently or non-transiently transfected with
one or more vectors described herein, or cell lines derived from
such cells are used in assessing one or more test compounds.
[0147] In some embodiments, one or more vectors described herein
are used to produce a non-human transgenic animal or transgenic
plant. In some embodiments, the transgenic animal is a mammal, such
as a mouse, rat, or rabbit. In certain embodiments, the organism or
subject is a plant. In certain embodiments, the organism or subject
or plant is algae. Methods for producing transgenic plants and
animals are known in the art, and generally begin with a method of
cell transfection, such as described herein.
[0148] In one aspect, the invention provides for methods of
modifying a target polynucleotide in a eukaryotic cell. In some
embodiments, the method comprises allowing a CRISPR complex to bind
to the target polynucleotide to effect cleavage of said target
polynucleotide thereby modifying the target polynucleotide, wherein
the CRISPR complex comprises a CRISPR enzyme complexed with a guide
sequence hybridized to a target sequence within said target
polynucleotide, wherein said guide sequence is linked to a tracr
mate sequence which in turn hybridizes to a tracr sequence.
[0149] In one aspect, the invention provides a method of modifying
expression of a polynucleotide in a eukaryotic cell. In some
embodiments, the method comprises allowing a CRISPR complex to bind
to the polynucleotide such that said binding results in increased
or decreased expression of said polynucleotide; wherein the CRISPR
complex comprises a CRISPR enzyme complexed with a guide sequence
hybridized to a target sequence within said polynucleotide, wherein
said guide sequence is linked to a tracr mate sequence which in
turn hybridizes to a tracr sequence.
[0150] With recent advances in crop genomics, the ability to use
CRISPR-Cas systems to perform efficient and cost effective gene
editing and manipulation will allow the rapid selection and
comparison of single and multiplexed genetic manipulations to
transform such genomes for improved production and enhanced traits.
In this regard reference is made to US patents and publications:
U.S. Pat. No. 6,603,061--Agrobacterium-Mediated Plant
Transformation Method; U.S. Pat. No. 7,868,149--Plant Genome
Sequences and Uses Thereof and US 2009/0100536--Transgenic Plants
with Enhanced Agronomic Traits, all the contents and disclosure of
each of which are herein incorporated by reference in their
entirety. In the practice of the invention, the contents and
disclosure of Morrell et al "Crop genomics:advances and
applications" Nat Rev Genet. 2011 Dec. 29; 13(2):85-96 are also
herein incorporated by reference in their entirety. In an
advantageous embodiment of the invention, the CRISPR/Cas9 system is
used to engineer microalgae (Example 15). Accordingly, reference
herein to animal cells may also apply, mutatis mutandis, to plant
cells unless otherwise apparent.
[0151] In one aspect, the invention provides for methods of
modifying a target polynucleotide in a eukaryotic cell, which may
be in vivo, ex vivo or in vitro. In some embodiments, the method
comprises sampling a cell or population of cells from a human or
non-human animal or plant (including micro-algae), and modifying
the cell or cells. Culturing may occur at any stage ex vivo. The
cell or cells may even be re-introduced into the non-human animal
or plant (including micro-algae).
[0152] In plants, pathogens are often host-specific. For example,
Fusarium oxysporum f. sp. lycopersici causes tomato wilt but
attacks only tomato, and F. oxysporum f dianthii Puccinia graminis
f. sp. tritici attacks only wheat. Plants have existing and induced
defenses to resist most pathogens. Mutations and recombination
events across plant generations lead to genetic variability that
gives rise to susceptibility, especially as pathogens reproduce
with more frequency than plants. In plants there can be non-host
resistance, e.g., the host and pathogen are incompatible. There can
also be Horizontal Resistance, e.g., partial resistance against all
races of a pathogen, typically controlled by many genes and
Vertical Resistance, e.g., complete resistance to some races of a
pathogen but not to other races, typically controlled by a few
genes. In a Gene-for-Gene level, plants and pathogens evolve
together, and the genetic changes in one balance changes in other.
Accordingly, using Natural Variability, breeders combine most
useful genes for Yield, Quality, Uniformity, Hardiness, Resistance.
The sources of resistance genes include native or foreign
Varieties, Heirloom Varieties, Wild Plant Relatives, and Induced
Mutations, e.g., treating plant material with mutagenic agents.
Using the present invention, plant breeders are provided with a new
tool to induce mutations. Accordingly, one skilled in the art can
analyze the genome of sources of resistance genes, and in Varieties
having desired characteristics or traits employ the present
invention to induce the rise of resistance genes, with more
precision than previous mutagenic agents and hence accelerate and
improve plant breeding programs.
[0153] In one aspect, the invention provides kits containing any
one or more of the elements disclosed in the above methods and
compositions. In some embodiments, the kit comprises a vector
system and instructions for using the kit. In some embodiments, the
vector system comprises (a) a first regulatory element operably
linked to a tracr mate sequence and one or more insertion sites for
inserting a guide sequence upstream of the tracr mate sequence,
wherein when expressed, the guide sequence directs
sequence-specific binding of a CRISPR complex to a target sequence
in a eukaryotic cell, wherein the CRISPR complex comprises a CRISPR
enzyme complexed with (1) the guide sequence that is hybridized to
the target sequence, and (2) the tracr mate sequence that is
hybridized to the tracr sequence; and/or (b) a second regulatory
element operably linked to an enzyme-coding sequence encoding said
CRISPR enzyme comprising a nuclear localization sequence. Elements
may be provide individually or in combinations, and may be provided
in any suitable container, such as a vial, a bottle, or a tube. In
some embodiments, the kit includes instructions in one or more
languages, for example in more than one language.
[0154] In some embodiments, a kit comprises one or more reagents
for use in a process utilizing one or more of the elements
described herein. Reagents may be provided in any suitable
container. For example, a kit may provide one or more reaction or
storage buffers. Reagents may be provided in a form that is usable
in a particular assay, or in a form that requires addition of one
or more other components before use (e.g. in concentrate or
lyophilized form). A buffer can be any buffer, including but not
limited to a sodium carbonate buffer, a sodium bicarbonate buffer,
a borate buffer, a Tris buffer, a MOPS buffer, a HEPES buffer, and
combinations thereof. In some embodiments, the buffer is alkaline.
In some embodiments, the buffer has a pH from about 7 to about 10.
In some embodiments, the kit comprises one or more oligonucleotides
corresponding to a guide sequence for insertion into a vector so as
to operably link the guide sequence and a regulatory element. In
some embodiments, the kit comprises a homologous recombination
template polynucleotide.
[0155] In one aspect, the invention provides methods for using one
or more elements of a CRISPR system. The CRISPR complex of the
invention provides an effective means for modifying a target
polynucleotide. The CRISPR complex of the invention has a wide
variety of utility including modifying (e.g., deleting, inserting,
translocating, inactivating, activating) a target polynucleotide in
a multiplicity of cell types. As such the CRISPR complex of the
invention has a broad spectrum of applications in, e.g., gene
therapy, drug screening, disease diagnosis, and prognosis. An
exemplary CRISPR complex comprises a CRISPR enzyme complexed with a
guide sequence hybridized to a target sequence within the target
polynucleotide. The guide sequence is linked to a tracr mate
sequence, which in turn hybridizes to a tracr sequence.
[0156] The target polynucleotide of a CRISPR complex can be any
polynucleotide endogenous or exogenous to the eukaryotic cell. For
example, the target polynucleotide can be a polynucleotide residing
in the nucleus of the eukaryotic cell. The target polynucleotide
can be a sequence coding a gene product (e.g., a protein) or a
non-coding sequence (e.g., a regulatory polynucleotide or a junk
DNA). Without wishing to be bound by theory, it is believed that
the target sequence should be associated with a PAM (protospacer
adjacent motif); that is, a short sequence recognized by the CRISPR
complex. The precise sequence and length requirements for the PAM
differ depending on the CRISPR enzyme used, but PAMs are typically
2-5 base pair sequences adjacent the protospacer (that is, the
target sequence) Examples of PAM sequences are given in the
examples section below, and the skilled person will be able to
identify further PAM sequences for use with a given CRISPR
enzyme.
[0157] The target polynucleotide of a CRISPR complex may include a
number of disease-associated genes and polynucleotides as well as
signaling biochemical pathway-associated genes and polynucleotides
as listed in U.S. provisional patent applications 61/736,527 and
61/748,427 having Broad reference BI-2011/008/WSGR Docket No.
44063-701.101 and BI-2011/008/WSGR Docket No. 44063-701.102
respectively, both entitled SYSTEMS METHODS AND COMPOSITIONS FOR
SEQUENCE MANIPULATION filed on Dec. 12, 2012 and Jan. 2, 2013,
respectively, the contents of all of which are herein incorporated
by reference in their entirety.
[0158] Examples of target polynucleotides include a sequence
associated with a signaling biochemical pathway, e.g., a signaling
biochemical pathway-associated gene or polynucleotide. Examples of
target polynucleotides include a disease associated gene or
polynucleotide. A "disease-associated" gene or polynucleotide
refers to any gene or polynucleotide which is yielding
transcription or translation products at an abnormal level or in an
abnormal form in cells derived from a disease-affected tissues
compared with tissues or cells of a non disease control. It may be
a gene that becomes expressed at an abnormally high level; it may
be a gene that becomes expressed at an abnormally low level, where
the altered expression correlates with the occurrence and/or
progression of the disease. A disease-associated gene also refers
to a gene possessing mutation(s) or genetic variation that is
directly responsible or is in linkage disequilibrium with a gene(s)
that is responsible for the etiology of a disease. The transcribed
or translated products may be known or unknown, and may be at a
normal or abnormal level.
[0159] Examples of disease-associated genes and polynucleotides are
available from McKusick-Nathans Institute of Genetic Medicine,
Johns Hopkins University (Baltimore, Md.) and National Center for
Biotechnology Information, National Library of Medicine (Bethesda,
Md.), available on the World Wide Web.
[0160] Examples of disease-associated genes and polynucleotides are
listed in Tables A and B. Disease specific information is available
from McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University (Baltimore, Md.) and National Center for Biotechnology
Information, National Library of Medicine (Bethesda, Md.),
available on the World Wide Web. Examples of signaling biochemical
pathway-associated genes and polynucleotides are listed in Table
C.
[0161] Mutations in these genes and pathways can result in
production of improper proteins or proteins in improper amounts
which affect function. Further examples of genes, diseases and
proteins are hereby incorporated by reference from U.S. Provisional
application 61/736,527 filed on Dec. 12, 2012 and 61/748,427 filed
on Feb. 2, 2013. Such genes, proteins and pathways may be the
target polynucleotide of a CRISPR complex.
TABLE-US-00001 TABLE A DISEASE/ DISORDERS GENE(S) Neoplasia PTEN;
ATM; ATR; EGFR; ERBB2; ERBB3; ERBB4; Notch1; Notch2; Notch3;
Notch4; AKT; AKT2; AKT3; HIF; HIF1a; HIF3a; Met; HRG; Bcl2; PPAR
alpha; PPAR gamma; WT1 (Wilms Tumor); FGF Receptor Family members
(5 members: 1, 2, 3, 4, 5); CDKN2a.; APC; RB (retinoblastoma);
MEN1; VHL; BRCA1; BRCA2; AR (Androgen Receptor); TSG101; IGF; IGF
Receptor; Igf1 (4 variants); Igf2 (3 variants); Igf 1 Receptor; Igf
2 Receptor; Bax; Bcl2; caspases family (9 members: 1, 2, 3, 4, 6,
7, 8, 9, 12); Kras; Apc Age-related Aber; Ccl2; Cc2; cp
(ceruloplasmin); Timp3; cathepsinD; Macular Vldlr; Ccr2
Degeneration Schizophrenia Neuregulin1 (Nrg1); Erb4 (receptor for
Neuregulin); Complexin1 (Cplx1); Tph1 Tryptophan hydroxylase; Tph2
Tryptophan hydroxylase 2; Neurexin 1; GSK3; GSK3a; GSK3b Disorders
5-HTT (Slc6a4); COMT; DRD (Drd1a); SLC6A3; DAOA; DTNBP1; Dao (Dao1)
Trinucleotide HTT (Huntington's Dx); SBMA/SMAX1/AR (Kennedy's
Repeat Dx); FXN/X25 (Friedrich's Ataxia); ATX3 (Machado- Disorders
Joseph's Dx); ATXN1 and ATXN2 (spinocerebellar ataxias); DMPK
(myotonic dystrophy); Atrophin-1 and Atn1 (DRPLA Dx); CBP
(Creb-BP--global instability); VLDLR (Alzheimer's); Atxn7; Atxn10
Fragile X FMR2; FXR1; FXR2; mGLUR5 Syndrome Secretase APH-1 (alpha
and beta); Presenilin (Psen1); nicastrin Related (Ncstn); .PEN-2
Disorders Others Nos1: Parp1; Nat1; Nat2 Prion--related Prp
disorders ALS SOD1; ALS2; STEX; FUS; TARDBP; VEGF (VEGF-a; VEGF-b;
VEGF-c) Drug Prkce (alcohol); Drd2; Drd4; ABAT (alcohol); GRIA2;
addiction Grm5; Grin1; Htr1b; Grin2a; Drd3; Pdyn; Gria1 (alcohol)
Autism Mecp2; BZRAP1; MDGA2; Sema5A.; Neurexin 1; Fragile X (FMR2
(AFF2); FXR1; FXR2; Mglur5) Alzheimer's E1; CHIP; UCH; UBB; Tau;
LRP; PICALM; Clusterin; Disease PS1; SORL1; CR1; Vldlr; Ubal; Uba3;
CHIP28 (Aqp1, Aquaporin 1); Uchl1; Uchl3; APP Inflammation IL-10;
IL-1 (IL-1a; IL-1b); IL-13; IL-17 (IL-17a (CTLA8); IL-17b; IL-17c;
IL-17d; :IL-17f); II-23; Cx3cr1; ptpn22; TNfa; NOD2/CARD15 for IBD;
IL-6; IL-12 (IL-12a; IL- 12b); CTLA4; Cx3cl1 Parkinson's
x-Synuclein; DJ-1; LRRK2; Parkin; PINK1 Disease
TABLE-US-00002 TABLE B Blood and Anemia (CDAN1, CDA1, RPS19, DBA,
PKLR, PK1, NT5C3, UMPH1, coagulation diseases PSN1, RHAG, RH50A,
NRAMP2, SPTB, ALAS2, ANH1, ASB, and disorders ABCB7, ABC7, ASAT);
Bare lymphocyte syndrome (TAPBP, TPSN, TAP2, ABCB3, PSF2, RING11,
MHC2TA, C2TA, RFX5, RFXAP, RFX5), Bleeding disorders (TBXA2R,
P2RX1, P2X1); Factor H and factor H-like 1 (HF1, CFH, HUS); Factor
V and factor VIII (MCFD2); Factor VII deficiency (F7); Factor X
deficiency (F10); Factor XI deficiency (F11); Factor XII deficiency
(F12, HAF); Factor XIIIA deficiency (F13A1, F13A); Factor XIIIB
deficiency (F13B); Fanconi anemia (FANCA, FACA, FA1, FA, FAA,
FAAP95, FAAP90, FLJ34064, FANCB, FANCC, FACC, BRCA2, FANCD1,
FANCD2, FANCD, FACD, FAD, FANCE, FACE, FANCT; XRCC9, FANCG, BRIP1,
BACH1, FANCJ, PHF9, FANCL, FANCM, KIAA1596); Hemophagocytic
lymphohistiocytosis disorders (PRF1, HPLH2, UNC13D, MUNC13-4,
HPLH3, HLH3, FHL3); Hemophilia A (F8, F8C, HEMA); Hemophilia B (F9,
HEMB), Hemorrhagic disorders (PI, ATT, F5); Leukocyde deficiencies
and disorders (ITGB2, CD18, LCAMB, LAD, EIF2B1, EIF2BA, EIF2B2,
EIF2B3, EIF2B5, LVWM, CACH, CLE, EIF2B4); Sickle cell anemia (HBB);
Thalassemia (HBA2, HBB, HBD, LCRB, HBA1) Cell dysregulation B-cell
non-Hodgkin lymphoma. (BCL7A, BCL7); Leukemia (TAL1, and oncology
TCL5, SCL, TAL2, FLT3, NBS1, NBS, ZNFN1A1, IK1, LYF1, diseases and
disorders HOXD4, HOX4B, BCR, CML, PHL, ALL, ARNT, KRAS2, RASK2,
GMPS, AF10, ARHGEF12, LARG, KIAA0382, CALM, CLTH, CEBPA, CEBP,
CHIC2, BTL, FLT3, KIT, PBT, LPP, NPM1, NUP214, D9S46E, CAN, CAIN,
RUNX1, CBFA2, AML1, WHSC1L1, NSD3, FLT3, AF1Q, NPM1, NUMA1, ZNF145,
PLZF, PML, MYL, STAT5B, AF10, CALM, CLTH, ARL11, ARLTS1, P2RX7,
P2X7, BCR, CML, PHL, ALL, GRAF, NF1, VRNF, WSS, NFNS, PTPN11,
PTP2C, SHP2, NS1, BCL2, CCND1, PRAD1, BCL1, TCRA, GATA1, GF1,
ERYF1, NFE1, ABL1, NQO1, DIA4, NMOR1, NUP214, D9S46E, CAN, CAIN).
Inflammation and AIDS (KIR3DL1, NKAT3, NKB1, AMB11, KIR3DS1, IFNG,
CXCL12, immune related SDF1); Autoimmune lymphoproliferative
syndrome (TNFRSF6, APT1, diseases and disorders FAS, CD95, ALPS1A);
Combined immunodeficiency, (IL2RG, SCIDX1, SCIDX, IMD4); HIV-1
(CCL5, SCYA5, D17S136E, TCP228), HIV susceptibility or infection
(IL10, CSIF, CMKBR2, CCR2, CMKBR5, CCCKR5 (CCR5));
Immunodeficiencies (CD3E, CD3G, AICDA, AID, HIGM2, TNFRSF5, CD40,
UNG, DGU, HIGM4, TNFSF5, CD40LG, HIGM1, IGM, FOXP3, IPEX, AIID,
XPID, PIDX, TNFRSF14B, TACI); Inflammation (IL-10, IL-1 (IL-1a,
IL-1b), IL-13, IL-17 (IL-17a (CTLA8), IL-17b, IL-17c, IL-17d,
IL-17f), II-23, Cx3cr1, ptpn22, TNFa, NOD2/CARD15 for IBD, IL-6,
IL-12 (IL-12a, IL-12b), CTLA4, Cx3cl1); Severe combined
immunodeficiencies (SCIDs)(JAK3, JAKL, DCLRE1C, ARTEMIS, SCIDA,
RAG1, RAG2, ADA, PTPRC, CD45, LCA, IL7R, CD3D, T3D, IL2RG, SCIDX1,
SCIDX, IMD4). Metabolic, liver. Amyloid neuropathy (TTR, PALB);
Amyloidosis APOA1, APP, AAA, kidney and protein CVAP, AD1, GSN,
FGA, LYZ, TTR, PALB); Cirrhosis (KRT18, KRT8, diseases and
disorders CIRH1A, NAIC, TEX292, KIAA1988); Cystic fibrosis (CFTR,
ABCC7, CF, MRP7); Glycogen storage diseases (SLC2A2, GLUT2, G6PC,
G6PT, G6PT1, GAA, LAMP2, LAMPB, AGL, GDE, GRE1, GYS2, PYGL. PFKM);
Hepatic adenoma, 142330 (TCF1, HNF1A, MODY3), Hepatic failure,
early onset, and neurologic disorder (SCOD1, SCO1), Hepatic lipase
deficiency (LIPC), Hepatoblastoma, cancer and carcinomas (CTNNB1,
PDGFRL, PDGRL, PRLTS, AXIN1, AXIN, CTNNB1, TP53, P53, LFS1, IGF2R,
MPRI, MET, CASP8, MCH5; Medullary cystic kidney disease (UMOD,
HNFJ, FJHN, MCKD2, ADMCKD2); Phenylketonuria (PAH, PKU1, QDPR,
DHPR, PTS); Polycystic kidney and hepatic disease (FCYT, PKHD1,
ARPKD, PKD1, PKD2, PKD4, PKDTS, PRKCSH, G19P1, PCLD, SEC63).
Muscular/Skeletal Becker muscular dystrophy (DMD, BMD, MYF6),
Duchenne Muscular diseases and disorders Dystrophy (DMD, BMD);
Emery-Dreifuss muscular dystrophy (LMNA, LMN1, EMD2, FPLD, CMD1A,
HGPS, LGMD1B, LMNA, LMN1, EMD2, FPLD, CMD1A); Facioscapulohumeral
muscular dystrophy (FSHMD1A, FSHD1A); Muscular dystrophy (FKRP,
MDC1C, LGMD2I, LAMA2, LAMM, LARGE, KIAA0609, MDC1D, FCMD, TTID,
MYOT, CAPN3, CANP3, DYSF, LGMD2B, SGCG, LGMD2C, DMDA1, SCG3, SGCA,
ADL, DAG2, LGMD2D, DMDA2, SGCB, LGMD2E, SGCD, SGD, LGMD2F, CMD1L,
TCAP, LGMD2G, CMD1N, TRIM32, HT2A, LGMD2H, FKRP, MDC1C, LGMD2I,
TTN, CMD1G, TMD, LGMD2J, POMT1, CAV3, LGMD1C, SEPN1, SELN, RSMD1,
PLEC1, PLTN, EBS1); Osteopetrosis (LRP5, BMND1, LRP7, LR3, OPPG,
VBCH2, CLCN7, CLC7, OPTA2, OSTM1, GL, TCIRG1, TIRC7, OC116, OPTB1);
Muscular atrophy (VAPB, VAPC, ALS8, SMN1, SMA1, SMA2, SMA3, SMA4,
BSCL2, SPG17, GARS, SMAD1, CMT2D, HEXB, IGHMBP2, SMUBP2, CATF I,
SMARD1). Neurological and ALS (SOD1, ALS2, STEX, FUS, TARDBP, VEGF
(VEGF-a, VEGF-b, neuronal diseases and VEGF-c); Alzheimer disease
(APP, AAA, CVAP, AD1, APOE, AD2, disorders PSEN2, AD4, STM2, APBB2,
FE65L1, NOS3, PLAU, URK, ACE, DCP1, ACE1, MPO, PACIP1, PAXIP1,
PTIP, A2M, BLMH, BMH, PSEN1, AD3); Autism (Mecp2, BZRAP1, MDGA2,
Sema5A, Neurexin 1, GLO1, MECP2, RTT, PPMX, MRX16, MRX79, NLGN3,
NLGN4, KIAA1260, AUTSX2); Fragile X Syndrome (FMR2, FXR1, FXR2,
mGLUR5); Huntington's disease and disease like disorders (HD, IT15,
PRNP, PRIP, JPH3, JP3, HDL2, TBP, SCA17); Parkinson disease (NR4A2,
NURR1, NOT, TINUR, SNCAIP, TBP, SCA17, SNCA, NACP, PARK1, PARK4,
DJ1, PARK7, LRRK2, PARK8, PINK1, PARK6, UCHL1, PARK5, SNCA, NACP,
PARK1, PARK4, PRKN, PARK2, PDJ, DBH, NDUFV2); Rett syndrome (MECP2,
RTT, PPMX, MRX16, MRX79, CDKL5, STK9, MECP2, RTT, PPMX, MRX16,
MRX79, x-Synuclein, DJ-1); Schizophrenia (Neuregulin1 (Nrg1), Erb4
(receptor for Neuregulin), Complexin1 (Cplx1), Tph1 Tryptophan
hydroxylase, Tph2, Tryptophan hydroxylase 2, Neurexin 1, GSK3,
GSK3a, GSK3b, 5-HTT (Slc6a4), COMT, DRD (Drd1a), SLC6A3, DAOA,
DTNBP1, Dao (Dao1)); Secretase Related Disorders (APH-1 (alpha and
beta), Presenilin (Psen1), nicastrin, (Ncstn), PEN-2, Nos1, Parp1,
Nat1, Nat2); Trinucleotide Repeat Disorders (HTT (Huntington's Dx),
SBMA/SMAX1/AR (Kennedy's Dx), FXN/X25 (Friedrich's Ataxia), ATX3
(Machado- Joseph's Dx), ATXN1 and ATXN2 (spinocerebellar ataxias),
DMPK (myotonic dystrophy), Atrophin-1 and Atn1 (DRPLA Dx), CBP
(Creb-BP--global instability), VLDLR (Alzheimer's), Atxn7, Atxn10).
Occular diseases and Age-related macular degeneration (Abcr, Ccl2,
Cc2, cp (ceruloplasmin), disorders Timp3, cathepsinD, Vldlr, Ccr2);
Cataract (CRYAA, CRYA1, CRYBB2, CRYB2, PTI X3, .13FSP2, CP49, CP47,
(RYAN., CRY A1, PAX6, AN2, MGDA, CRYBA1, CRYB1, CRYGC, CRYG3, CCL,
LIM2, MP19, CRYGD, CRYG4, BFSP2, CP49, CP47, HSF4, CTM, HSF4, CTM,
MIP, AQP0, CRYAB, CRYA2 CTPP2, CRYBB1, CRYGD, CRYG4, CRYBB2, CRYB2,
CRYGC, CRYG3, CCL, CRYAA, CRYA1, GJA8, CX50, CAE1, GJA3, CX46,
CZP3, CAE3, CCM1, CAM, KRIT1); Corneal clouding and dystrophy
(APOA1, TGFBI, CSD2, CDGG1, CSD, BIGH3, CDG2, TACSTD2, TROP2, M1S1,
VSX1, RINX, PPCD, PPD, KTCN, COL8A2, FECD, PPCD2, PIP5K3, CFD);
Cornea plana congenital (KERA, CNA2); Glaucoma (MYOC, TIGR, GLC1A,
JOAG, GPOA, OPTN, GLC1E, FIP2, HYPL, NRP, CYP1B1, GLC3A, OPA1 NTG,
NPG, CYP1B1, GLC3A); Leber congenital amaurosis (CRB1, RP12, CRX,
CORD2, CRD, RPGRIP1, LCA6, CORD9, RPE65, RP20, AIPL1, LCA4, GUCY2D,
GUC2D, LCA1, CORD6, RDH12, LCA3); Macular dystrophy (ELOVL4, ADMD,
STGD2, STGD3, RDS, RP7, PRPH2, PRPH, AVMD, AOFMD, VMD2).
TABLE-US-00003 TABLE C CELLULAR FUNCTION GENES PI3K/AKT Signaling
PRKCE; ITGAM; ITGA5; IRAK1; PRKAA2; EIF2AK2; PTEN; EIF4E; PRKCZ;
GRK6; MAPK1; TSC1; PLK1; AKT2; IKBKB; PIK3CA; CDK8; CDKN1B; NFKB2;
BCL2; PIK3CB; PPP2R1A; MAPK8; BCL2L1; MAPK3; TSC2; ITGA1; KRAS;
EIF4EBP1; RELA; PRKCD; NOS3; PRKAA1; MAPK9; CDK2; PPP2CA; PIM1;
ITGB7; YWHAZ; ILK; TP53; RAF1; IKBKG; RELB; DYRK1A; CDKN1A; ITGB1;
MAP2K2; JAK1; AKT1; JAK2; PIK3R1; CHUK ; PDPK1; PPP2R5C; CTNNB1 ;
MAP2K1; NFKB1; PAK3; ITGB3; CCND1; GSK3A; FRAP1; SFN; ITGA2; TTK;
CSNK1A1; BRAF; GSK3B; AKT3; FOXO1; SGK; HSP9OAA1; RPS6KB1 ERK/MAPK
Signaling PRKCE; ITGAM; ITGA5; HSPB1; IRAK1; PRKAA2; EIF2AK2; RAC1;
RAP1A; TLN1; EIF4E; ELK1; GRK6; MAPK1; RAC2; PLK1; AKT2; PIK3CA;
CDK8; CREB1; PRKCI; PTK2; FOS; RPS6KA4; PIK3CB; PPP2R1A; PIK3C3;
MAPK8; MAPK3; ITGA1; ETS1; KRAS; MYCN; EIF4EBP1; PPARG; PRKCD;
PRKAA1; MAPK9; SRC; CDK2; PPP2CA; PIM1; PIK3C2A; ITGB7; YWHAZ;
PPP1CC; KSR1; PXN; RAF1; FYN; DYRK1A; ITGB1; MAP2K2; PAK4; PIK3R1;
STAT3; PPP2R5C; MAP2K1; PAK3; ITGB3; ESR1; ITGA2; MYC; TTK;
CSNK1A1; CRKL; BRAT; ATF4; PRKCA; SRF; STAT1; SGK Glucocorticoid
Receptor RAC1; TAF4B; EP300; SMAD2; TRAF6; PCAF; ELK1; Signaling
MAPK1; SMAD3; AKT2; IKBKB; NCOR2; UBE2I; PIK3CA; CREB1; FOS; HSPA5;
NFKB2; BCL2; MAP3K14; STAT5B; PIK3CB; PIK3C3; MAPK8; BCL2L1; MAPK3;
TSC22D3; MAPK10; NRIP1; KRAS; MAPK13; RELA; STAT5A; MAPK9; NOS2A;
PBX1; NR3C1; PIK3C2A; CDKN1C; TRAF2; SERPINE1; NCOA3; MAPK14; TNF;
RAF1; IKBKG; MAP3K7; CREBBP CDKN1A; MAP2K2; JAK1; IL8; NCOA2; AKT1;
JAK2; PIK3R1; CHUK; STAT3; MAP2K1; NFKB1; TGFBR1; ESR1; SMAD4;
CEBPB; JUN; AR; AKT3; CCL2; MMP1; STAT1; IL6; HSP90AA1 Axonal
Guidance PRKCE; ITGAM; ROCK1; ITGA5; CXCR4; ADAM12; Signaling IGF1;
RAC1; RAP1A; EIF4E; PRKCZ; NRP1; NTRK2; ARHGEF7; SMO; ROCK2; MAPK1;
PGF; RAC2; PTPN11; GNAS; AKT2; PIK3CA; ERBB2; PRKCI; PTK2; CFL1;
GNAQ; PIK3CB; CXCL12; PIK3C3; WNT11; PRKD1; GNB2L1; ABLI; MAPK3;
ITGA1; KRAS; RHOA; PRKCD; PIK3C2A; ITGB7; GLI2; PXN; VASP; RAF1;
FYN; ITGB1; MAP2K2; PAK4; ADAM17; AKT1; PIK3R1; GLI1; WNT5A;
ADAM10; MAP2K1; PAK3; ITGB3; CDC42; VEGFA; ITGA2; EPHA8; CRKL;
RND1; GSK3B; AKT3; PRKCA Ephrin Receptor PRKCE; ITGAM; ROCK1;
ITGA5; CXCR4; IRAK1; Signaling PRKAA2; EIF2AK2; RAC1; RAP1A; GRK6;
ROCK2; MAPK1; PGF; RAC2; PTPN11; GNAS; PLK1; AKT2; DOK1; CDK8;
CREB1; PTK2; CFL1; GNAQ; MAP3K14; CXCL12; MAPK8; GNB2L1; ABL1;
MAPK3; ITGA1; KRAS; RHOA; PRKCD; PRKAA1; MAPK9; SRC; CDK2; PIM1;
ITGB7; PXN; RAF1; FYN; DYRK1A; ITGB1 MAP2K2; PAK4; AKT1; JAK2;
STAT3; ADAM10; MAP2K1; PAK3; ITGB3; CDC42; VEGFA; ITGA2; EPHA8;
TTK; CSNK1A1; CRKL; BRAF; PTPN13; ATF4; AKT3; SGK Actin
Cytoskeleton ACTN4; PRKCE; ITGAM; ROCK1; ITGA5; IRAK1; Signaling
PRKAA2; EIF2AK2; RAC1; INS; ARHGEF7; GRK6; ROCK2; MAPK1; RAC2;
PLK1; AKT2; PIK3CA; CDK8; PTK2; CFL1; PIK3CB; MYH9; DIAPH1; PIK3C3;
MAPK8; F2R; MAPK3; SLC9A1; ITGA1; KRAS; RHOA; PRKCD; PRKAA1; MAPK9;
CDK2; PIM1; PIK3C2A; ITGB7; PPP1CC; PXN; VIL2; RAF1; GSN; DYRK1A;
ITGB1; MAP2K2; PAK4; PIP5K1A; PIK3R1; MAP2K1; PAK3; ITGB3; CDC42;
APC; ITGA2; TTK; CSNK1A1; CRKL; BRAF; VAV3; SGK Huntington's
Disease PRKCE; IGF1; EP300; RCOR1; PRKCZ; HDAC4; TGM2; Signaling
MAPK1; CAPNS1; AKT2; EGFR; NCOR2; SP1; CAPN2; PIK3CA; HDAC5; CREB1;
PRKCI; HSPA5; REST; GNAQ; PIK3CB; PIK3C3; MAPK8; IGF1R; PRKD1;
GNB2L1; BCL2L1; CAPN1; MAPK3; CASP8; HDAC2; HDAC7A; PRKCD; HDAC11;
MAPK9; HDAC9; PIK3C2A; HDAC3; TP53; CASP9; CREBBP; AKT1; PIK3R1;
PDPK1; CASP1; APAF1; FRAP1; CASP2; JUN; BAX; ATF4; AKT3; PRKCA;
CLTC; SGK; HDAC6; CASP3 Apoptosis Signaling PRKCE; ROCK1; BID;
IRAK1; PRKAA2; EIF2AK2; BAK1; BIRC4; GRK6; MAPK1; CAPNS1; PLK1;
AKT2; IKBKB; CAPN2; CDK8; FAS; NFKB2; BCL2; MAP3K14; MAPK8; BCL2L1;
CAPN1; MAPK3; CASP8; KRAS; RELA; PRKCD; PRKAA1; MAPK9; CDK2; PIM1;
TP53; TNF; RAF1; IKBKG; RELB; CASP9; DYRK1A; MAP2K2; CHUK; APAF1;
MAP2K1; NFKB1; PAK3; LMNA; CASP2; BIRC2; TTK; CSNK1A1; BRAF; BAX;
PRKCA; SGK; CASP3; BIRC3; PARP1 B Cell Receptor RAC1; PTEN; LYN;
ELK1; MAPK1; RAC2; PTPN11; Signaling AKT2; IKBKB; PIK3CA; CREB1;
SYK; NFKB2; CAMK2A.; MAP3K14; PIK3CB; PIK3C3; MAPK8; BCL2L1; ABL1;
MAPK3; ETS1; KRAS; MAPK13; RELA; PTPN6; MAPK9; EGR1; PIK3C2A; BTK;
MAPK14; RAF1; IKBKG; RELB; MAP3K7; MAP2K2; AKT1; PIK3R1; CHUK;
MAP2K1; NFKB1; CDC42; GSK3A; FRAP1; BCL6; BCL10; JUN; GSK3B; ATF4;
AKT3; VAV3; RPS6KB1 Leukocyte Extravasation ACTN4; CD44; PRKCE;
ITGAM; ROCK1; CXCR4; CYBA; Signaling RAC1; RAP1A; PRKCZ; ROCK2;
RAC2; PTPN11; MMP14; PIK3CA; PRKCI; PTK2; PIK3CB; CXCL12; PIK3C3;
MAPK8; PRKD1; ABL1; MAPK10; CYBB; MAPK13; RHOA; PRKCD; MAPK9; SRC;
PIK3C2A; BTK; MAPK14; NOX1; PXN; VIL2; VASP; ITGB1; MAP2K2; CTNND1;
PIK3R1; CTNNB1; CLDN1; CDC42; F11R; ITK; CRKL; VAV3; CTTN; PRKCA;
MMP1; MMP9 Integrin Signaling ACTN4; ITGAM; ROCK1; ITGA5; RAC1;
PTEN; RAP1A; TLN1; ARHGEF7; MAPK1; RAC2; CAPNS1; AKT2; CAPN2;
PIK3CA; PTK2; PIK3CB; PIK3C3; MAPK8; CAV1; CAPN1; ABL1; MAPK3;
ITGA1; KRAS; RHOA; SRC; PIK3C2A; ITGB7; PPP1CC; ILK; PXN; VASP;
RAF1; FYN; ITGB1; MAP2K2; PAK4; AKT1; PIK3R1; TNK2; MAP2K1; PAK3;
ITGB3; CDC42; RND3; ITGA2; CRKL; BRAF; GSK3B; AKT3 Acute Phase
Response IRAK1; SOD2; MYD88; TRAF6; ELK1; MAPK1; PTPN11; Signaling
AKT2; IKBKB; PIK3CA; FOS; NFKB2; MAP3K14; PIK3CB; MAPK8; RIPK1;
MAPK3; IL6ST; KRAS; MAPK13; IL6R; RELA; SOCS1; MAPK9; FTL; NR3C1;
TRAF2; SERPINE1; MAPK14; TNF; RAF1; PDK1; IKBKG; RELB; MAP3K7;
MAP2K2; AKT1; JAK2; PIK3R1; CHUK; STAT3; MAP2K1; NFKB1; FRAP1;
CEBPB; JUN; AKT3; IL1R1; IL6 PTEN Signaling ITGAM; ITGA5; RAC1;
PTEN; PRKCZ; BCL2L11; MAPK1; RAC2; AKT2; EGFR; IKBKB; CBL; PIK3CA;
CDKN1B; PTK2; NFKB2; BCL2; PIK3CB; BCL2L1; MAPK3; ITGA1; KRAS;
ITGB7; ILK; PDGFRB; INSR; RAF1; IKBKG; CASP9; CDKN1A; ITGB1;
MAP2K2; AKT1; PIK3R1; CHUK; PDGFRA; PDPK1; MAP2K1; NFKB1; ITGB3;
CDC42; CCND1; GSK3A; ITGA2; GSK3B; AKT3; FOXO1; CASP3; RPS6KB1 p53
Signaling PTEN; EP300; BBC3; PCAF; FASN; BRCA1; GADD45A; BIRC5;
AKT2; PIK3CA; CHEK1; TP53LNP1; BCL2; PIK3CB; PIK3C3; MAPK8; THBS1;
ATR; BCL2L1; E2F1 PMAIP1; CHEK2; TNFRSF10B; TP73; RB1; HDAC9; CDK2;
PIK3C2A; MAPK14; TP53; LRDD; CDKN1A; HIPK2; AKT1; PIK3R1; RRM2B;
APAF1; CTNNB1; SIRT1; CCND1; PRKDC; ATM; SFN; CDKN2A; JUN; SNAI2;
GSK3B; BAX; AKT3 Aryl Hydrocarbon HSPB1; EP300; FASN; TGM2; RXRA;
MAPK1; NQO1; Receptor NCOR2; SP1; ARNT; CDKN1B; FOS; CHEK1;
Signaling SMARCA4; NFKB2; MAPK8; ALDH1A1; ATR; E2F1; MAPK3; NRIP1;
CHEK2; RELA; TP73; GSTP1; RB1; SRC; CDK2; AHR; NFE2L2; NCOA3; TP53;
TNF; CDKN1A; NCOA2; APAF1; NFKB1; CCND1; ATM; ESR1; CDKN2A; MYC;
JUN; ESR2; BAX; IL6; CYP1B1; HSP90AA1 Xenobiotic Metabolism PRKCE;
EP300; PRKCZ; RXRA; MAPK1; NQO1; Signaling NCOR2; PIK3CA; ARNT;
PRKCI; NFKB2; CAMK2A; PIK3CB; PPP2R1A; PIK3C3; MAPK8; PRKD1;
ALDH1A1; MAPK3; NRIP1; KRAS; MAPK13; PRKCD; GSTP1; MAPK9; NOS2A;
ABCB1; AHR; PPP2CA; FTL; NFE2L2; PIK3C2A; PPARGC1A; MAPK14; TNF;
RAF1; CREBBP; MAP2K2; PIK3R1; PPP2R5C; .MAP2K1; NFKB1; KEAP1;
PRKCA; EIF2AK3; IL6; CYP1B1; HSP90AA1 SAPK/JNK Signaling PRKCE;
IRAK1; PRKAA2; EIF2AK2; RAC1; ELK1; GRK6; MAPK1; GADD45A; RAC2;
PLK1; AKT2; PIK3CA; FADD; CDK8; PIK3CB; PIK3C3; MAPK8; RIPK1;
GNB2L1; IRS1; MAPK3; MAPK10; DAXX; KRAS; PRKCD; PRKAA1; MAPK9;
CDK2; PIM1; PIK3C2A; TRAF2; TP53; LCK; MAP3K7; DYRK1A; MAP2K2;
PIK3R1; MAP2K1; PAK3; CDC42; JUN; TTK; CSNK1A1; CRKL; BRAF; SGK
PPAr/RXR Signaling PRKAA2; EP300; INS; SMAD2; TRAF6; PPARA; FASN;
RXRA; MAPK1; SMAD3; GNAS; IKBKB; NCOR2; ABCA1; GNAQ; NFKB2;
MAP3K14; STAT5B; MAPK8; IRS1; MAPK3; KRAS; RELA; PRKAA1; PPARGC1A;
NCOA3; MAPK14; INSR; RAF1; IKBKG; RELB; MAP3K7; CREBBP; MAP2K2;
JAK2; CHUK; MAP2K1; NFKB1; TGFBR1; SMAD4; JUN; IL1R1; PRKCA; IL6;
HSP90AA1; ADIPOQ NF-KB Signaling IRAK1; EIF2AK2; EP300; INS; MYD88;
PRKCZ; TRAF6; TBK1; AKT2; EGFR; IKBKB; PIK3CA; BTRC; NFKB2;
MAP3K14; PIK3CB; PIK3C3; MAPK8; RIPK1; HDAC2; KRAS; RELA; PIK3C2A;
TRAF2; TLR4; PDGFRB; TNF; INSR; LCK; IKBKG; RELB; MAP3K7; CREBBP;
AKT1; PIK3R1; CHUK; PDGFRA; NFKB1; TLR2; BCL10; GSK3B; AKT3;
TNFAIP3; IL1R1 Neuregulin Signaling ERBB4; PRKCE; ITGAM; ITGA5;
PTEN; PRKCZ; ELK1; MAPK1; PTPN11; AKT2; EGFR; ERBB2; PRKCI; CDKN1B;
STAT5B; PRKD1; MAPK3; ITGA1; KRAS; PRKCD; STAT5A; SRC; ITGB7; RAF1;
ITGB1; MAP2K2; ADAM17; AKT1; PIK3R1; PDPK1; MAP2K1; ITGB3; EREG;
FRAP1; PSEN1; ITGA2; MYC; NRG1; CRKL; AKT3; PRKCA; HSP90AA1;
RPS6KB1 Wnt & Beta catenin CD44; EP300; LRP6; DVL3; CSNK1E;
GJA1; SMO; Signaling AKT2; PIN1; CDH1; BTRC; GNAQ; MARK2; PPP2R1A;
WNT11; SRC; DKK1; PPP2CA; SOX6; SFRP2; ILK; LEF1; SOX9; TP53;
MAP3K7; CREBBP; TCF7L2; AKT1; PPP2R5C; WNT5A; LRP5; CTNNB1; TGFBR1;
CCND1; GSK3A; DVL1; APC; CDKN2A; MYC; CSNK1A1; GSK3B; AKT3; SOX2
Insulin Receptor PTEN; INS; EIF4E; PTPN1; PRKCZ; MAPK1; TSC1;
Signaling PTPN11; AKT2; CBL; PIK3CA; PRKCI; PIK3CB; PIK3C3; MAPK8;
IRS1; MAPK3; TSC2; KRAS; EIF4EBP1; SLC2A4; PIK3C2A; PPP1CC; INSR;
RAF1; FYN; MAP2K2; JAK1; AKT1; JAK2; PIK3R1; PDPK1; MAP2K1; GSK3A;
FRAP1; CRKL; GSK3B; AKT3; FOXO1; SGK; RPS6KB1 IL-6 Signaling HSPB1;
TRAF6; MAPKAPK2; ELK1; MAPK1; PTPN11; IKBKB; FOS; NFKB2; MAP3K14;
MAPK8; MAPK3; MAPK10; IL6ST; KRAS; MAPK13; IL6R; RELA; SOCS1;
MAPK9; ABCB1; TRAF2; MAPK14; TNF; RAF1; IKBKG; RELB; MAP3K7;
MAP2K2; IL8; JAK2; CHUK; STAT3; MAP2K1; NFKB1; CEBPB; JUN; IL1R1;
SRF; IL6 Hepatic Cholestasis PRKCE; IRAK1; INS; MYD88; PRKCZ;
TRAF6; PPARA; RXRA; IKBKB ; PRKCI; NFKB2; MAP3K14; MAPK8; PRKD1;
MAPK10; RELA; PRKCD; MAPK9; ABCB1; TRAF2; TLR4; TNF; INSR; IKBKG;
RELB; MAP3K7; IL8; CHUK; NR1H2; TJP2; NFKB1; ESR1; SREBF1; FGFR4;
JUN; IL1R1; PRKCA; IL6 IGF-1 Signaling IGF1; PRKCZ; ELK1; MAPK1;
PTPN11; NEDD4; AKT2; PIK3CA; PRKCZ; PTK2; FOS; PIK3CB; PIK3C3;
MAPK8; IGF1R; IRS1; MAPK3; IGFBP7; KRAS; PIK3C2A; YWHAZ; PXN; RAF1;
CASP9; MAP2K2; AKT1; PIK3R1; PDPK1; MAP2K1; ICFBP2; SFN; JUN;
CYR61; AKT3; FOXO1; SRF; CTGF; RPS6KB1 NRF2-mediated PRKCE; EP300;
SOD2; PRKCZ; MAPK1; SQSTM1; Oxidative NQO1; PIK3CA; PRKCI; FOS;
PIK3CB; PIK3C3; MAPK8; Stress Response PRKD1; MAPK3; KRAS; PRKCD;
GSTP1; MAPK9; FTL; NFE2L2; PIK3C2A; MAPK14; RAF1; MAP3K7; CREBBP;
MAP2K2; AKT1; PIK3R1; MAP2K1; PPIB; JUN; KEAP1 GSK3B; ATF4; PRKCA;
EIF2AK3; HSP90AA1 Hepatic Fibrosis/Hepatic EDN1; IGF1; KDR; FLT1;
SMAD2; FGFR1; MET; PGF; Stellate Cell Activation SMAD3; EGFR; FAS;
CSF1; NFKB2; BCL2; MYH9 IGF1R; IL6R; RELA; TLR4; PDGFRB; TNF; RELB;
IL8; PDGFRA; NFKB1; TGFBR1; SMAD4; VEGFA; BAX; IL1R1; CCL2; HGF;
MMP1; STAT1; IL6; CTGF; MMP9 PPAR Signaling EP300; INS; TRAF6;
PPARA; RXRA; MAPK1; IKBKB; NCOR2; FOS; NFKB2; MAP3K14; STAT5B;
MAPK3; NRIP1; KRAS; PPARG; RELA; STAT5A; TRAF2; PPARGC1A; PDGFRB;
TNF; INSR; RAF1; IKBKG; RELB; MAP3K7; CREBBP; MAP2K2; CHUK; PDGFRA;
MAP2K1; NFKB1; JUN; IL1R1; HSP90AA1 Fc Epsilon RI Signaling PRKCE;
RAC1; PRKCZ; LYN; MAPK1; RAC2; PTPN11; AKT2; PIK3CA; SYK; PRKCI;
PIK3CB; PIK3C3; MAPK8; PRKD1; MAPK3; MAPK10; KRAS; MAPK13; PRKCD;
MAPK9; PIK3C2A; BTK; MAPK14; TNF; RAF1; FYN MAP2K2; AKT1; PIK3R1;
PDPK1; MAP2K1; AKT3; VANT3; PRKCA G-Protein Coupled PRKCE; RAP1A;
RGS16; MAPK1; GNAS; AKT2; IKBKB; Receptor Signaling PIK3CA; CREB1;
GNAQ; NEKB2; CAMK2A; PIK3CB; PIK3C3; MAPK3; KRAS; RELA; SRC;
PIK3C2A; RAF1; IKBKG; RELB; FYN; MAP2K2; NK11; PIK3R1; CHUK; PDPK1;
STAT3; MAP2K1; NFKB1; BRAF; ATF4; AKT3; PRKCA Inositol Phosphate
PRKCE; IRAK1; PRKAA2; EIF2AK2; PTEN; GRK6; Metabolism MAPK1; PLK1;
AKT2; PIK3CA; CDK8; PIK3CB; PIK3C3; MAPK8; MAPK3; PRKCD; PRKAA1;
MAPK9; CDK2; PIM1; PIK3C2A; DYRK1A; MAP2K2; PIP5K1A; PIK3R1;
MAP2K1; PAK3; ATM; TTK; CSNK1A1; BRAF; SGK PDGF Signaling EIF2AK2;
ELK1; ABL2; MAPK1; PIK3CA; FOS; PIK3CB; PIK3C3; MAPK8; CAV1; ABL1;
MAPK3; KRAS; SRC; PIK3C2A; PDGFRB; RAF1; MAP2K2; JAK1; JAK2;
PIK3R1; PDGFRA; STAT3; SPHK1; MAP2K1; MYC; JUN; CRKL; PRKCA; SRF;
STAT1; SPHK2 VEGF Signaling ACTN4; ROCK1; KDR; FLT1; ROCK2; MAPK1;
PGF; AKT2; PIK3CA; ARNT; PTK2; BCL2; PIK3CB; PIK3C3; BCL2L1; MAPK3;
KRAS; HIF1A; NOS3; PIK3C2A; PXN; RAF1; MAP2K2; ELAVL1; AKT1;
PIK3R1; MAP2K1; SFN; VEGFA; AKT3; FOXO1; PRKCA Natural Killer Cell
PRKCE; RAC1; PRKCZ; MAPK1; RAC2; PTPN11; Signaling KIR2DL3; AKT2;
PIK3CA; SYK; PRKCI; PIK3CB; PIK3C3; PRKD1; MAPK3; KRAS; PRKCD;
PTPN6; PIK3C2A; LCK; RAF1; FYN; MAP2K2; PAK4; AKT1; PIK3R1; MAP2K1;
PAK3; AKT3; VAV3; PRKCA Cell Cycle: G1/S HDAC4; SMAD3; SUV39H1;
HDAC5; CDKN1B; BTRC; Checkpoint Regulation ATR; ABL1; E2F1; HDAC2;
FIDAC7A; RB1; HDAC11; HDAC9; CDK2; E2F2; HDAC3; TP53; CDKN1A;
CCND1; E2F4; ATM; RBL2; SMAD4; CDKN2A; MYC; NRG1; GSK3B; RBL1;
HDAC6 T Cell Receptor RAC1; ELK1; MAPK1; IKBKB; CBL; PIK3CA; FOS;
Signaling NFKB2; PIK3CB; PIK3C3; MAPK8; MAPK3; KRAS; RELA; PIK3C2A;
BTK; LCK; RAF1; IKBKG; RELB; FYN; MAP2K2; PIK3R1; CHUK; MAP2K1;
NFKB1; ITK; BCL10; JUN; VAV3 Death Receptor Signaling CRADD; HSPB1;
BID; BIRC4; TBK1; IKBKB; FADD; FAS; NFKB2; BCL2; MAP3K14; MAPK8;
RIPK1; CASP8; DAXX; TNFRSF10B; RELA; TRAF2; TNF; IKBKG; RELB;
CASP9; CHUK; APAF1; NFKB1; CASP2; BIRC2; CASP3; BIRC3 FGF Signaling
RAC1; FGFR1; MET; MAPKAPK2; MAPK1; PTPN11; AKT2; PIK3CA; CREB1;
PIK3CB; PIK3C3; MAPK8; MAPK3; MAPK13; PTPN6; PIK3C2A; MAPK14; RAF1;
AKT1; PIK3R1; STAT3; MAP2K1; FGFR4; CRKL; ATF4; AKT3; PRKCA; HGF
GM-CSF Signaling LYN; ELK1; MAPK1; PTPN11; AKT2; PIK3CA; CAMK2A;
STAT5B; PIK3CB; PIK3C3; GNB2L1; BCL2L1; MAPK3; ETS1; KRAS; RUNX1;
PIM1; PIK3C2A; RAF1; MAP2K2; AKT1; JAK2; PIK3R1; STAT3; MAP2K1;
CCND1; AKT3; STAT1 Amyotrophic Lateral BID; IGF1; RAC1; BIRC4; PGF;
CAPNS1; CAPN2; Sclerosis Signaling PIK3CA; BCL2; PIK3CB; PIK3C3;
BCL2L1; CAPN1; PIK3C2A; TP53; CASP9; PIK3R1; RAB5A; CASP1; APAF1;
VEGFA; BIRC2; BAX; AKT3; CASP3; BIRC3 JAK/Stat Signaling PTPN1;
MAPK1; PTPN11; AKT2; PIK3CA; STAT5B; PIK3CB; PIK3C3; MAPK3; KRAS;
SOCS1; STAT5A; PTPN6; PIK3C2A; RAF1; CDKN1A; MAP2K2; JAK1 AKT1;
JAK2; PIK3R1; STAT3; MAP2K1; FRAP1; AKT3; STAT1 Nicotinate and
PRKCE; IRAK1; PRKAA2; EIF2AK2; GRK6; MAPK1; Nicotinamide PLK1;
AKT2; CDK8; MAPK8; MAPK3; PRKCD; PRKAA1; Metabolism PBEF1; MAPK9;
CDK2; PIM1; DYRK1A; MAP2K2; MAP2K1; PAK3; NT5E; TTK; CSNK1A1; BRAF;
SGK Chemokine Signaling CXCR4; ROCK2; MAPK1; PTK2; FOS; CFL1; GNAQ;
CAMK2A; CXCL12; MAPK8; MAPK3; KRAS; MAPK13; RHOA; CCR3; SRC; PPP1CC
; MAPK14; NOX1; RAF1; MAP2K2; MAP2K1; JUN; CCL2; PRKCA IL-2
Signaling ELK1; MAPK1; PTPN11; AKT2; PIK3CA; SYK; FOS; STAT5B;
PIK3CB; PIK3C3; MAPK8; MAPK3; KRAS; SOCS1; STAT5A; PIK3C2A; LCK;
RAF1; MAP2K2; JAK1; AKT1; PIK3R1; MAP2K1; JUN; AKT3 Synaptic Long
Term PRKCE; IGF1; PRKCZ; PRDX6; LYN; MAPK1; GNAS; Depression PRKCI;
GNAQ; PPP2R1A; IGF1R; PRKD1; MAPK3; KRAS; GRN; PRKCD; NOS3; NOS2A;
PPP2CA; YWHAZ; RAF1; MAP2K2; PPP2R5C; MAP2K1; PRKCA Estrogen
Receptor TAF4B; EP300; CARM1; PCAF; MAPK1; NCOR2; Signaling
SMARCA4; MAPK3; NRIP1; KRAS; SRC; NR3C1; HDAC3; PPARGC1A; RBM9;
NCOA3; RAF1; CREBBP; MAP2K2; NCOA2; MAP2K1; PRKDC; ESR1; ESR2
Protein Ubiquitination TRAF6; SMURF1; BIRC4; BRCA1; UCHL1; NEDD4;
Pathway CBL; UBE2I; BTRC; HSPA5; USP7; USP10; FBXW7; USP9X; STUB1;
USP22; B2M; BIRC2; PARK2; USP8; USP1; VHL; USP90AA1; BIRC3 IL-10
Signaling TRAF6; CCR1; ELK1; IKBKB; SP1; FOS; NFKB2; MAP3K14;
MAPK8; MAPK13; RELA; MAPK14; TNF; IKBKG; RELB; MAP3K7; JAK1; CHUK;
STAT3; NFKB1; JUN; IL1R1; IL6 VDR/RXR Activation PRKCE; EP300;
PRKCZ; RXRA; GADD45A; HES1; NCOR2; SP1; PRKCI; CDKN1B; PRKD1;
PRKCD; RUNX2; KLF4; YY1; NCOA3; CDKN1A; NCOA2; SPP1; LRP5; CEBPB;
FOXO1; PRKCA TGF-beta Signaling EP300; SMAD2; SMURF1; MAPK1; SMAD3;
SMAD1; FOS; MAPK8; MAPK3; KRAS; MAPK9; RUNX2; SERPINE1; RAF1;
MAP3K7; CREBBP; MAP2K2; MAP2K1; TGFBR1; SMAD4; JUN; SMAD5 Toll-like
Receptor IRAK1; EIF2AK2; MYD88; TRAF6; PPARA; ELK1; Signaling
IKBKB; FOS; NFKB2; MAP3K14; MAPK8; MAPK13; RELA; TLR4; MAPK14;
IKBKG; RELB; MAP3K7; CHUK; NFKB1; TLR2; JUN p38 MAPK Signaling
HSPB1; IRAK1; TRAF6; MAPKAPK2; ELK1; FADD; FAS; CREB1; DDIT3;
RPS6KA4; DAXX; MAPK13; TRAF2; MAPK14; TNF; MAP3K7; TGFBR1; MYC;
ATF4; IL1R1; SRF; STAT1 Neurotrophin/TRK NTRK2; MAPK1; PTPN11;
PIK3CA; CREB1; FOS; Signaling PIK3CB; PIK3C3; MAPK8; MAPK3; KRAS;
PIK3C2A; RAF1; .MAP2K2; AKT1; PIK3R1; PDPK1; MAP2K1; CDC42; JUN;
ATF4 FXR/RXR Activation INS; PPARA; FASN; RXRA; AKT2; SDC1; MAPK8;
APOB; MAPK10; PPARG; MTTP; MAPK9; PPARGC1A; TNF; CREBBP; AKT1;
SREBF1; FGFR4; AKT3; FOXO1 Synaptic Long Term PRKCE; RAP1A; EP300;
PRKCZ; MAPK1; CREB1; Potentiation PRKCI; GNAQ; CAMK2A; PRKD1;
MAPK3; KRAS; PRKCD; PPP1CC; RAF1; CREBBP; MAP2K2; MAP2K1; ATF4;
PRKCA Calcium Signaling RAP1A; EP300; HDAC4; MAPK1; HDAC5; CREB1;
CAMK2A; MYH9; MAPK3; HDAC2; HDAC7A; HDAC11; HDAC9; HDAC3; CREBBP;
CALR; CAMKK2; ATF4; HDAC6 EGF Signaling ELK1; MAPK1; EGFR; PIK3CA;
FOS; PIK3CB; PIK3C3; MAPK8; MAPK3; PIK3C2A; RAF1; JAK1; PIK3R1;
STAT3; MAP2K1; JUN; PRKCA; SRF; STAT1 Hypoxia Signaling in the
EDN1; PTEN; EP300; NQO1; UBE2I; CREB1; ARNT; Cardiovascular System
HIF1A; SLC2A4; NOS3; TP53; LDHA; AKT1; ATM; VEGFA; JUN; ATF4; VHL;
HSP90AA1 LPS/IL-1 Mediated IRAK1; MYD88; TRAF6; PPARA; RXRA; ABCA1;
Inhibition of RXR MAPK8; ALDH1A1; GSTP1; MAPK9; ABCB1; TRAF2;
Function TLR4; TNF; MAP3K7; NR1H2; SREBF1; JUN; IL1R1 LXR/RXR
Activation FASN; RXRA; NCOR2; ABCA1; NFKB2; IRF3; RELA; NOS2A;
TLR4; TNF; RELB; LDLR; NR1H2; NFKB1; SREBF1; IL1R1; CCL2; IL6; MMP9
Amyloid Processing PRKCE; CSNK1E; MAPK1; CAPNS1; AKT2; CAPN2;
CAPN1; MAPK3; MAPK13; MAPT; MAPK14; AKT1; PSEN1; CSNK1A1; GSK3B;
AKT3; APP IL-4 Signaling AKT2; PIK3CA; PIK3CB; PIK3C3; RS1; KRAS;
SOCS1; PTPN6; NR3C1; PIK3C2A; JAK1; AKT1; JAK2; PIK3R1; FRAP1;
AKT3; RPS6KB1 Cell Cycle: G2/M DNA EP300; PCAF; BRCA1; GADD45A;
PLK1; BTRC; Damage Checkpoint CHEK1; ATR; CHEK2; YWHAZ; TP53;
CDKN1A; Regulation PRKDC; ATM; SFN; CDKN2A Nitric Oxide Signaling
KDR; FLT1; PGF; AKT2; PIK3CA; PIK3CB; PIK3C3; in the CAV1; PRKCD;
NOS3; PIK3C2A; AKT1; PIK3R1; Cardiovascular System VEGFA; AKT3;
HSP90AA1 Purine Metabolism NME2; SMARCA4; MYH9; RRM2; ADAR;
EIF2AK4; PKM2; ENTPD1; RAD51; RRM2B; TJP2; RAD51C; NT5E; POLD1;
NME1 cAMP-mediated RAP1A; MAPK1; GNAS; CREB1; CAMK2A; MAPK3;
Signaling SRC; RAF1; MAP2K2; STAT3; MAP2K1; BRAF; ATF4
Mitochondrial SOD2; MAPK8; CASP8; .MAPK10; MAPK9; CASP9;
Dysfunction PARK7; PSEN1; PARK2; APP; CASP3 Notch Signaling HES1;
JAG1; NUMB; NOTCH4; ADAM17; NOTCH2; PSEN1; NOTCH3; NOTCH1; DLL4
Endoplasmic Reticulum HSPA5; MAPK8; XBP1; TRAF2; ATF6; CASP9; ATF4;
Stress Pathway EIF2AK3; CASP3 Pyrimidine Metabolism NME2; AICDA;
RRM2; EIF2AK4; ENTPD1; RRM2B; NT5E; POLD1; NME1 Parkinson's
Signaling UCHL1; MAPK8; MAPK13; MAPK14; CASP9; PARK7; RARK2; CASP3
Cardiac & Beta GNAS; GNAQ; PPP2R1A; GNB2L1; PPP2CA; PPP1CC;
Adrenergic Signaling PPP2R5C Glycolysis/ HK2; GCK; GPI; ALDH1A1;
PKM2; LDHA; HK1 Gluconeogenesis Interferon Signaling IRF1; SOCS1;
JAK1; JAK2; IFITM1; STAT1; IFIT3 Sonic Hedgehog ARRB2; SMO; GLI2;
DYRK1A; GLI1; GSK3B; DYRK1B Signaling Glycerophospholipid PLD1;
GRN; GPAM; YWHAZ; SPHK1; SPHK2 Metabolism Phospholipid PRDX6; PLD1;
GRN; YWHAZ; SPFIK1; SPHK2 Degradation Tryptophan Metabolism SIAH2;
PRMT5; NEDD4; ALDH1A1; CYP1B1; SIAH1 Lysine Degradation SUV39H1;
EHMT2; NSD1; SETD7; PPP2R5C Nucleotide Excision ERCC5; ERCC4; XPA;
XPC; ERCC1 Repair Pathway Starch and Sucrose UCHL1; HK2; GCK; GPI;
HK1 Metabolism Aminosugars Metabolism NQO1; HK2; GCK; HK1
Arachidonic Acid PRDX6; GRN; YWHAZ; CYP1B1 Metabolism Circadian
Rhythm CSNK1E; CREB1; ATF4; NR1D1 Signaling Coagulation System
BDKRB1; F2R; SERPINE1; F3 Dopamine Receptor PPP2R1A; PPP2CA;
PPP1CC; PPP2R5C Signaling Glutathione Metabolism IDH2; GSTP1;
ANPEP; IDH1 Glycerolipid Metabolism ALDH1A1; GPAM; SPHK1; SPHK2
Linoleic Acid PRDX6; GRN; YWHAZ; CYP1B1 Metabolism Methionine
Metabolism DNMT1; DNMT3B; AHCY; DNMT3A Pyruvate Metabolism GLO1;
ALDH1A1; PKM2; LDHA Arginine and Proline ALDH1A1; NOS3; NOS2A
Metabolism Eicosanoid Signaling PRDX6; GRN; YWHAZ Fructose and
Mannose HK2; GCK; HK1 Metabolism Galactose Metabolism HK2; GCK; HK1
Stilbene, Coumarine and PRDX6; PRDX1; TYR Lignin Biosynthesis
Antigen Presentation CALR; B2M Pathway Biosynthesis of Steroids
NQO1; DHCR7 Butanoate Metabolism ALDH1A1; NLGN1 Citrate Cycle IDH2;
IDH1 Fatty Acid Metabolism ALDH1A1; CYP1B1 Glycerophospholipid
PRDX6; CHKA Metabolism Histidine Metabolism PRMT5; ALDH1A1 Inositol
Metabolism ERO1L; APEX1 Metabolism of GSTP1; CYP1B1 Xenobiotics by
Cytochrome p450 Methane Metabolism PRDX6; PRDX1 Phenylalanine
PRDX6; PRDX1 Metabolism Propanoate Metabolism ALDH1A1; LDHA
Selenoamino Acid PRMT5; AHCY Metabolism Sphingolipid Metabolism
SPHK1; SPHK2 Aminophosphonate PRMT5 Metabolism Androgen and
Estrogen PRMT5 Metabolism Ascorbate and Aldarate ALDH1A1 Metabolism
Bile Acid Biosynthesis ALDH1A1 Cysteine Metabolism LDHA Fatty Acid
Biosynthesis FASN Glutamate Receptor GNB2L1 Signaling NRF2-mediated
PRDX1 Oxidative Stress Response Pentose Phosphate GPI Pathway
Pentose and Glucuronate UCHL1 Interconversions Retinol Metabolism
ALDH1A1 Riboflavin Metabolism TYR Tyrosine Metabolism PRMT5, TYR
Ubiquinone Biosynthesis PRMT5 Valine, Leucine and ALDH1A1
Isoleucine Degradation Glycine; Serine and CHKA Threonine
Metabolism Lysine Degradation ALDH1A1 Pain/Taste TRPM5; TRPA1 Pain
TRPM7; TRPC5; TRPC6; TRPC1; Cnr1; cnr2; Grk2; Trpa1; Pomc; Cgrp;
Crf; Pka; Era; Nr2b; TRPM5; Prkaca; Prkacb; Prkar1a; Prkar2a
Mitochondrial Function AIF; CytC; SMAC (Diablo); Aifm-1; Aifm-2
Developmental BMP-4; Chordin (Chrd); Noggin (Nog); WNT (Wnt2;
Neurology Wnt2b; Wnt3a; Wnt4; Wnt5a; Wnt6; Wnt7b; Wnt8b; Wnt9a;
Wnt9b; Wnt10a; Wnt10b; Wnt16); beta-catenin; Dkk-1; Frizzled
related proteins; Otx-2; Gbx2; FGF-8; Reelin; Dab1; unc-86 (Pou4f1
or Brn3a); Numb; Reln
[0162] Embodiments of the invention also relate to methods and
compositions related to knocking out genes, amplifying genes and
repairing particular mutations associated with DNA repeat
instability and neurological disorders (Robert D. Wells, Tetsuo
Ashizawa, Genetic Instabilities and Neurological Diseases, Second
Edition, Academic Press, Oct. 13, 2011--Medical). Specific aspects
of tandem repeat sequences have been found to be responsible for
more than twenty human diseases (New insights into repeat
instability: role of RNA*DNA hybrids. McIvor E I, Polak U,
Napierala M. RNA Biol. 2010 September-October; 7(5):551-8). The
CRISPR-Cas system may be harnessed to correct these defects of
genomic instability.
[0163] A further aspect of the invention relates to utilizing the
CRISPR-Cas system for correcting defects in the EMP2A and EMP2B
genes that have been identified to be associated with Lafora
disease. Lafora disease is an autosomal recessive condition which
is characterized by progressive myoclonus epilepsy which may start
as epileptic seizures in adolescence. A few cases of the disease
may be caused by mutations in genes yet to be identified. The
disease causes seizures, muscle spasms, difficulty walking,
dementia, and eventually death. There is currently no therapy that
has proven effective against disease progression. Other genetic
abnormalities associated with epilepsy may also be targeted by the
CRISPR-Cas system and the underlying genetics is further described
in Genetics of Epilepsy and Genetic Epilepsies, edited by Giuliano
Avanzini, Jeffrey L. Noebels, Mariani Foundation Paediatric
Neurology: 20; 2009).
[0164] In yet another aspect of the invention, the CRISPR-Cas
system may be used to correct ocular defects that arise from
several genetic mutations further described in Genetic Diseases of
the Eye, Second Edition, edited by Elias I. Traboulsi, Oxford
University Press, 2012.
[0165] Several further aspects of the invention relate to
correcting defects associated with a wide range of genetic diseases
which are further described on the website of the National
Institutes of Health under the topic subsection Genetic Disorders
(website at health.nih.gov/topic/GeneticDisorders). The genetic
brain diseases may include but are not limited to
Adrenoleukodystrophy, Agenesis of the Corpus Callosum, Aicardi
Syndrome, Alpers' Disease, Alzheimer's Disease, Barth Syndrome,
Batten Disease, CADASIL, Cerebellar Degeneration, Fabry's Disease,
Gerstmann-Straussler-Scheinker Disease, Huntington's Disease and
other Triplet Repeat Disorders, Leigh's Disease, Lesch-Nyhan
Syndrome, Menkes Disease, Mitochondrial Myopathies and NINDS
Colpocephaly. These diseases are further described on the website
of the National Institutes of Health under the subsection Genetic
Brain Disorders.
[0166] In some embodiments, the condition may be neoplasia. In some
embodiments, where the condition is neoplasia, the genes to be
targeted are any of those listed in Table A (in this case PTEN and
so forth). In some embodiments, the condition may be Age-related
Macular Degeneration. In some embodiments, the condition may be a
Schizophrenic Disorder. In some embodiments, the condition may be a
Trinucleotide Repeat Disorder. In some embodiments, the condition
may be Fragile X Syndrome. In some embodiments, the condition may
be a Secretase Related Disorder. In some embodiments, the condition
may be a Prion--related disorder. In some embodiments, the
condition may be ALS. In some embodiments, the condition may be a
drug addiction. In some embodiments, the condition may be Autism.
In some embodiments, the condition may be Alzheimer's Disease. In
some embodiments, the condition may be inflammation. In some
embodiments, the condition may be Parkinson's Disease.
[0167] Examples of proteins associated with Parkinson's disease
include but are not limited to .alpha.-synuclein, DJ-1, LRRK2,
PINK1, Parkin, UCHL1, Synphilin-1, and NURR1.
[0168] Examples of addiction-related proteins may include ABAT for
example.
[0169] Examples of inflammation-related proteins may include the
monocyte chemoattractant protein-1 (MCP 1) encoded by the Ccr2
gene, the C-C chemokine receptor type 5 (CCR5) encoded by the Ccr5
gene, the IgG receptor IIB (FCGR2b, also termed CD32) encoded by
the Fcgr2b gene, or the Fc epsilon R1g (FCER1g) protein encoded by
the Fcer1g gene, for example.
[0170] Examples of cardiovascular diseases associated proteins may
include IL1B (interleukin 1, beta), XDH (xanthine dehydrogenase),
TP53 (tumor protein p53), PTGIS (prostaglandin 12 (prostacyclin)
synthase), MB (myoglobin), 1L4 (interleukin 4), ANGPT 1I
(angiopoietin 1), ABCG8 (ATP-binding cassette, sub-family G
(WHITE), member 8), or CTSK (cathepsin K), for example.
[0171] Examples of Alzheimer's disease associated proteins may
include the very low density lipoprotein receptor protein (VLDLR)
encoded by the VLDLR gene, the ubiquitin-like modifier activating
enzyme 1 (UBA1) encoded by the UBA1 gene, or the NEDD8-activating
enzyme E1 catalytic subunit protein (UBEIC) encoded by the UBA3
gene, for example.
[0172] Examples of proteins associated Autism Spectrum Disorder may
include the benzodiazapine receptor (peripheral) associated protein
1 (BZRAP1) encoded by the BZRAP1 gene, the AF4/FMR2 family member 2
protein (AFF2) encoded by the AFF2 gene (also termed MFR2), the
fragile X mental retardation autosomal homolog 1 protein (FXR1)
encoded by the FXR1 gene, or the fragile X mental retardation
autosomal homolog 2 protein (FXR2) encoded by the FXR2 gene, for
example.
[0173] Examples of proteins associated Macular Degeneration may
include the ATP-binding cassette, sub-family A (ABC1) member 4
protein (ABCA4) encoded by the ABCR gene, the apolipoprotein E
protein (APOE) encoded by the APOE gene, or the chemokine (C-C
motif) Ligand 2 protein (CCL2) encoded by the CCL2 gene, for
example.
[0174] Examples of proteins associated Schizophrenia may include
NRG1, ErbB4, CPLX1, TPH1, TPH2, NRXN1, GSK3A, BDNF, DISC1, GSK3B,
and combinations thereof.
[0175] Examples of proteins involved in tumor suppression may
include ATM (ataxia telangiectasia mutated), ATR (ataxia
telangiectasia and Rad3 related), EGFR (epidermal growth factor
receptor), ERBB2 (v-erb-b2 erythroblastic leukemia viral oncogene
homolog 2), ERBB3 (v-erb-b2 erythroblastic leukemia viral oncogene
homolog 3), ERBB4 (v-erb-b2 erythroblastic leukemia viral oncogene
homolog 4), Notch 1, Notch2, Notch 3, or Notch 4, for example.
[0176] Examples of proteins associated with a secretase disorder
may include PSENEN (presenilin enhancer 2 homolog (C. elegans)),
CTSB (cathepsin B), PSEN1 (presenilin 1), APP (amyloid beta (A4)
precursor protein), APHIB (anterior pharynx defective I homolog B
(C. elegans)), PSEN2 (presenilin 2 (Alzheimer disease 4)), or BACE1
(beta-site APP-cleaving enzyme 1), for example.
[0177] Examples of proteins associated with Amyotrophic Lateral
Sclerosis may include SODI (superoxide dismutase 1), ALS2
(amyotrophic lateral sclerosis 2), FUS (fused in sarcoma), TARDBP
(TAR DNA binding protein), VAGFA (vascular endothelial growth
factor A), VAGFB (vascular endothelial growth factor B), and VAGFC
(vascular endothelial growth factor C), and any combination
thereof.
[0178] Examples of proteins associated with prion diseases may
include SODI (superoxide dismutase 1), ALS2 (amyotrophic lateral
sclerosis 2), FUS (fused in sarcoma), TARDBP (TAR DNA binding
protein), VAGFA (vascular endothelial growth factor A), VAGFB
(vascular endothelial growth factor B), and VAGFC (vascular
endothelial growth factor C), and any combination thereof.
[0179] Examples of proteins related to neurodegenerative conditions
in prion disorders may include A2M (Alpha-2-Macroglobulin), AATF
(Apoptosis antagonizing transcription factor), ACPP (Acid
phosphatase prostate), ACTA2 (Actin alpha 2 smooth muscle aorta),
ADAM22 (ADAM metallopeptidase domain), ADORA3 (Adenosine A3
receptor), or ADRAID (Alpha-1D adrenergic receptor for Alpha-1D
adrenoreceptor), for example.
[0180] Examples of proteins associated with Immunodeficiency may
include A2M [alpha-2-macroglobulin]; AANAT [arylalkylamine
N-acetyltransferase]; ABCA1 [ATP-binding cassette, sub-family A
(ABC1), member 1]; ABCA2 [ATP-binding cassette, sub-family A
(ABC1), member 2]; or ABCA3 [ATP-binding cassette, sub-family A
(ABC1), member 3]; for example.
[0181] Examples of proteins associated with Trinucleotide Repeat
Disorders include AR (androgen receptor), FMR1 (fragile X mental
retardation 1), HTT (huntingtin), or DMPK (dystrophia
myotonica-protein kinase), FXN (frataxin), ATXN2 (ataxin 2), for
example.
[0182] Examples of proteins associated with Neurotransmission
Disorders include SST (somatostatin), NOS1 (nitric oxide synthase 1
(neuronal)), ADRA2A (adrenergic, alpha-2A-, receptor), ADRA2C
(adrenergic, alpha-2C-, receptor), TACR1 (tachykinin receptor 1),
or HTR2c (5-hydroxytryptamine (serotonin) receptor 2C), for
example.
[0183] Examples of neurodevelopmental-associated sequences include
A2BP1 [ataxin 2-binding protein 1], AADAT [aminoadipate
aminotransferase], AANAT [arylalkylamine N-acetyltransferase], ABAT
[4-aminobutyrate aminotransferase], ABCA1 [ATP-binding cassette,
sub-family A (ABC1), member 1], or ABCA13 [ATP-binding cassette,
sub-family A (ABC1), member 13], for example.
[0184] Further examples of preferred conditions treatable with the
present system include may be selected from: Aicardi-Goutieres
Syndrome; Alexander Disease; Allan-Herndon-Dudley Syndrome;
POLG-Related Disorders; Alpha-Mannosidosis (Type II and III);
Alstrom Syndrome; Angelman; Syndrome; Ataxia-Telangiectasia;
Neuronal Ceroid-Lipofuscinoses; Beta-Thalassemia; Bilateral Optic
Atrophy and (Infantile) Optic Atrophy Type 1; Retinoblastoma
(bilateral); Canavan Disease; Cerebrooculofacioskeletal Syndrome 1
[COFSI]; Cerebrotendinous Xanthomatosis; Cornelia de Lange
Syndrome; MAPT-Related Disorders; Genetic Prion Diseases; Dravet
Syndrome; Early-Onset Familial Alzheimer Disease; Friedreich Ataxia
[FRDA]; Fryns Syndrome; Fucosidosis; Fukuyama Congenital Muscular
Dystrophy; Galactosialidosis; Gaucher Disease; Organic Acidemias;
Hemophagocytic Lymphohistiocytosis; Hutchinson-Gilford Progeria
Syndrome; Mucolipidosis II; Infantile Free Sialic Acid Storage
Disease; PLA2G6-Associated Neurodegeneration; Jervell and
Lange-Nielsen Syndrome; Junctional Epidermolysis Bullosa;
Huntington Disease; Krabbe Disease (Infantile); Mitochondrial
DNA-Associated Leigh Syndrome and NARP; Lesch-Nyhan Syndrome;
LIS1-Associated Lissencephaly; Lowe Syndrome; Maple Syrup Urine
Disease; MECP2 Duplication Syndrome; ATP7A-Related Copper Transport
Disorders; LAMA2-Related Muscular Dystrophy; Arylsulfatase A
Deficiency; Mucopolysaccharidosis Types I, II or III; Peroxisome
Biogenesis Disorders, Zellweger Syndrome Spectrum;
Neurodegeneration with Brain Iron Accumulation Disorders; Acid
Sphingomyelinase Deficiency; Niemann-Pick Disease Type C; Glycine
Encephalopathy; ARX-Related Disorders; Urea Cycle Disorders;
COL1A1/2-Related Osteogenesis Imperfecta; Mitochondrial DNA
Deletion Syndromes; PLP1-Related Disorders; Perry Syndrome;
Phelan-McDermid Syndrome; Glycogen Storage Disease Type II (Pompe
Disease) (Infantile); MAPT-Related Disorders; MECP2-Related
Disorders; Rhizomelic Chondrodysplasia Punctata Type 1; Roberts
Syndrome; Sandhoff Disease; Schindler Disease-Type 1; Adenosine
Deaminase Deficiency; Smith-Lemli-Opitz Syndrome; Spinal Muscular
Atrophy; Infantile-Onset Spinocerebellar Ataxia; Hexosaminidase A
Deficiency; Thanatophoric Dysplasia Type 1; Collagen Type
VI-Related Disorders; Usher Syndrome Type I; Congenital Muscular
Dystrophy; Wolf-Hirschhorn Syndrome; Lysosomal Acid Lipase
Deficiency; and Xeroderma Pigmentosum.
[0185] As will be apparent, it is envisaged that the present system
can be used to target any polynucleotide sequence of interest. Some
examples of conditions or diseases that might be usefully treated
using the present system are included in the Tables above and
examples of genes currently associated with those conditions are
also provided there. However, the genes exemplified are not
exhaustive.
EXAMPLES
[0186] The following examples are given for the purpose of
illustrating various embodiments of the invention and are not meant
to limit the present invention in any fashion. The present
examples, along with the methods described herein are presently
representative of preferred embodiments, are exemplary, and are not
intended as limitations on the scope of the invention. Changes
therein and other uses which are encompassed within the spirit of
the invention as defined by the scope of the claims will occur to
those skilled in the art.
Example 1
CRISPR Complex Activity in the Nucleus of a Eukaryotic Cell
[0187] An example type II CRISPR system is the type II CRISPR locus
from Streptococcus pyogenes SF370, which contains a cluster of four
genes Cas9, Cas1, Cas2, and Csn1, as well as two non-coding RNA
elements, tracrRNA and a characteristic array of repetitive
sequences (direct repeats) interspaced by short stretches of
non-repetitive sequences (spacers, about 30 bp each). In this
system, targeted DNA double-strand break (DSB) is generated in four
sequential steps (FIG. 2A). First, two non-coding RNAs, the
pre-crRNA array and tracrRNA, are transcribed from the CRISPR
locus. Second, tracrRNA hybridizes to the direct repeats of
pre-crRNA, which is then processed into mature crRNAs containing
individual spacer sequences. Third, the mature crRNA:tracrRNA
complex directs Cas9 to the DNA target consisting of the
protospacer and the corresponding PAM via heteroduplex formation
between the spacer region of the crRNA and the protospacer DNA.
Finally, Cas9 mediates cleavage of target DNA upstream of PAM to
create a DSB within the protospacer (FIG. 2A). This example
describes an example process for adapting this RNA-programmable
nuclease system to direct CRISPR complex activity in the nuclei of
eukaryotic cells.
[0188] Cell Culture and Transfection
[0189] Human embryonic kidney (HEK) cell line HEK 293FT (Life
Technologies) was maintained in Dulbecco's modified Eagle's Medium
(DMEM) supplemented with 10% fetal bovine serum (HyClone), 2 mM
GlutaMAX (Life Technologies), 100 U/mL penicillin, and 100 .mu.g/mL
streptomycin at 37.degree. C. with 5.degree. % CO.sub.2 incubation.
Mouse neuro2A (N2A) cell line (ATCC) was maintained with DMEM
supplemented with 5% fetal bovine serum (HyClone), 2 mM GlutaMAX
(Life Technologies), 100 U/mL penicillin, and 100 .mu.g/mL
streptomycin at 37.degree. C. with 5% CO.sub.2.
[0190] HEK 293FT or N2A cells were seeded into 24-well plates
(Corning) one day prior to transfection at a density of 200,000
cells per well. Cells were transfected using Lipofectamine 2000
(Life Technologies) following the manufacturer's recommended
protocol. For each well of a 24-well plate a total of 800 ng of
plasmids were used.
[0191] Surveyor Assay and Sequencing Analysis for Genome
Modification
[0192] HEK 293FT or N2A cells were transfected with plasmid DNA as
described above.
[0193] After transfection, the cells were incubated at 37.degree.
C. for 72 hours before genomic DNA extraction. Genomic DNA was
extracted using the QuickExtract DNA extraction kit (Epicentre)
following the manufacturer's protocol. Briefly, cells were
resuspended in QuickExtract solution and incubated at 65.degree. C.
for 15 minutes and 98.degree. C. for 10 minutes. Extracted genomic
DNA was immediately processed or stored at -20.degree. C.
[0194] The genomic region surrounding a CRISPR target site for each
gene was PCR amplified, and products were purified using QiaQuick
Spin Column (Qiagen) following manufacturer's protocol. A total of
400 ng of the purified PCR products were mixed with 2 .mu.l
10.times.Taq polymerase PCR buffer (Enzymatics) and ultrapure water
to a final volume of 20 .mu.l, and subjected to a re-annealing
process to enable heteroduplex formation: 95.degree. C. for 10 min,
95.degree. C. to 85.degree. C. ramping at -2.degree. C./s,
85.degree. C. to 25.degree. C. at -0.25.degree. C./s, and
25.degree. C. hold for 1 minute. After re-annealing, products were
treated with Surveyor nuclease and Surveyor enhancer S
(Transgenomics) following the manufacturer's recommended protocol,
and analyzed on 4-20% Novex TBE poly-acrylamide gels (Life
Technologies). Gels were stained with SYBR Gold DNA stain (Life
Technologies) for 30 minutes and imaged with a Gel Doc gel imaging
system (Bio-rad). Quantification was based on relative band
intensities, as a measure of the fraction of cleaved DNA. FIG. 8
provides a schematic illustration of this Surveyor assay.
[0195] Restriction fragment length polymorphism assay for detection
of homologous recombination
[0196] HEK 293FT and N2A cells were transfected with plasmid DNA,
and incubated at 37.degree. C. for 72 hours before genomic DNA
extraction as described above. The target genomic region was PCR
amplified using primers outside the homology arms of the homologous
recombination (HR) template. PCR products were separated on a 1%
agarose gel and extracted with MinElute GelExtraction Kit (Qiagen).
Purified products were digested with HindIII (Fermentas) and
analyzed on a 6% Novex TBE poly-acrylamide gel (Life
Technologies).
[0197] RNA Secondary Structure Prediction and Analysis
[0198] RNA secondary structure prediction was performed using the
online webserver RNAfold developed at Institute for Theoretical
Chemistry at the University of Vienna, using the centroid structure
prediction algorithm (see e.g. A. R. Gruber et al., 2008, Cell
106(1): 23-24; and PA Carr and GM Church, 2009, Nature
Biotechnology 27(12): 1151-62).
[0199] Bacterial Plasmid Transformation Interference Assay
[0200] Elements of the S. pyogenes CRISPR locus 1 sufficient for
CRISPR activity were reconstituted in E. coli using pCRISPR plasmid
(schematically illustrated in FIG. 10A). pCRISPR contained
tracrRNA, SpCas9, and a leader sequence driving the crRNA array.
Spacers (also referred to as "guide sequences") were inserted into
the crRNA array between BsaI sites using annealed oligonucleotides,
as illustrated. Challenge plasmids used in the interference assay
were constructed by inserting the protospacer (also referred to as
a "target sequence") sequence along with an adjacent CRISPR motif
sequence (PAM) into pUC19 (see FIG. 10B). The challenge plasmid
contained ampicillin resistance. FIG. 10C provides a schematic
representation of the interference assay. Chemically competent E.
coli strains already carrying pCRISPR and the appropriate spacer
were transformed with the challenge plasmid containing the
corresponding protospacer-PAM sequence. pUC19 was used to assess
the transformation efficiency of each pCRISPR-carrying competent
strain. CRISPR activity resulted in cleavage of the pPSP plasmid
carrying the protospacer, precluding ampicillin resistance
otherwise conferred by pUC19 lacking the protospacer. FIG. 10D
illustrates competence of each pCRISPR-carrying E. coli strain used
in assays illustrated in FIG. 4C.
[0201] RNA Purification
[0202] HEK 293FT cells were maintained and transfected as stated
above. Cells were harvested by trypsinization followed by washing
in phosphate buffered saline (PBS). Total cell RNA was extracted
with TRI reagent (Sigma) following manufacturer's protocol.
Extracted total RNA was quantified using Naonodrop (Thermo
Scientific) and normalized to same concentration.
[0203] Northern Blot Analysis of crRNA and tracrRNA Expression in
Mammalian Cells
[0204] RNAs were mixed with equal volumes of 2X loading buffer
(Ambion), heated to 95.degree. C. for 5 min, chilled on ice for 1
min, and then loaded onto 8% denaturing polyacrylamide gels
(SequaGel, National Diagnostics) after pre-running the gel for at
least 30 minutes. The samples were electrophoresed for 1.5 hours at
40 W limit. Afterwards, the RNA was transferred to Hybond N+
membrane (GE Healthcare) at 300 mA in a semi-dry transfer apparatus
(Bio-rad) at room temperature for 1.5 hours. The RNA was
crosslinked to the membrane using autocrosslink button on
Stratagene UV Crosslinker the Stratalinker (Stratagene). The
membrane was pre-hybridized in ULTRAhyb-Oligo Hybridization Buffer
(Ambion) for 30 min with rotation at 42.degree. C., and probes were
then added and hybridized overnight. Probes were ordered from IDT
and labeled with [gamma-.sup.32P]ATP (Perkin Elmer) with T4
polynucleotide kinase (New England Biolabs). The membrane was
washed once with pre-warmed (42.degree. C.) 2.times.SSC, 0.5% SDS
for 1 min followed by two 30 minute washes at 42.degree. C. The
membrane was exposed to a phosphor screen for one hour or overnight
at room temperature and then scanned with a phosphorimager
(Typhoon).
[0205] Bacterial CRISPR System Construction and Evaluation
[0206] CRISPR locus elements, including tracrRNA, Cas9, and leader
were PCR amplified from Streptococcus pyogenes SF370 genomic DNA
with flanking homology arms for Gibson Assembly. Two BsaI type IIS
sites were introduced in between two direct repeats to facilitate
easy insertion of spacers (FIG. 9). PCR products were cloned into
EcoRV-digested pACYC184 downstream of the tet promoter using Gibson
Assembly Master Mix (NEB). Other endogenous CRISPR system elements
were omitted, with the exception of the last 50 bp of Csn2. Oligos
(Integrated DNA Technology) encoding spacers with complimentary
overhangs were cloned into the BsaI-digested vector pDC000 (NEB)
and then ligated with T7 ligase (Enzymatics) to generate pCRISPR
plasmids. Challenge plasmids containing spacers with PAM sequences
(also referred to herein as "CRISPR motif sequences") were created
by ligating hybridized oligos carrying compatible overhangs
(Integrated DNA Technology) into BamHI-digested pUC19. Cloning for
all constructs was performed in E. co/i strain JM109 (Zymo
Research).
[0207] pCRISPR-carrying cells were made competent using the
Z-Competent E. coli Transformation Kit and Buffer Set (Zymo
Research, T3001) according to manufacturer's instructions. In the
transformation assay, 50 uL aliquots of competent cells carrying
pCRISPR were thawed on ice and transformed with 1 ng of spacer
plasmid or pUC19 on ice for 30 minutes, followed by 45 second heat
shock at 42.degree. C. and 2 minutes on ice. Subsequently, 250 ul
SOC (Invitrogen) was added followed by shaking incubation at
37.degree. C. for lhr, and 100 uL of the post-SOC outgrowth was
plated onto double selection plates (12.5 ug/ml chloramphenicol,
100 ug/ml ampicillin). To obtain cfu/ng of DNA, total colony
numbers were multiplied by 3.
[0208] To improve expression of CRISPR components in mammalian
cells, two genes from the SF370 locus 1 of Streptococcus pyogenes
(S. pyogenes) were codon-optimized, Cas9 (SpCas9) and RNase III
(SpRNase III). To facilitate nuclear localization, a nuclear
localization signal (NLS) was included at the amino (N)- or
carboxyl (C)-termini of both SpCas9 and SpRNase III (FIG. 2B). To
facilitate visualization of protein expression, a fluorescent
protein marker was also included at the N- or C-termini of both
proteins (FIG. 2B). A version of SpCas9 with an NLS attached to
both N- and C-termini (2.times.NLS-SpCas9) was also generated.
Constructs containing NLS-fused SpCas9 and SpRNase III were
transfected into 293FT human embryonic kidney (HEK) cells, and the
relative positioning of the NLS to SpCas9 and SpRNase III was found
to affect their nuclear localization efficiency. Whereas the
C-terminal NLS was sufficient to target SpRNase III to the nucleus,
attachment of a single copy of these particular NLS's to either the
N- or C-terminus of SpCas9 was unable to achieve adequate nuclear
localization in this system. In this example, the C-terminal NLS
was that of nucleoplasmin (KRPAATKKAGQAKKKK (SEQ ID NO: 2)), and
the C-terminal NLS was that of the SV40 large T-antigen (PKKKRKV
(SEQ ID NO: 1)). Of the versions of SpCas9 tested, only
2.times.NLS-SpCas9 exhibited nuclear localization (FIG. 2B).
[0209] The tracrRNA from the CRISPR locus of S. pyogenes SF370 has
two transcriptional start sites, giving rise to two transcripts of
89-nucleotides (nt) and 171 nt that are subsequently processed into
identical 75 nt mature tracrRNAs. The shorter 89 nt tracrRNA was
selected for expression in mammalian cells (expression constructs
illustrated in FIG. 7A, with functionality as determined by results
of the Surveyor assay shown in FIG. 7B). Transcription start sites
are marked as +1, and transcription terminator and the sequence
probed by northern blot are also indicated. Expression of processed
tracrRNA was also confirmed by Northern blot. FIG. 7C shows results
of a Northern blot analysis of total RNA extracted from 293FT cells
transfected with U6 expression constructs carrying long or short
tracrRNA, as well as SpCas9 and DR-EMX1(1)-DR. Left and right
panels are from 293FT cells transfected without or with SpRNase
III, respectively. U6 indicate loading control blotted with a probe
targeting human U6 snRNA. Transfection of the short tracrRNA
expression construct led to abundant levels of the processed form
of tracrRNA (.about.75 bp). Very low amounts of long tracrRNA are
detected on the Northern blot.
[0210] To promote precise transcriptional initiation, the RNA
polymerase III-based U6 promoter was selected to drive the
expression of tracrRNA (FIG. 2C). Similarly, a U6 promoter-based
construct was developed to express a pre-crRNA array consisting of
a single spacer flanked by two direct repeats (DRs, also
encompassed by the term "tracr-mate sequences"; FIG. 2C). The
initial spacer was designed to target a 33-base-pair (bp) target
site (30-bp protospacer plus a 3-bp CRISPR motif (PAM) sequence
satisfying the NGG recognition motif of Cas9) in the human EMY1
locus (FIG. 2C), a key gene in the development of the cerebral
cortex.
[0211] To test whether heterologous expression of the CRISPR system
(SpCas9, SpRNase III, tracrRNA, and pre-crRNA) in mammalian cells
can achieve targeted cleavage of mammalian chromosomes, HEK 293FT
cells were transfected with combinations of CRISPR components.
Since DSBs in mammalian nuclei are partially repaired by the
non-homologous end joining (NHEJ) pathway, which leads to the
formation of indels, the Surveyor assay was used to detect
potential cleavage activity at the target EMX1 locus (FIG. 8) (see
e.g. Guschin el al., 2010, Methods Mol Biol 649: 247).
Co-transfection of all four CRISPR components was able to induce up
to 5.0% cleavage in the protospacer (see FIG. 2D). Co-transfection
of all CRISPR components minus SpRNase III also induced up to 4.7%
indel in the protospacer, suggesting that there may be endogenous
mammalian RNases that are capable of assisting with crRNA
maturation, such as for example the related Dicer and Drosha
enzymes. Removing any of the remaining three components abolished
the genome cleavage activity of the CRISPR system (FIG. 2D). Sanger
sequencing of amplicons containing the target locus verified the
cleavage activity: in 43 sequenced clones, 5 mutated alleles
(11.6%) were found. Similar experiments using a variety of guide
sequences produced indel percentages as high as 29% (see FIGS. 4-7,
12, and 13). These results define a three-component system for
efficient CRISPR-mediated genome modification in mammalian cells.
To optimize the cleavage efficiency, Applicants also tested whether
different isoforms of tracrRNA affected the cleavage efficiency and
found that, in this example system, only the short (89-bp)
transcript form was able to mediate cleavage of the human EMX1
genomic locus (FIG. 7B).
[0212] FIG. 14 provides an additional Northern blot analysis of
crRNA processing in mammalian cells. FIG. 14A illustrates a
schematic showing the expression vector for a single spacer flanked
by two direct repeats (DR-EMX1(1)-DR). The 30 bp spacer targeting
the human EMX1 locus protospacer 1 (see FIG. 6) and the direct
repeat sequences are shown in the sequence beneath FIG. 14A. The
line indicates the region whose reverse-complement sequence was
used to generate Northern blot probes for EMX1(1) crRNA detection.
FIG. 14B shows a Northern blot analysis of total RNA extracted from
293FT cells transfected with U6 expression constructs carrying
DR-EMX1(1)-DR. Left and right panels are from 293FT cells
transfected without or with SpRNase III respectively. DR-EMX1(1)-DR
was processed into mature crRNAs only in the presence of SpCas9 and
short tracrRNA and was not dependent on the presence of SpRNase
III. The mature crRNA detected from transfected 293FT total RNA is
.about.33 bp and is shorter than the 39-42 bp mature crRNA from S.
pyogenes. These results demonstrate that a CRISPR system can be
transplanted into eukaryotic cells and reprogrammed to facilitate
cleavage of endogenous mammalian target polynucleotides.
[0213] FIG. 2 illustrates the bacterial CRISPR system described in
this example. FIG. 2A illustrates a schematic showing the CRISPR
locus 1 from Streptococcus pyogenes SF370 and a proposed mechanism
of CRISPR-mediated DNA cleavage by this system. Mature crRNA
processed from the direct repeat-spacer array directs Cas9 to
genomic targets consisting of complimentary protospacers and a
protospacer-adjacent motif (PAM). Upon target-spacer base pairing,
Cas9 mediates a double-strand break in the target DNA. FIG. 2B
illustrates engineering of S. pyogenes Cas9 (SpCas9) and RNase III
(SpRNase III) with nuclear localization signals (NLSs) to enable
import into the mammalian nucleus. FIG. 2C illustrates mammalian
expression of SpCas9 and SpRNase III driven by the constitutive
EF1.alpha. promoter and tracrRNA and pre-crRNA array (DR-Spacer-DR)
driven by the RNA Po13 promoter U6 to promote precise transcription
initiation and termination. A protospacer from the human EMX1 locus
with a satisfactory PAM sequence is used as the spacer in the
pre-crRNA array. FIG. 2D illustrates surveyor nuclease assay for
SpCas9-mediated minor insertions and deletions. SpCas9 was
expressed with and without SpRNase III, tracrRNA, and a pre-crRNA
array carrying the EMX1-target spacer. FIG. 2E illustrates a
schematic representation of base pairing between target locus and
EMX1-targeting crRNA, as well as an example chromatogram showing a
micro deletion adjacent to the SpCas9 cleavage site. FIG. 2F
illustrates mutated alleles identified from sequencing analysis of
43 clonal amplicons showing a variety of micro insertions and
deletions. Dashes indicate deleted bases, and non-aligned or
mismatched bases indicate insertions or mutations. Scale bar=10
.mu.m.
[0214] To further simplify the three-component system, a chimeric
crRNA-tracrRNA hybrid design was adapted, where a mature crRNA
(comprising a guide sequence) is fused to a partial tracrRNA via a
stem-loop to mimic the natural crRNA:tracrRNA duplex (FIG. 3A). To
increase co-delivery efficiency, a bicistronic expression vector
was created to drive co-expression of a chimeric RNA and SpCas9 in
transfected cells (FIGS. 3A and 8). In parallel, the bicistronic
vectors were used to express a pre-crRNA (DR-guide sequence-DR)
with SpCas9, to induce processing into crRNA with a separately
expressed tracrRNA (compare FIG. 13B top and bottom). FIG. 9
provides schematic illustrations of bicistronic expression vectors
for pre-crRNA array (FIG. 9A) or chimeric crRNA (represented by the
short line downstream of the guide sequence insertion site and
upstream of the EF1.alpha. promoter in FIG. 9B) with hSpCas9,
showing location of various elements and the point of guide
sequence insertion. The expanded sequence around the location of
the guide sequence insertion site in FIG. 9B also shows a partial
DR sequence (GTTTTAGAGCTA (SEQ ID NO: 27)) and a partial tracrRNA
sequence (TAGCAAGTTAAAATAAGGCTAGTCCGTTTTT (SEQ ID NO: 28)). Guide
sequences can be inserted between BbsI sites using annealed
oligonucleotides. Sequence design for the oligonucleotides are
shown below the schematic illustrations in FIG. 9, with appropriate
ligation adapters indicated. WPRE represents the Woodchuck
hepatitis virus post-transcriptional regulatory element. The
efficiency of chimeric RNA-mediated cleavage was tested by
targeting the same EMX1 locus described above. Using both Surveyor
assay and Sanger sequencing of amplicons, Applicants confirmed that
the chimeric RNA design facilitates cleavage of human EMX1 locus
with approximately a 4.7% modification rate (FIG. 4).
[0215] Generalizability of CRISPR-mediated cleavage in eukaryotic
cells was tested by targeting additional genomic loci in both human
and mouse cells by designing chimeric RNA targeting multiple sites
in the human EMX1 and PVALB, as well as the mouse Th loci. FIG. 15
illustrates the selection of some additional targeted protospacers
in human PVALB (FIG. 15A) and mouse Th (FIG. 15B) loci. Schematics
of the gene loci and the location of three protospacers within the
last exon of each are provided. The underlined sequences include 30
bp of protospacer sequence and 3 bp at the 3' end corresponding to
the PAM sequences. Protospacers on the sense and anti-sense strands
are indicated above and below the DNA sequences, respectively. A
modification rate of 6.3% and 0.75% was achieved for the human
PVALB and mouse Th loci respectively, demonstrating the broad
applicability of the CRISPR system in modifying different loci
across multiple organisms (FIGS. 3B and 6). While cleavage was only
detected with one out of three spacers for each locus using the
chimeric constructs, all target sequences were cleaved with
efficiency of indel production reaching 27% when using the
co-expressed pre-crRNA arrangement (FIG. 6).
[0216] FIG. 13 provides a further illustration that SpCas9 can be
reprogrammed to target multiple genomic loci in mammalian cells.
FIG. 13A provides a schematic of the human EMX1 locus showing the
location of five protospacers, indicated by the underlined
sequences. FIG. 13B provides a schematic of the pre-crRNA/trcrRNA
complex showing hybridization between the direct repeat region of
the pre-crRNA and tracrRNA (top), and a schematic of a chimeric RNA
design comprising a 20 bp guide sequence, and tracr mate and tracr
sequences consisting of partial direct repeat and tracrRNA
sequences hybridized in a hairpin structure (bottom). Results of a
Surveyor assay comparing the efficacy of Cas9-mediated cleavage at
five protospacers in the human EMX1 locus is illustrated in FIG.
13C. Each protospacer is targeted using either processed
pre-crRNA/tracrRNA complex (crRNA) or chimeric RNA (chiRNA).
[0217] Since the secondary structure of RNA can be crucial for
intermolecular interactions, a structure prediction algorithm based
on minimum free energy and Boltzmann-weighted structure ensemble
was used to compare the putative secondary structure of all guide
sequences used in our genome targeting experiment (FIG. 3B) (see
e.g. Gruber et al., 2008, Nucleic Acids Research, 36: W70).
Analysis revealed that in most cases, the effective guide sequences
in the chimeric crRNA context were substantially free of secondary
structure motifs, whereas the ineffective guide sequences were more
likely to form internal secondary structures that could prevent
base pairing with the target protospacer DNA. It is thus possible
that variability in the spacer secondary structure might impact the
efficiency of CRISPR-mediated interference when using a chimeric
crRNA.
[0218] FIG. 3 illustrates example expression vectors. FIG. 3A
provides a schematic of a bi-cistronic vector for driving the
expression of a synthetic crRNA-tracrRNA chimera (chimeric RNA) as
well as SpCas9. The chimeric guide RNA contains a 20-bp guide
sequence corresponding to the protospacer in the genomic target
site. FIG. 3B provides a schematic showing guide sequences
targeting the human EMX1, PVALB, and mouse Th loci, as well as
their predicted secondary structures. The modification efficiency
at each target site is indicated below the RNA secondary structure
drawing (EMX1 n=216 amplicon sequencing reads; PVALB, n=224 reads;
Th, n=265 reads). The folding algorithm produced an output with
each base colored according to its probability of assuming the
predicted secondary structure, as indicated by a rainbow scale that
is reproduced in FIG. 3B in gray scale. Further vector designs for
SpCas9 are shown in FIG. 44, which illustrates single expression
vectors incorporating a U6 promoter linked to an insertion site for
a guide oligo, and a Cbh promoter linked to SpCas9 coding sequence.
The vector shown in FIG. 44b includes a tracrRNA coding sequence
linked to an H1 promoter.
[0219] To test whether spacers containing secondary structures are
able to function in prokaryotic cells where CRISPRs naturally
operate, transformation interference of protospacer-bearing
plasmids were tested in an E. coli strain heterologously expressing
the S. pyogenes SF370 CRISPR locus 1 (FIG. 10). The CRISPR locus
was cloned into a low-copy E. coli expression vector and the crRNA
array was replaced with a single spacer flanked by a pair of DRs
(pCRISPR). E. coli strains harboring different pCRISPR plasmids
were transformed with challenge plasmids containing the
corresponding protospacer and PAM sequences (FIG. 10C). In the
bacterial assay, all spacers facilitated efficient CRISPR
interference (FIG. 4C). These results suggest that there may be
additional factors affecting the efficiency of CRISPR activity in
mammalian cells.
[0220] To investigate the specificity of CRISPR-mediated cleavage,
the effect of single-nucleotide mutations in the guide sequence on
protospacer cleavage in the mammalian genome was analyzed using a
series of EMX1-targeting chimeric crRNAs with single point
mutations (FIG. 4A). FIG. 4B illustrates results of a Surveyor
nuclease assay comparing the cleavage efficiency of Cas9 when
paired with different mutant chimeric RNAs. Single-base mismatch up
to 12-bp 5' of the PAM substantially abrogated genomic cleavage by
SpCas9, whereas spacers with mutations at farther upstream
positions retained activity against the original protospacer target
(FIG. 4B). In addition to the PAM, SpCas9 has single-base
specificity within the last 12-bp of the spacer. Furthermore,
CRISPR is able to mediate genomic cleavage as efficiently as a pair
of TALE nucleases (TALEN) targeting the same EMX1 protospacer. FIG.
4C provides a schematic showing the design of TALENs targeting
EMX1, and FIG. 4D shows a Surveyor gel comparing the efficiency of
TALEN and Cas9 (n=3).
[0221] Having established a set of components for achieving
CRISPR-mediated gene editing in mammalian cells through the
error-prone NHEJ mechanism, the ability of CRISPR to stimulate
homologous recombination (HR), a high fidelity gene repair pathway
for making precise edits in the genome, was tested. The wild type
SpCas9 is able to mediate site-specific DSBs, which can be repaired
through both NHEJ and HR. In addition, an aspartate-to-alanine
substitution (D10A) in the RuvC 1 catalytic domain of SpCas9 was
engineered to convert the nuclease into a nickase (SpCas9n;
illustrated in FIG. 5A) (see e.g. Sapranauskas et al., 2011,
Nucleic Acids Research, 39: 9275; Gasiunas et al., 2012, Proc.
Natl. Acad. Sci. USA, 109:E2579), such that nicked genomic DNA
undergoes the high-fidelity homology-directed repair (HDR).
Surveyor assay confirmed that SpCas9n does not generate indels at
the EMX1 protospacer target. As illustrated in FIG. 5B,
co-expression of EMX1-targeting chimeric crRNA with SpCas9 produced
indels in the target site, whereas co-expression with SpCas9n did
not (n=3). Moreover, sequencing of 327 amplicons did not detect any
indels induced by SpCas9n. The same locus was selected to test
CRISPR-mediated HR by co-transfecting HEK 293FT cells with the
chimeric RNA targeting EMX1, hSpCas9 or hSpCas9n, as well as a HR
template to introduce a pair of restriction sites (HindIII and
NheI) near the protospacer. FIG. 5C provides a schematic
illustration of the HR strategy, with relative locations of
recombination points and primer annealing sequences (arrows).
SpCas9 and SpCas9n indeed catalyzed integration of the HR template
into the EMX1 locus. PCR amplification of the target region
followed by restriction digest with HindIII revealed cleavage
products corresponding to expected fragment sizes (arrows in
restriction fragment length polymorphism gel analysis shown in FIG.
5D), with SpCas9 and SpCas9n mediating similar levels of HR
efficiencies. Applicants further verified HR using Sanger
sequencing of genomic amplicons (FIG. 5E). These results
demonstrate the utility of CRISPR for facilitating targeted gene
insertion in the mammalian genome. Given the 14-bp (12-bp from the
spacer and 2-bp from the PAM) target specificity of the wild type
SpCas9, the availability of a nickase can significantly reduce the
likelihood of off-target modifications, since single strand breaks
are not substrates for the error-prone NHEJ pathway.
[0222] Expression constructs mimicking the natural architecture of
CRISPR loci with arrayed spacers (FIG. 2A) were constructed to test
the possibility of multiplexed sequence targeting. Using a single
CRISPR array encoding a pair of EMX1- and PVALB-targeting spacers,
efficient cleavage at both loci was detected (FIG. 4F, showing both
a schematic design of the crRNA array and a Surveyor blot showing
efficient mediation of cleavage). Targeted deletion of larger
genomic regions through concurrent DSBs using spacers against two
targets within EMX1 spaced by 119 bp was also tested, and a 1.6%
deletion efficacy (3 out of 182 amplicons; FIG. 4G) was detected.
This demonstrates that the CRISPR system can mediate multiplexed
editing within a single genome.
Example 2
CRISPR System Modifications and Alternatives
[0223] The ability to use RNA to program sequence-specific DNA
cleavage defines a new class of genome engineering tools for a
variety of research and industrial applications. Several aspects of
the CRISPR system can be further improved to increase the
efficiency and versatility of CRISPR targeting. Optimal Cas9
activity may depend on the availability of free Mg.sup.2+ at levels
higher than that present in the mammalian nucleus (see e.g. Jinek
et al., 2012, Science, 337:816), and the preference for an NGG
motif immediately downstream of the protospacer restricts the
ability to target on average every 12-bp in the human genome (FIG.
11, evaluating both plus and minus strands of human chromosomal
sequences). Some of these constraints can be overcome by exploring
the diversity of CRISPR loci across the microbial metagenome (see
e.g. Makarova et al., 2011, Nat Rev Microbiol, 9:467). Other CRISPR
loci may be transplanted into the mammalian cellular milieu by a
process similar to that described in Example 1. For example, FIG.
12 illustrates adaptation of the Type II CRISPR system from CRISPR
1 of Streptococcus thermophilus LMD-9 for heterologous expression
in mammalian cells to achieve CRISPR-mediated genome editing. FIG.
12A provides a Schematic illustration of CRISPR 1 from S.
thermophilus LMD-9. FIG. 12B illustrates the design of an
expression system for the S. thermophilus CRISPR system. Human
codon-optimized hStCa9 is expressed using a constitutive EF1.alpha.
promoter. Mature versions of tracrRNA and crRNA are expressed using
the U6 promoter to promote precise transcription initiation.
Sequences from the mature crRNA and tracrRNA are illustrated. A
single base indicated by the lower case "a" in the crRNA sequence
is used to remove the polyU sequence, which serves as a RNA polIII
transcriptional terminator. FIG. 12C provides a schematic showing
guide sequences targeting the human EMX1 locus as well as their
predicted secondary structures. The modification efficiency at each
target site is indicated below the RNA secondary structures. The
algorithm generating the structures colors each base according to
its probability of assuming the predicted secondary structure,
which is indicated by a rainbow scale reproduced in FIG. 12C in
gray scale. FIG. 12D shows the results of hStCas9-mediated cleavage
in the target locus using the Surveyor assay. RNA guide spacers 1
and 2 induced 14% and 6.4%, respectively. Statistical analysis of
cleavage activity across biological replica at these two
protospacer sites is also provided in FIG. 6. FIG. 16 provides a
schematic of additional protospacer and corresponding PAM sequence
targets of the S. thermophilus CRISPR system in the human EMX1
locus. Two protospacer sequences are highlighted and their
corresponding PAM sequences satisfying NNAGAAW motif are indicated
by underlining 3' with respect to the corresponding highlighted
sequence. Both protospacers target the anti-sense strand.
Example 3
Sample Target Sequence Selection Algorithm
[0224] A software program is designed to identify candidate CRISPR
target sequences on both strands of an input DNA sequence based on
desired guide sequence length and a CRISPR motif sequence (PAM) for
a specified CRISPR enzyme. For example, target sites for Cas9 from
S. pyogenes, with PAM sequences NGG, may be identified by searching
for 5'-N.sub.x-NGG-3' both on the input sequence and on the
reverse-complement of the input. Likewise, target sites for Cas9 of
S. thermophilus CRISPR1, with PAM sequence NNAGAAW, may be
identified by searching for 5'-N-NNAGAAW-3' (SEQ ID NO: 29) both on
the input sequence and on the reverse-complement of the input.
Likewise, target sites for Cas9 of S. thermophilus CRISPR3, with
PAM sequence NGGNG, may be identified by searching for
5'-N-NGGNG-3' both on the input sequence and on the
reverse-complement of the input. The value "x" in N.sub.x may be
fixed by the program or specified by the user, such as 20.
[0225] Since multiple occurrences in the genome of the DNA target
site may lead to nonspecific genome editing, after identifying all
potential sites, the program filters out sequences based on the
number of times they appear in the relevant reference genome. For
those CRISPR enzymes for which sequence specificity is determined
by a `seed` sequence, such as the 11-12 bp 5' from the PAM
sequence, including the PAM sequence itself, the filtering step may
be based on the seed sequence. Thus, to avoid editing at additional
genomic loci, results are filtered based on the number of
occurrences of the seed:PAM sequence in the relevant genome. The
user may be allowed to choose the length of the seed sequence. The
user may also be allowed to specify the number of occurrences of
the seed:PAM sequence in a genome for purposes of passing the
filter. The default is to screen for unique sequences. Filtration
level is altered by changing both the length of the seed sequence
and the number of occurrences of the sequence in the genome. The
program may in addition or alternatively provide the sequence of a
guide sequence complementary to the reported target sequence(s) by
providing the reverse complement of the identified target
sequence(s).
[0226] Further details of methods and algorithms to optimize
sequence selection can be found in U.S. application Ser. No.
61/836,080 (attorney docket 44790.11.2022); incorporated herein by
reference.
Example 4
Evaluation of Multiple Chimeric crRNA-tracrRNA Hybrids
[0227] This example describes results obtained for chimeric RNAs
(chiRNAs; comprising a guide sequence, a tracr mate sequence, and a
tracr sequence in a single transcript) having tracr sequences that
incorporate different lengths of wild-type tracrRNA sequence. FIG.
18a illustrates a schematic of a bicistronic expression vector for
chimeric RNA and Cas9. Cas9 is driven by the CBh promoter and the
chimeric RNA is driven by a U6 promoter. The chimeric guide RNA
consists of a 20 bp guide sequence (Ns) joined to the tracr
sequence (running from the first "U" of the lower strand to the end
of the transcript), which is truncated at various positions as
indicated. The guide and tracr sequences are separated by the
tracr-mate sequence GUUUUAGAGCUA (SEQ ID NO: 30) followed by the
loop sequence GAAA. Results of SURVEYOR assays for Cas9-mediated
indels at the human EMX1 and PVALB loci are illustrated in FIGS.
18b and 18c, respectively. Arrows indicate the expected SURVEYOR
fragments. ChiRNAs are indicated by their "+n" designation, and
crRNA refers to a hybrid RNA where guide and tracr sequences are
expressed as separate transcripts. Quantification of these results,
performed in triplicate, are illustrated by histogram in FIGS. 19a
and 19b, corresponding to FIGS. 18b and 18c, respectively ("N.D."
indicates no indels detected). Protospacer IDs and their
corresponding genomic target, protospacer sequence, PAM sequence,
and strand location are provided in Table D. Guide sequences were
designed to be complementary to the entire protospacer sequence in
the case of separate transcripts in the hybrid system, or only to
the underlined portion in the case of chimeric RNAs.
TABLE-US-00004 TABLE D proto- protospacer spacer genomic sequence
ID target (5' to 3') PAM strand 1 EMX1 GGACATCGATGTCACCTCCAATG TGG
+ ACTAGGG (SEQ ID NO: 31) 2 EMX1 CATTGGAGGTGACATCGATGTCC TGG -
TCCCCAT (SEQ ID NO: 32) 3 EMX1 GGAAGGGCCTGAGTCCGAGCAGA GGG +
AGAAGAA (SEQ ID NO: 33) 4 PVALB GGTGGCGAGAGGGGCCGAGATTG AGG +
GGTGTTC (SEQ ID NO: 34) 5 PVALB ATGCAGGAGGGTGGCGAGAGGGG TGG +
CCGAGAT (SEQ ID NO: 35)
[0228] Cell Culture and Transfection
[0229] Human embryonic kidney (HEK) cell line 293FT (Life
Technologies) was maintained in Dulbecco's modified Eagle's Medium
(DMEM) supplemented with 10% fetal bovine serum (HyClone), 2 mM
GlutaMAX (Life Technologies), 100 U/mL penicillin, and 100 g/mL
streptomycin at 37.degree. C. with 5% CO.sub.2 incubation. 293FT
cells were seeded onto 24-well plates (Corning) 24 hours prior to
transfection at a density of 150,000 cells per well. Cells were
transfected using Lipofectamine 2000 (Life Technologies) following
the manufacturer's recommended protocol. For each well of a 24-well
plate, a total of 500 ng plasmid was used.
[0230] SURVEYOR Assay for Genome Modification
[0231] 293FT cells were transfected with plasmid DNA as described
above. Cells were incubated at 37.degree. C. for 72 hours
post-transfection prior to genomic DNA extraction. Genomic DNA was
extracted using the QuickExtract DNA Extraction Solution
(Epicentre) following the manufacturer's protocol. Briefly,
pelleted cells were resuspended in QuickExtract solution and
incubated at 65.degree. C. for 15 minutes and 98.degree. C. for 10
minutes. The genomic region flanking the CRISPR target site for
each gene was PCR amplified (primers listed in Table E), and
products were purified using QiaQuick Spin Column (Qiagen)
following the manufacturer's protocol. 400 ng total of the purified
PCR products were mixed with 2 .mu.l 10.times.Taq DNA Polymerase
PCR buffer (Enzymatics) and ultrapure water to a final volume of 20
.mu.l, and subjected to a re-annealing process to enable
heteroduplex formation: 95.degree. C. for 10 min, 95C to 85.degree.
C. ramping at -2.degree. C./s, 85.degree. C. to 25.degree. C. at
-0.25.degree. C./s, and 25.degree. C. hold for 1 minute. After
re-annealing, products were treated with SURVEYOR nuclease and
SURVEYOR enhancer S (Transgenomics) following the manufacturer's
recommended protocol, and analyzed on 4-20% Novex TBE
poly-acrylamide gels (Life Technologies). Gels were stained with
SYBR Gold DNA stain (Life Technologies) for 30 minutes and imaged
with a Gel Doc gel imaging system (Bio-rad). Quantification was
based on relative band intensities.
TABLE-US-00005 TABLE E primer genomic primer sequence name target
(5' to 3') Sp-EMX1-F EMX1 AAAACCACCCTTCTCTCTGGC (SEQ ID NO: 36)
Sp-EMX1-R EMX1 GGAGATTGGAGACACGGAGAG (SEQ ID NO: 37) Sp-PVALB-F
PVALB CTGGAAAGCCAATGCCTGAC (SEQ ID NO: 38) Sp-PVALB-R PVALB
GGCAGCAAACTCCTTGTCCT (SEQ ID NO: 39)
[0232] Computational Identification of Unique CRISPR Target
Sites
[0233] To identify unique target sites for the S. pyogenes SF370
Cas9 (SpCas9) enzyme in the human, mouse, rat, zebrafish, fruit
fly, and C. elegans genome, we developed a software package to scan
both strands of a DNA sequence and identify all possible SpCas9
target sites. For this example, each SpCas9 target site was
operationally defined as a 20 bp sequence followed by an NGG
protospacer adjacent motif (PAM) sequence, and we identified all
sequences satisfying this 5'-N.sub.20-NGG-3' definition on all
chromosomes. To prevent non-specific genome editing, after
identifying all potential sites, all target sites were filtered
based on the number of times they appear in the relevant reference
genome. To take advantage of sequence specificity of Cas9 activity
conferred by a `seed` sequence, which can be, for example,
approximately 11-12 bp sequence 5' from the PAM sequence,
5'-NNNNNNNNNN-NGG-3' sequences were selected to be unique in the
relevant genome. All genomic sequences were downloaded from the
UCSC Genome Browser (Human genome hg19, Mouse genome mm9, Rat
genome rn5, Zebrafish genome danRer7, D. melanogaster genome dm4
and C. elegans genome ce10). The full search results are available
to browse using UCSC Genome Browser information. An example
visualization of some target sites in the human genome is provided
in FIG. 21.
[0234] Initially, three sites within the EMX1 locus in human HEK
293FT cells were targeted. Genome modification efficiency of each
chiRNA was assessed using the SURVEYOR nuclease assay, which
detects mutations resulting from DNA double-strand breaks (DSBs)
and their subsequent repair by the non-homologous end joining
(NHEJ) DNA damage repair pathway. Constructs designated chiRNA(+n)
indicate that up to the +n nucleotide of wild-type tracrRNA is
included in the chimeric RNA construct, with values of 48, 54, 67,
and 85 used for n. Chimeric RNAs containing longer fragments of
wild-type tracrRNA (chiRNA(+67) and chiRNA(+85)) mediated DNA
cleavage at all three EMX1 target sites, with chiRNA(+85) in
particular demonstrating significantly higher levels of DNA
cleavage than the corresponding crRNA/tracrRNA hybrids that
expressed guide and tracr sequences in separate transcripts (FIGS.
18b and 19a). Two sites in the PVALB locus that yielded no
detectable cleavage using the hybrid system (guide sequence and
tracr sequence expressed as separate transcripts) were also
targeted using chiRNAs. chiRNA(+67) and chiRNA(+85) were able to
mediate significant cleavage at the two PVALB protospacers (FIGS.
18c and 19b).
[0235] For all five targets in the EMX1 and PVALB loci, a
consistent increase in genome modification efficiency with
increasing tracr sequence length was observed. Without wishing to
be bound by any theory, the secondary structure formed by the 3'
end of the tracrRNA may play a role in enhancing the rate of CRISPR
complex formation. An illustration of predicted secondary
structures for each of the chimeric RNAs used in this example is
provided in FIG. 21. The secondary structure was predicted using
RNAfold using minimum free energy and partition function algorithm.
Pseudocolor for each based (reproduced in grayscale) indicates the
probability of pairing. Because chiRNAs with longer tracr sequences
were able to cleave targets that were not cleaved by native CRISPR
crRNA/tracrRNA hybrids, it is possible that chimeric RNA may be
loaded onto Cas9 more efficiently than its native hybrid
counterpart. To facilitate the application of Cas9 for
site-specific genome editing in eukaryotic cells and organisms, all
predicted unique target sites for the S. pyogenes Cas9 were
computationally identified in the human, mouse, rat, zebra fish, C.
elegans, and D. melanogaster genomes. Chimeric RNAs can be designed
for Cas9 enzymes from other microbes to expand the target space of
CRISPR RNA-programmable nucleases.
[0236] FIG. 22 illustrates an exemplary bicistronic expression
vector for expression of chimeric RNA including up to the +85
nucleotide of wild-type tracr RNA sequence, and SpCas9 with nuclear
localization sequences. SpCas9 is expressed from a CBh promoter and
terminated with the bGH polyA signal (bGH pA). The expanded
sequence illustrated immediately below the schematic corresponds to
the region surrounding the guide sequence insertion site, and
includes, from 5' to 3', 3'-portion of the U6 promoter (first
shaded region), BbsI cleavage sites (arrows), partial direct repeat
(tract: mate sequence CIFFITAGAGCTA (SEQ ID NO: 27), underlined),
loop sequence GAAA, and +85 tracr sequence (underlined sequence
following loop sequence) An exemplary guide sequence insert is
illustrated below the guide sequence insertion site, with
nucleotides of the guide sequence for a selected target represented
by an "N".
[0237] Sequences desctibed in the above examples are as follows
(polynucleotide sequences are 5' to 3'):
TABLE-US-00006 U6-short tracrRNA (Streptococcus pyogenes SF370):
(SEQ ID NO: 40) GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGG
CTGTTAGAGAGATAATTGGAATTAATTTGACTGTAAACACAAAGATATT
AGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCA
GTTTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTT
GAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAA
CACCGGAACCATTCAAAACAGCATAGCAAGTTAAAATAAGGCTAGTCCG
TTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT (bold = tracrRNA
sequence; underline = terminator sequence) U6-long tracrRNA
(Streptococcus pyogenes SF370): (SEQ ID NO: 41)
GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGG
CTGTTAGAGAGATAATTGGAATTAATTTGACTGTAAACACAAAGATATT
AGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCA
GTTTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTT
GAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAA
CACCGGTAGTATTAAGTATTGTTTTATGGCTGATAAATTTCTTTGAATT
TCTCCTTGATTATTTGTTATAAAAGTTATAAAATAATCTTGTTGGAACC
ATTCAAAACAGCATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTT
GAAAAAGTGGCACCGAGTCGGTGCTTTTTTT U6-DR-BbsI backbone-DR
(Streptococcus pyogenes SF370): (SEQ ID NO: 42)
GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGG
CTGTTAGAGAGATAATTGGAATTAATTTGACTGTAAACACAAAGATATT
AGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCA
GTTTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTT
GAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAA
CACCGGGTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAACGGGTCTT
CGAGAAGACGTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC U6-chimeric RNA-BbsI
backbone (Streptococcus pyogenes SF370) (SEQ ID NO: 43)
GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGG
CTGTTAGAGAGATAATTGGAATTAATTTGACTGTAAACACAAAGATATT
AGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCA
GTTTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTT
GAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAA
CACCGGGTCTTCGAGAAGACCTGTTTTAGAGCTAGAAATAGCAAGTTAA AATAAGGCTAGTCCG
NLS-SpCas9-EGFP: (SEQ ID NO: 44)
MDYKDUDGDYKDMDIDYKDDDDKMAPKKKRKVGIHGVPAADKKYSIGLD
IGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETA
EATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVE
EDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLA
LAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGV
DAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSN
FDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSD
ILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFD
QSKNGYAGIDGGASQEEFYKFIKPILEKNlDGTEELLVKLNREDIXRKQ
RTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYY
VGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDK
NLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIV
DLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLL
KIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKV
MKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQL
IHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVD
ELVKVMGRHKPENIVIEMARENQTTOKGQKNSRERMKRIEEGIKELGSQ
ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVP
QSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLI
TQRKFDNLTKAERGGLSELDKAGF1KRQLVETRQITKHVAQILDSRMNI
KYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLN
AWGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYS
NIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSM
PQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPT
VAYSVLVVAKVEKGKSKKIASVKELLGITIMERSSFFKNPIDFLEAKGY
KEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFL
YLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADA
NLDKVLSAYNKIIRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDR
KRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDAAAVSKGEELFTGV
VPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL
VTTLTYGVQCFSRYPDHMKOHDFFKSAMPEGYVQERTIFFKDDGNYKTR
AEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQK
NGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSAL
SKDPNEKRDHMVLLEFVTAAGITLGMDELYK SpCas9-EGFP-NLS: (SEQ ID NO. 45)
MDKKYSIGLDIGTNSVGVVAVITDEYKVPSKKFKVLGNTDRHSIKKNLI
GALLFDSGETAEATRLKRTARRRYTRRKNRICYLQHIFSNEMAKVDDSF
FFIRLEESFLVEHDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDS
IDKADLRLIYLALAHMIKFRGFIFLIEGDLNPDNSDVDKLFIQLVQTYN
QLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLI
ALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFL
AAKNLSDAILLSDILRVNTEITKAPLSASMfKRYDEHHQDLTLLKALVR
QQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEEL
LVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNRE
KIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGAS
AQSFIERMTNFDKNLPNEKVLPKIISLLYEYFTVYNELTKVKYVTEGMR
KPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVE
DRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIE
ERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDF
LKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSP
AKKGILQTVKVVDELVKVVIGRIIKPENIVIEMARENQTTQKGQKNSRE
RMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQEL
DINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVK
KMKNYWRQLLNAKIJTQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQ
ITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKV
REINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAK
SEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIV
WDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIAR
KKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMER
SSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGEL
QKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDII
EQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLG
APAAFKYFDTTTDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD
AAAVSKGEELFTGWPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFI
CTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQER
TIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNY
NSHNVYIMADKQKNGIKVTSTKIRHNIEDGSVQLADHYQQNTPIGDGPV
LLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGFFLGMDELYKKRPA ATKKAGQAKKKK
NLS-SpCas9-EGFP-NLS: (SEQ ID NO: 46)
MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGTHGWAADKKYSIGLDI
GTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAE
ATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEE
DKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTQKADLRLIYLAL
AHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYMQLFEENPINASGVD
AKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNF
DLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDI
LRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQ
SKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQR
TFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYV
GPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKN
LPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVD
LLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLK
IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMK
QLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIH
DDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKWDELV
KVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILK
EHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF
LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQR
KFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYD
ENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVV
GTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKWFYSNMN
FFKTEITLANGEIRKRPLIETNGETGEIVDKGRDFATVRKVLSMPQVNI
VKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSV
LVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKK
DLIIKLPKYSLFELENGIIKRMLASAGELOKGNELALPSKYVNFLYLAS
HYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDK
VLSAYNKHRDKPIREOAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTS
TKEVLDATLIHQSITGLYETRIDLSQLGGDAAAVSKGEELFTGVVPILV
ELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVTWPTLVTTLT
YGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKF
EGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV
NFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPN
EKRDHMVLLEFVTAAGITLGMDELYKKRPAATKKAGQAKKKK NLS-SpCas9-NLS: (SEQ ID
NO: 47) MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGIHGVPAADKKYSIGLD
IGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETA
EATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVE
EDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLA
LARVIIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASG
VDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKS
NFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLS
DILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFF
DQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRK
QRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNPILEKIEKILTFRI
PYWGPLARGNSRFAWMTRKSEETITPWNFEEWDKGASAQSFIERMTNFD
KNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAI
VDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDL
LKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDK
VMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQ
LIHDDSLTFKEDIQKAQVSGQGDSLHEHIAMAGSPAIKKGILQTVKVVD
ELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQ
ILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVP
QSFLKDDSIDNKVLTRSDKNRGKSDNWSEEVVKKMKNYWRQLLNAKLIT
QRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTK
YDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNA
VVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYS
NIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSM
PQVNIVKKTEVQTGGFSKESILPKRNSDKLLARKKDVVDPKKYGGFDSP
TVAYSVLVVAKVEKGKSKKLKSVKELLGITLMERSSFEKNPIDFLEAKG
YKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNF
LYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILAD
ANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDR
KRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDKRPAATKKAGQAKK KK
NLS-mCherry-SpRNase3: (SEQ ID NO: 48)
MFLFLSLTSFLSSSRTLVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFE
IEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPA
DIPDYLKLSFPEGFKWERVMNTEDGGVVTVTQDSSLQDGEFIYKVKLRG
TNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYDA
EVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRFIST
GGMDELYKGSKQLEELLSTSFDIQFNDLTLLETAFTHTSYANEHRLLNV
SHNERLEFLGDAVLQLIISEYLFAKYPKKTEGDMSKLRSMIVREESLAG
FSRFCSFDAYIKLGKGEEKSGGRRRDTILGDLFEAFLGALLLDKGIDAV
RRFLKQVMIPQVEKGNFERVKDYKTCLQEFLQTKGDVAIDYQVISEKGP
AHAKQFEVSIVVNGAVLSKGLGKSKKLAEQDAAKNALAQLSEV SpRNase3-mCherry-NLS:
(SEQ ID NO: 49) MKQLEELLSTSFDIQFNDLTLLETAFTHTSYANEHRLLNVSHNERLEFL
GDAVLQLIISEYLFAKYPKKTEGDMSKLRSMIVREESLAGFSRPCSFDA
YIKLGKGEEKSGGRRRDTILGDLFEAFLGALLLDKGIDAVRRFLKQVMI
PQVEKGNFERVKDYKTCLQEFLQTKGDVAIDYQVISEKGPAHAKQFEVS
IVVNGAVLSKGLGKSKKLAEQDAAKNALAQLSEVGSVSKGEEDNMAIIK
EFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAW
DILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTV
TQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGA
LKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVMKLDITSHNE
DYTIVEQYERAEGRHSTGGMDELYKKRPAATKKAGQAKKKK NLS-SpCas9n-NLS (the D10A
nickase mutation is lowercase): (SEQ ID NO: 50)
MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGIHGVPAADKKYSIGLa
IGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETA
EATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVE
EDKKHERFIPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYL
ALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASG
VDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKS
NFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLS
DILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQIPFKYKEIFF
DQSKNGYAGYIDGGASQEEFYKFDCPILEKMDGTEFXLVKLNREDLLRK
QRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPY
YVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFD
KNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAI
VDLLITCTMIKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHD
LLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDD
KVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFM
QLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKW
DELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGKELGSQ
ILKEHPVENTQLQNEKLYLYYLQNGRDNlYVDQELDINRLSDYDVDHIV
PQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKL
ITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMN
TKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYL
NAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFF
YSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVL
SMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDS
PTVAYSVLWAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKG
YKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNF
LYLASFFYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILA
DANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTID
RKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDKRPAATKKAGQAK KKK hEMX1-HR
Template-HindII-NheI: (SEQ ID NO: 51)
GAATGCTGCCCTCAGACCCGCTTCCTCCCTGTCCTTGTCTGTCCAAGGA
GAATGAGGTCTCACTGGTGGATTTCGGACTACCCTGAGGAGCTGGCACC
TGAGGGACAAGGCCCCCCACCTGCCCAGCTCCAGCCTCTGATGAGGGGT
GGGAGAGAGCTACATGAGGTTGCTAAGAAAGCCTCCCCTGAAGGAGACC
ACACAGTGTGTGAGGTTGGAGTCTCTAGCAGCGGGTTCTGTGCCCCCAG
GGATAGTCTGGCTGTCCAGGCACTGCTCTTGATATAAACACCACCTCCT
AGTTATGAAACCATGCCCATTCTGCCTCTCTGTATGGAAAAGAGCATGG
GGCTGGCCCGTGGGGTGGTGTCCACTTTAGGCCCTGTGGGAGATCATGG
GAACCCACGCAGTGGGTCATAGGCTCTCTCATTTACTACTCACATCCAC
TCTGTGAAGAAGCGATTATGATCTCTCCTCTAGAAACTCGTAGAGTCCC
ATGTCTGCCGGCTTCCAGAGCCTGCACTCCTCCACCTTGGCTTGGCTTT
GCTGGGGCTAGAGGAGCTAGGATGCACAGCAGCTCTGTGACCCTTTGTT
TGAGAGGAACAGGAAAACCACCCTTCTCTCTGGCCCACTGTGTCCTCTT
CCTGCCCTGCCATCCCCTTCTGTGAATGTTAGACCCATGGGAGCAGCTG
GTCAGAGGGGACCCCGGCCTGGGGCCCCTAACCCTATGTAGCCTCAGTC
TTCCCATCAGGCTCTCAGCTCAGCCTGAGTGTTGAGGCCCCAGTGGCTG
CTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCC
AGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTACAAACGGCAGAA
GCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCAT
CACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATGGGGAGGACA
TCGATGTCACCTCCAATGACaagcttgctagcGGTGGGCAACCACAAAC
CCACGAGGGCAGAGTGCTGCTTGCTGCTGGCCAGGCCCCTGCGTGGGCC
CAAGCTGGACTCTGGCCACTCCCTGGCCAGGCTTTGGGGAGGCCTGGAG
TCATGGCCCCACAGGGCTTGAAGCCCGGGGCCGCCATTGACAGAGGGAC
AAGCAATGGGCTGGCTGAGGCCTGGGACCACTTGGCCTTCTCCTCGGAG
AGCCTGCCTGCCTGGGCGGGCCCGCCCGCCACCGCAGCCTCCCAGCTGC
TCTCCGTGTCTCCAATCTCCCTTTTGTTTTGATGCATTTCTGTTTTAAT
TTATTTTCCAGGCACCACTGTAGTTTAGTGATCCCCAGTGTCCCCCTTC
CCTATGGGAATAATAAAAGTCTCTCTCTTAATGACACGGGCATCCAGCT
CCAGCCCCAGAGCCTGGGGTGGTAGATTCCGGCTCTGAGGGCCAGTGGG
GGCTGGTAGAGCAAACGCGTTCAGGGCCTGGGAGCCTGGGGTGGGGTAC
TGGTGGAGGGGGTCAAGGGTAATTCATTAACTCCTCTCTTTTGTTGGGG
GACCCTGGTCTCTACCTCCAGCTCCACAGCAGGAGAAACAGGCTAGACA
TAGGGAAGGGCCATCCTGTATCTTGAGGGAGGACAGGCCCAGGTCTTTC
TTAACGTATTGAGAGGTGGGAATCAGGCCCAGGTAGTTCAATGGGAGAG
GGAGAGTGCTTCCCTCTGCCTAGAGACTCTGGTGGCTTCTCCAGTTGAG
GAGAAACCAGAGGAAAGGGGAGGATTGGGGTCTGGGGGAGGGAACACCA
TTCACAAAGGCTGACGGTTCCAGTCCGAAGTCGTGGGCCCACCAGGATG
CTCACCTGTCCTTGGAGAACCGCTGGGCAGGTTGAGACTGCAGAGACAG
GGCTTAAGGCTGAGCCTGCAACCAGTCCCCAGTGACTCAGGGCCTCCTC
AGCCCAAGAAAGAGCAACGTGCCAGGGCCCGCTGAGCTCTTGTGTTCAC CTG
NLS-StCsn1-NLS: (SEQ ID NO 52)
MKRPAATKKAGQAKKKKSDLVLGLDIGIGSVGVGILNKVTGEIIHKNSR
IFPAAQAENNLVRRTNRQGRRLARRKKHRRVRLNRLFEESGLITDFTKI
SINLNPYQLRVKGLTDELSNEELFIALKNMVKHRGISYLDDASDDGNSS
VGDYAQIVKENSKQLETKTPGQIQLERYQTYGQLRGDFTVEKDGKKHRL
INVFPTSAYRSEALRILQTQQEFNPQITDEFINRYLEILTGKRKYYHGP
GNEKSRTDYGRYRTSGETLDNIFGILIGKCTFYPDEFRAAKASYTAQEF
NLLNDLNNLTWTETKKLSKEQKNQIINYVKNEKAMGPAKLFKYIAKLLS
CDVADIKGYRIDKSGKAEIHTFEAYRKMKTLETLDIEQMDREILDKLAY
VLTLNTEREGIQEALEHEFADGSFSOKQVDELVQFRKANSSIFGKGWHN
FSVKLMMELIPELYETSEEQMTILTRLGKQKTTSSSNKTKYIDEKLLTE
EIYNPWAKSVRQAIKIVNAAIKEYGDFDNIVIEMARETNEDDEKKAIQK
IQKANKDEKDAAMLKAANQYNGKAELPHSVFHGHKQLATKIRLWHQQGE
RCLYTGKTISIHDLINNSNQFEVDHILPLSITFDDSLANKVLVYATANQ
EKGQRTPYQALDSMDDAWSFRELKAFVRESKTLSNKKKEYLLTEEDISK
FDVRKKFIERNLVDTRYASRWLNALQEHFRAHKIDTKVSVVRGQFTSQL
RRHWGTEKTRDTYHHHAVDALIIAASSQLNLWKKQKNTLVSYSEDQLLD
IETGELISDDEYKESVTKAPYQHFVDTLKSKEFEDSILFSYQVDSKFNR
KISDATIYATRQAKVGKDKADETYVLGKIKDIYTQDGYDAFMKIYKKDK
SKFLMYRHDPQTFEKVIEPILENYPNKQINEKGKEVPCNPFLKYKEEHG
YIRKYSKKGNGPEIKSLKYYDSKLGNHIDITPKDSNMCVVLQSVSPWRA
DWFNKTTGKYEILGLKYADLQFEKGTGTYKISQEKYNDIKKKEGVDSDS
EFKFTLYKNDLLLVKDTETKEQQLFRFLSRTMPKQKHYVELKPYDKQKF
EGGEALIKVLGNVANSGQCKKGLGKSNISIYKVRTDVLGNQHIIKNEGD
KPKLDFKRPAATKKAGQAKKKK U6-St_tracrRNA(7-97): (SEQ ID NO: 53)
GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGG
CTGTTAGAGAGATAATTGGAATTAATTTGACTGTAAACACAAAGATATT
AGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCA
GTTTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTT
GAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAA
CACCGTTACTTAAATCTTGCAGAAGCTACAAAGATAAGGCTTCATGCCG
AAATCAACACCCTGTCATTTTATGGCAGGGTGTTTTCGTTATTTAA U6-DR-spacer-DR (S.
pyogenes SF370) (SEQ ID NO: 54)
gagggcctatttcccatgattccttcatatttgcatatacgatacaagg
ctgttagagagataattggaattaatttgactgtaaacacaaagatatt
agtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgca
gttttaaaattatgttttaaaatggactatcatatgcttaccgtaactt
gaaagtatttcgatttcttggctttatatatcttgtggaaaggacgaaa
caccgggttttagagctatgctgttttgaatggtcccaaaacNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNgttttagagctatgctgttttgaatg gtcccaaaacTTTTTTT
(lowercase underline = direct repeat; N = guide sequence; bold =
terminator) Chimeric RNA containing +48 tracr RNA (S. pyogenes
SF370) (SEQ ID NO: 55)
gagggcctatttcccatgattccttcatatttgcatatacgatacaagg
ctgttagagagataattggaattaatttgactgtaaacacaaagatatt
agtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgca
gttttaaaattatgttttaaaatggactatcatatgcttaccgtaactt
gaaagtatttcgatttcaggctttatatatcttgtggaaaggacgaaac
accNNNNNNNNNNNNNNNNNNNNgttttagagctagaaatagcaagtta
aaataaggctagtccgTTTTTTT (N = guide sequence; first underline =
tracr mate sequence; second underline = tracr sequence; bold =
terminator) Chimeric RNA containing +54 tracr RNA (S. pyogenes
SF370) (SEQ ID NO: 56)
gagggcctatttcccatgattccttcatatttgcatatacgatacaagg
ctgttagagagataattggaattaatttgactgtaaacacaaagatatt
agtacaaaatacgtgacgtagaaagtaataatttatgggtagtagcagt
tttaaaattatgattaaaatggactatcatatgcttaccgtaacttgaa
agtatttgatttcttggctttatatatcttgtggaaaggacgaaacacc
NNNNNNNNNNNNNNNNNNNNgttttagagctagaaatagcaagttaaaa
taaggctagtccgttatcaTTTTTTTT (N = guide sequence; first underline =
tracr mate sequence; second underline = tracr sequence; bold =
terminator) Chimeric RNA containing +67 tracr RNA (S. pyogenes
SF370) (SEQ ID NO: 57)
gagggcctatttcccatgattccttcatatttgcatatacgatacaagg
ctgttagagagataattggaattaatttgactgtaaacacaaagatatt
agtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgca
gttttaaaattatgattaaaatggactatcatatgcttaccgtaacttg
aaagtatttcgatttcaggctttatatatcttgtggaaaggacgaaaca
ccNNNNNNNNNNNNNNNNNNNNgtttagagctagaaatagcaagttaaa
ataaggctagtccgttatcaacttgaaaaagtaTTTTTTTT (N = guide sequence;
first underline = tracr mate sequence; second underline = tracr
sequence; bold = terminator) Chimeric RNA containing +85 tracr RNA
(S. pyogenes SF370) (SEQ ID NO: 58)
gagggcctatacccatgattccttcatatttgcatatacgatacaaggc
tgttagagagataattggaattaatttgactgtaaacacaaagatatta
gtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgcag
ttttaaaattatgttttaaaatggactatcatatgcttaccgtaacttg
aaagtatttcgatttcttggctttatatatcttgtggaaaggacgaaac
accNNNNNNNNNNNNNNNNNNNNgttttagagctagaaatagcaagtta
aaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcggtg cTTTTTTTT (N =
guide sequence; first underline = tracr mate sequence; second
underline = tracr sequence; bold = terminator) CBh-NLS-SpCas9-NLS
(SEQ ID NO: 59) CGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCAACGAC
CCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAA
TAGGGACTTTCCATTGACGTCAATGGGTGGAGTATTTACGGTAAACTGC
CCACTTGGCAGTACATCAAGTGTATCATATGCCAAGTACGCCCCCTATT
GACGTCAATGACGGTAAATGGCCCGCCTGGCATTATGCCCAGTACATGA
CCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTATTAGTCATCGC
TATTACCATGGTCGAGGTGAGCCCCACGTTCTGCTTCACTCTCCCCATC
TCCCCCCCCTCCCCACCCCCAATTTTGTATTTATTTATTTTTTAATTAT
TTTGTGCAGCGATGGGGGCGGGGGGGGGGGGGGGGCGCGCGCCAGGCGG
GGCGGGGCGGGGCGAGGGGCGGGGCGGGGCGAGGCGGAGAGGTGCGGCG
GCAGCCAATCAGAGCGGCGCGCTCCGAAAGTTTCCTTTTATGGCGAGGC
GGCGGCGGCGGCGGCCCTATAAAAAGCGAAGCGCGCGGCGGGCGGGAGT
CGCTGCGACGCTGCCTTCGCCCCGTGCCCCGCTCCGCCGCCGCCTCGCG
CCGCCCGCCCCGGCTCTGACTGACCGCGTTACTCCCACAGGTGAGCGGG
CGGGACGGCCCTTCTCCTCCGGGCTGTAATTAGCTGAGCAAGAGGTAAG
GGATTAAGGGATGGTTGGTTGGTGGGGTATTAATGTTTAATTACCTGGA
GCACCTGCCTGAAATCACTTTTTTTCAGGTTGGaccaataccaccATGG
ACTATAAGGACCACGACGGAGACTACAAGGATCATGATATTGATTACAA
AGACGATGACGATAAGATGGCCCCAAAGAAGAAGCGGAAGGTCGGTATC
CACGGAGTCCCAGCAGCCGACAAGAAGTACAGCATCGGCCTGGACATCG
GCACCAACTCTGTGGGCTGGGCCGTGATCACCGACGAGTACAAGGTGCC
CAGCAAGAAATTCAAGGTGCTGGGCAACACCGACCGGCACAGCATCAAG
AAGAACCTGATCGGAGCCCTGCTGTTCGACAGCGGCGAAACAGCCGAGG
CCACCCGGCTGAAGAGAACCGCCAGAAGAAGATACACCAGACGGAAGAA
CCGGATCTGCTATCTGCAAGAGATCTTCAGCAACGAGATGGCCAAGGTG
GACGACAGCTTCTTCCACAGACTGGAAGAGTCCTTCCTGGTGGAAGAGG
ATAAGAAGCACGAGCGGCACCCCATCTTCGGCAACATCGTGGACGAGGT
GGCCTACCACGAGAAGTACCCCACCATCTACCACCTGAGAAAGAAACTG
GTGGACAGCACCGACAAGGCCGACCTGCGGCTGATCTATCTGGCCCTGG
CCCACATGATCAAGTTCCGGGGCCACTTCCTGATCGAGGGCGACCTGAA
CCCCGACAACAGCGACGTGGACAAGCTGTTCATCCAGCTGGTGCAGACC
TACAACCAGCTGTTCGAGGAAAACCCCATCAACGCCAGCGGCGTGGACG
CCAAGGCCATCCTGTCTGCCAGACTGAGCAAGAGCAGACGGCTGGAAAA
TCTGATCGCCCAGCTGCCCGGCGAGAAGAAGAATGGCCTGTTCGGCAAC
CTGATTGCCCTGAGCCTGGGCCTGACCCCCAACTTCAAGAGCAACTTCG
ACCTGGCCGAGGATGCCAAACTGCAGCTGAGCAAGGACACCTACGACGA
CGACCTGGACAACCTGCTGGCCCAGATCGGCGACCAGTACGCCGACCTG
TTTCTGGCCGCCAAGAACCTGTCCGACGCCATCCTGCTGAGCGACATCC
TGAGAGTGAACACCGAGATCACCAAGGCCCCCCTGAGCGCCTCTATGAT
CAAGAGATACGACGAGCACCACCAGGACCTGACCCTGCTGAAAGCTCTC
GTGCGGCAGCAGCTGCCTGAGAAGTACAAAGAGATTTTCTTCGACCAGA
GCAAGAACGGCTACGCCGGCTACATTGACGGCGGAGCCAGCCAGGAAGA
GTTCTACAAGTTCATCAAGCCCATCCTGGAAAAGATGGACGGCACCGAG
GAACTGCTCGTGAAGCTGAACAGAGAGGACCTGCTGCGGAAGCAGCGGA
CCTTCGACAACGGCAGCATCCCCCACCAGATCCACCTGGGAGAGCTGCA
CGCCATTCTGCGGCGGCAGGAAGATTTTTACCCATTCCTGAAGGACAAC
CGGGAAAAGATCGAGAAGATCCTGACCTTCCGCATCCCCTACTACGTGG
GCCCTCTGGCCAGGGGAAACAGCAGATTCGCCTGGATGACCAGAAAGAG
CGAGGAAACCATCACCCCCTGGAACTTCGAGGAAGTGGTGGACAAGGGC
GCTTCCGCCCAGAGCTTCATCGAGCGGATGACCAACTTCGATAAGAACC
TGCCCAACGAGAAGGTGCTGCCCAAGCACAGCCTGCTGTACGAGTACTT
CACCGTGTATAACGAGCTGACCAAAGTGAAATACGTGACCGAGGGAATG
AGAAAGCCCGCCTTCCTGAGCGGCGAGCAGAAAAAGGCCATCGTGGACC
TGCTGTTCAAGACCAACCGGAAAGTGACCGTGAAGCAGCTGAAAGAGGA
CTACTTCAAGAAAATCGAGTGCTTCGACTCCGTGGAAATCTCCGGCGTG
GAAGATCGGTTCAACGCCTCCCTGGGCACATACCACGATCTGCTGAAAA
TTATCAAGGACAAGGACTTCCTGGACAATGAGGAAAACGAGGACATTCT
GGAAGATATCGTGCTGACCCTGACACTGTTTGAGGACAGAGAGATGATC
GAGGAACGGCTGAAAACCTATGCCCACCTGTTCGACGACAAAGTGATGA
AGCAGCTGAAGCGGCGGAGATACACCGGCTGGGGCAGGCTGAGCCGGAA
GCTGATCAACGGCATCCGGGACAAGCAGTCCGGCAAGACAATCCTGGAT
TTCCTGAAGTCCGACGGCTTCGCCAACAGAAACTTCATGCAGCTGATCC
ACGACGACAGCCTGACCTTTAAAGAGGACATCCAGAAAGCCCAGGTGTC
CGGCCAGGGCGATAGCCTGGACGAGCACATTGCCAATCTGGCCGGCAGC
CCCGCCATTAAGAAGGGCATCCTGCAGACAGTGAAGGTGGTGGACGAGC
TCGTGAAAGTGATGGGCCGGCACAAGCCCGAGAACATCGTGATCGAAAT
GGCCAGAGAGAACCAGACCACCCAGAAGGGACAGAAGAACAGCCGCGAG
AGAATGAAGCGGATCGAAGAGGGCATCAAAGAGCTGGGCAGCCAGATCC
TGAAAGAACACCCCGTGGAAAACACCCAGCTGCAGAACGAGAAGCTGTA
CCTGTACTACCTGCAGAATGGGCGGGATATGTACGTGGACCAGGAACTG
GACATCAACCGGCTGTCCGACTACGATGTGGACCATATCGTGCCTCAGA
GCTTTCTGAAGGACGACTCCATCGACAACAAGGTGCTGACCAGAAGCGA
CAAGAACCGGGGCAAGAGCGACAACGTGCCCTCCGAAGAGGTCGTGAAG
AAGATGAAGAACTACTGGCGGCAGCTGCTGAACGCCAAGCTGATTACCC
AGAGAAAGTTCGACAATCTGACCAAGGCCGAGAGAGGCGGCCTGAGCGA
ACTGGATAAGGCCGGCTTCATCAAGAGACAGCTGGTGGAAACCCGGCAG
ATCACAAAGCACGTGGCACAGATCCTGGACTCCCGGATGAACACTAAGT
ACGACGAGAATGACAAGCTGATCCGGGAAGTGAAAGTGATCACCCTGAA
GTCCAAGCTGGTGTCCGATTTCCGGAAGGATTTCCAGTTTTACAAAGTG
CGCGAGATCAACAACTACCACCACGCCCACGACGCCTACCTGAACGCCG
TCGTGGGAACCGCCCTGATCAAAAAGTACCCTAAGCTGGAAAGCGAGTT
CGTGTACGGCGACTACAAGGTGTACGACGTGCGGAAGATGATCGCCAAG
AGCGAGCAGGAAATCGGCAAGGCTACCGCCAAGTACTTCTTCTACAGCA
ACATCATGAACTTTTTCAAGACCGAGATTACCCTGGCCAACGGCGAGAT
CCGGAAGCGGCCTCTGATCGAGACAAACGGCGAAACCGGGGAGATCGTG
TGGGATAAGGGCCGGGATTTTGCCACCGTGCGGAAAGTGCTGAGCATGC
CCCAAGTGAATATCGTGAAAAAGACCGAGGTGCAGACAGGCGGCTTCAG
CAAAGAGTCTATCCTGCCCAAGAGGAACAGCGATAAGCTGATCGCCAGA
AAGAAGGACTGGGACCCTAAGAAGTACGGCGGCTTCGACAGCCCCACCG
TGGCCTATTCTGTGCTGGTGGTGGCCAAAGTGGAAAAGGGCAAGTCCAA
GAAACTGAAGAGTGTGAAAGAGCTGCTGGGGATCACCATCATGGAAAGA
AGCAGCTTCGAGAAGAATCCCATCGACTTTCTGGAAGCCAAGGGCTACA
AAGAAGTGAAAAAGGACCTGATCATCAAGCTGCCTAAGTACTCCCTGTT
CGAGCTGGAAAACGGCCGGAAGAGAATGCTGGCCTCTGCCGGCGAACTG
CAGAAGGGAAACGAACTGGCCCTGCCCTCCAAATATGTGAACTTCCTGT
ACCTGGCCAGCCACTATGAGAAGCTGAAGGGCTCCCCCGAGGATAATGA
GCAGAAACAGCTGTTTGTGGAACAGCACAAGCACTACCTGGACGAGATC
ATCGAGCAGATCAGCGAGTTCTCCAAGAGAGTGATCCTGGCCGACGCTA
ATCTGGACAAAGTGCTGTCCGCCTACAACAAGCACCGGGATAAGCCCAT
CAGAGAGCAGCKrCGAGAATATCATCCACCTGTTTACCCTGACCAATCT
GGGAGCCCCTGCCGCCTTCAAGTACTTTGACACCACCATCGACCGGAAG
AGGTACACCAGCACCAAAGAGGTGCTGGACGCCACCCTGATCCACCAGA
GCATCACCGGCCTGTACGAGACACGGATCGACCTGTCTCAGCTGGGAGG
CGACTTTCTTTTTCTTAGCTTGACCAGCTTTCTTAGTAGCAGCAGGACG CTTTAA (underline
= NLS-hSpCas9-NLS) Example chimeric RNA for S. thermophilus LMD-9
CRISPR1 Cas9 (with PAM of NNAGAAW) (SEQ ID NO: 21)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaagatttaGAAAtaa
atcttgcagaagctacaaagataaggcttcatgccgaaatcaacaccct
gtcattttatggcagggtgttttacgttatttaaTTTTTT (N = guide sequence; first
underline = tracr mate sequence; second underline = tracr sequence;
bold = terminator) Example chimeric RNA for S. thermophilus LMD-9
CRISPR1 Cas9 (with PAM of NNAGAAW) (SEQ ID NO: 22)
NNNNNNNNNNNNNNNNNNNNgtattgtactctcaGAAAtgcagaagcta
caaaataacttcatgccgaaatcaacaccctgtcattttatggcagggt
gttacgttatttaaTTTTTT (N = guide sequence; first underline = tracr
mate sequence; second underline = tracr sequence; bold =
terminator) Example chimeric RNA for S. thermophilus LMD-9 CRISPR1
Cas9 (with PAM of NNAGAAW) (SEQ ID NO: 23)
NNNNNNNNNNNNNNNNNNNNgttttttgtactacaGAAAtgcagaagct
acaaagataaggcttcatgccgaaatcaacaccctgtcattttatggca gggtgtTTTTTT (N =
guide sequence; first underline = tracr mate sequence; second
underline = tracr sequence; bold = terminator) Example chimeric RNA
for S. thermophilus LMD-9 CRISPR1 Cas9 (with PAM of NNAGAAW) (SEQ
ID NO: 60) NNNNNNNNNNNNNNNNNNNNgttattgtactctcaagatttaGAAAtaa
atcttgcagaagctacaaagataaggatcatgccgaaatcaacaccctg
tcatatatggcagggtgttttcgttatttaaTTTTTT (N = guide sequence; first
underline = tracr mate sequence; second underline = tracr sequence;
bold = terminator) Example chimeric RNA for S. thermophilus LMD-9
CRISPR1 Cas9 (with PAM of NNAGAAW) (SEQ ID NO: 61)
NNNNNNNNNNNNNNNNNNNNgttattgtactctcaGAAAtgcagaagct
acaaagataaggcttcatgccgaaatcaacaccctgtcattttatggca
gggtgttttacgttatttaaTTTTTT (N = guide sequence; first underline =
tracr mate sequence; second underline = tracr sequence; bold =
terminator) Example chimeric RNA for S. thermophilus LMD-9 CRISPR1
Cas9 (with PAM of NNAGAAW) (SEQ ID NO: 62)
NNNNNNNNNNNNNNNNNNNNgttattgtactctcaGAAAtgcagaagct
acaaagataaggcttcatgccgaaatcaacaccctgtcattttatggca gggtgtTTTTTT (N =
guide sequence; first underline = tracr mate sequence; second
underline = tracr sequence; bold = terminator) Example chimeric RNA
for S. thermophilus LMD-9 CRISPR1 Cas9 (with PAM of NNAGAAW) (SEQ
ID NO: 63) NNNNNNNNNNNNNNNNNNNNgttattgtactctcaagatttaGAAAtaa
atcttcagaagctacaatgataaggcttcatgccgaaatcaacaccctg
tcattttatggcagggtgttttcgttatttaaTTTTTT (N = guide sequence; first
underline = tracr mate sequence; second underline = tracr sequence;
bold = terminator) Example chimeric RNA for S. thermophilus
LMD-9
CRISPR1 Cas9 (with PAM of NNAGAAW) (SEQ ID NO: 64)
NNNNNNNNNNNNNNNNNNNNgttattgtactctcaGAAAtgcagaagct
acaatgataaggcttcatgccgaaatcaacaccctgtcattttatggca
gggtgttttcgttatttaaTTTTTT (N = guide sequence; first underline =
tracr mate sequence; second underline = tracr sequence; bold =
terminator) Example chimeric RNA for S. thermophilus LMD-9 CRISPR1
Cas9 (with PAM of NNAGAAW) (SEQ ID NO: 65)
NNNNNNNNNNNNNNNNNNNNgttattgactctcaGAAAtgcagaagcta
caatgataaggcttcatgccgaaatcaacaccctgtcattttatggcag ggtgTTTTTT (N =
guide sequence; first underline = tracr mate sequence; second
underline = tracr sequence; bold = terminator) Example chimeric RNA
for S. thermophilus LMD-9 CRISPR3 Cas9 (with PAM of NGGNG) (SEQ ID
NO: 66) NNNNNNNNNNNNNNNNNNNNgttttagagctgtgGAAAcacagcgagtt
aaaataaggcttagtccgtactcaacttgaaaaggtggcaccgattcgg tgtTTTTTT (N =
guide sequence; first underline = tracr mate sequence; second
underline = tracr sequence; bold = terminator) Codon-optimized
version of Cas9 from S. thermophilus LMD-9 CRISPR3 locus (with an
NLS at both 5' and 3' ends) (SEQ ID NO: 67)
ATGAAAAGGCCGGCGGCCACGAAAAAGGCCGGCCAGGCAAAAAAGAAAA
AGACCAAGCCCTACAGCATCGGCCTGGACATCGGCACCAATAGCGTGGG
CTGGGCCGTGACCACCGACAACTACAAGGTGCCCAGCAAGAAAATGAAG
GTGCTGGGCAACACCTCCAAGAAGTACATCAAGAAAAACCTGCTGGGCG
TGCTGCTGTTCGACAGCGGCATTACAGCCGAGGGCAGACGGCTGAAGAG
AACCGCCAGACGGCGGTACACCCGGCGGAGAAACAGAATCCTGTATCTG
CAAGAGATCTTCAGCACCGAGATGGCTACCCTGGACGACGCCTTCTTCC
AGCGGCTGGACGACAGCITCCTGGTGCCCGACGACAAGCGGGACAGCAA
GTACCCCATCTTCGGCAACCTGGTGGAAGAGAAGGCCTACCACGACGAG
TTCCCCACCATCTACCACCTGAGAAAGTACCTGGCCGACAGCACCAAGA
AGGCCGACCTGAGACTGGTGTATCTGGCCCTGGCCCACATGATCAAGTA
CCGGGGCCACTTCCTGATCGAGGGCGAGTTCAACAGCAAGAACAACGAC
ATCCAGAAGAACTTCCAGGACTTCCTGGACACCTACAACGCCATCTTCG
AGAGCGACCTGTCCCTGGAAAACAGCAAGCAGCTGGAAGAGATCGTGAA
GGACAAGATCAGCAAGCTGGAAAAGAAGGACCGCATCCTGAAGCTGTTC
CCCGGCGAGAAGAACAGCGGAATCTTCAGCGAGTTTCTGAAGCTGATCG
TGGGCAACCAGGCCGACTTCAGAAAGTGCTTCAACCTGGACGAGAAAGC
CAGCCTGCACTTCAGCAAAGAGAGCTACGACGAGGACCTGGAAACCCTG
CTGGGATATATCGGCGACGACTACAGCGACGTGTTCCTGAAGGCCAAGA
AGCTGTACGACGCTATCCTGCTGAGCGGCTTCCTGACCGTGACCGACAA
CGAGACAGAGGCCCCACTGAGCAGCGCCATGATTAAGCGGTACAACGAG
CACAAAGAGGATCTGGCTCTGCTGAAAGAGTACATCCGGAACATCAGCC
TGAAAACCTACAATGAGGTGTTCAAGGACGACACCAAGAACGGCTACGC
CGGCTACATCGACGGCAAGACCAACCAGGAAGATTTCTATGTGTACCTG
AAGAAGCTGCTGGCCGAGTTCGAGGGGGCCGACTACTTTCTGGAAAAAA
TCGACCGCGAGGATTTCCTGCGGAAGCAGCGGACCTTCGACAACGGCAG
CATCCCCTACCAGATCCATCTGCAGGAAATGCGGGCCATCCTGGACAAG
CAGGCCAAGTTCTACCCATTCCTGGCCAAGAACAAAGAGCGGATCGAGA
AGATCCTGACCTTCCGCATCCCTTACTACGTGGGCCCCCTGGCCAGAGG
CAACAGCGATTTTGCCTGGTCCATCCGGAAGCGCAATGAGAAGATCACC
CCCTGGAACTTCGAGGACGTGATCGACAAAGAGTCCAGCGCCGAGGCCT
TCATCAACCGGATGACCAGCTTCGACCTGTACCTGCCCGAGGAAAAGGT
GCTGCCCAAGCACAGCCTGCTGTACGAGACATTCAATGTGTATAACGAG
CTGACCAAAGTGCGGTTTATCGCCGAGTCTATGCGGGACTACCAGTTCC
TGGACTCCAAGCAGAAAAAGGACATCGTGCGGCTGTACTTCAAGGACAA
GCGGAAAGTGACCGATAAGGACATCATCGAGTACCTGCACGCCATCTAC
GGCTACGATGGCATCGAGCTGAAGGGCATCGAGAAGCAGTTCAACTCCA
GCCTGAGCACATACCACGACCTGCTGAACATTATCAACGACAAAGAATT
TCTGGACGACTCCAGCAACGAGGCCATCATCGAAGAGATCATCCACACC
CTGACCATCTTTGAGGACCGCGAGATGATCAAGCAGCGGCTGAGCAAGT
TCGAGAACATCTTCGACAAGAGCGTGCTGAAAAAGCTGAGCAGACGGCA
CTACACCGGCTGGGGCAAGCTGAGCGCCAAGCTGATCAACGGCATCCGG
GACGAGAAGTCCGGCAACACAATCCTGGACTACCTGATCGACGACGGCA
TCAGCAACCGGAACTTCATGCAGCTGATCCACGACGACGCCCTGAGCTT
CAAGAAGAAGATCCAGAAGGCCCAGATCATCGGGGACGAGGACAAGGGC
AACATCAAAGAAGTCGTGAAGTCCCTGCCCGGCAGCCCCGCCATCAAGA
AGGGAATCCTGCAGAGCATCAAGATCGTGGACGAGCTCGTGAAAGTGAT
GGGCGGCAGAAAGCCCGAGAGCATCGTGGTGGAAATGGCTAGAGAGAAC
CAGTACACCAATCAGGGCAAGAGCAACAGCCAGCAGAGACTGAAGAGAC
TGGAAAAGTCCCTGAAAGAGCTGGGCAGCAAGATTCTGAAAGAGAATAT
CCCTGCCAAGCTGTCCAAGATCGACAACAACGCCCTGCAGAACGACCGG
CTGTACCTGTACTACCTGCAGAATGGCAAGGACATGTATACAGGCGACG
ACCTGGATATCGACCGCCTGAGCAACTACGACATCGACCATATTATCCC
CCAGGCCTTCCTGAAAGACAACAGCATTGACAACAAAGTGCTGGTGTCC
TCCGCCAGCAACCGCGGCAAGTCCGATGATGTGCCCAGCCTGGAAGTCG
TGAAAAAGAGAAAGACCTTCTGGTATCAGCTGCTGAAAAGCAAGCTGAT
TAGCCAGAGGAAGTTCGACAACCTGACCAAGGCCGAGAGAGGCGGCCTG
AGCCCTGAAGATAAGGCCGGCTTCATCCAGAGACAGCTGGTGGAAACCC
GGCAGATCACCAAGCACGTGGCCAGACTGCTGGATGAGAAGTTTAACAA
CAAGAAGGACGAGAACAACCGGGCCGTGCGGACCGTGAAGATCATCACC
CTGAAGTCCACCCTGGTGTCCCAGTTCCGGAAGGACTTCGAGCTGTATA
AAGTGCGCGAGATCAATGACTTTCACCACGCCCACGACGCCTACCTGAA
TGCCGTGGTGGCTTCCGCCCTGCTGAAGAAGTACCCTAAGCTGGAACCC
GAGTTCGTGTACGGCGACTACCCCAAGTACAACTCCTTCAGAGAGCGGA
AGTCCGCCACCGAGAAGGTGTACTTCTACTCCAACATCATGAATATCTT
TAAGAAGTCCATCTCCCTGGCCGATGGCAGAGTGATCGAGCGGCCCCTG
ATCGAAGTGAACGAAGAGACAGGCGAGAGCGTGTGGAACAAAGAAAGCG
ACCTGGCCACCGTGCGGCGGGTGCTGAGTTATCCTCAAGTGAATGTCGT
GAAGAAGGTGGAAGAACAGAACCACGGCCTGGATCGGGGCAAGCCCAAG
GGCCTGTTCAACGCCAACCTGTCCAGCAAGCCTAAGCCCAACTCCAACG
AGAATCTCGTGGGGGCCAAAGAGTACCTGGACCCTAAGAAGTACGGCGG
ATACGCCGGCATCTCCAATAGCTTCACCGTGCTCGTGAAGGGCACAATC
GAGAAGGGCGCTAAGAAAAAGATCACAAACGTGCTGGAATTTCAGGGGA
TCTCTATCCTGGACCGGATCAACTACCGGAAGGATAAGCTGAACTTTCT
GCTGGAAAAAGGCTACAAGGACATTGAGCTGATTATCGAGCTGCCTAAG
TACTCCCTGTTCGAACTGAGCGACGGCTCCAGACGGATGCTGGCCTCCA
TCCTGTCCACCAACAACAAGCGGGGCGAGATCCACAAGGGAAACCAGAT
CTTCCTGAGCCAGAAATTTGTGAAACTGCTGTACCACGCCAAGCGGATC
TCCAACACCATCAATGAGAACCACCGGAAATACGTGGAAAACCACAAGA
AAGAGTTTGAGGAACTGTTCTACTACATCCTGGAGTTCAACGAGAACTA
TGTGGGAGCCAAGAAGAACGGCAAACTGCTGAACTCCGCCTTCCAGAGC
TGGCAGAACCACAGCATCGACGAGCTGTGCAGCTCCTTCATCGGCCCTA
CCGGCAGCGAGCGGAAGGGACTGTTTGAGCTGACCTCCAGAGGCTCTGC
CGCCGACTTTGAGTTCCTGGGAGTGAAGATCCCCCGGTACAGAGACTAC
ACCCCCTCTAGTCTGCTGAAGGACGCCACCCTGATCCACCAGAGCGTGA
CCGGCCTGTACGAAACCCGGATCGACCTGGCTAAGCTGGGCGAGGGAAA
GCGTCCTGCTGCTACTAAGAAAGCTGGTCAAGCTAAGAAAAAGAAATAA
Example 5
RNA-Guided Editing of Bacterial Genomes Using CRLSPR-Cas
Systems
[0238] Applicants used the CRISPR-associated endonuclease Cas9 to
introduce precise mutations in the genomes of Streptococcus
pneumoniae and Escherichia coli. The approach relied on
Cas9-directed cleavage at the targeted site to kill unmutated cells
and circumvented the need for selectable markers or
counter-selection systems. Cas9 specificity was reprogrammed by
changing the sequence of short CRISPR RNA (crRNA) to make single-
and multi-nucleotide changes carried on editing templates.
Simultaneous use of two crRNAs enabled multiplex mutagenesis. In S.
pneumoniae, nearly 100% of cells that survived Cas9 cleavage
contained the desired mutation, and 65% when used in combination
with recombineering in E. coli. Applicants exhaustively analyzed
Cas9 target requirements to define the range of targetable
sequences and showed strategies for editing sites that do not meet
these requirements, suggesting the versatility of this technique
for bacterial genome engineering.
[0239] The understanding of gene function depends on the
possibility of altering DNA sequences within the cell in a
controlled fashion. Site-specific mutagenesis in eukaryotes is
achieved by the use of sequence-specific nucleases that promote
homologous recombination of a template DNA containing the mutation
of interest. Zinc finger nucleases (ZFNs), transcription
activator-like effector nucleases (TALENs) and homing meganucleases
can be programmed to cleave genomes in specific locations, but
these approaches require engineering of new enzymes for each target
sequence. In prokaryotic organisms, mutagenesis methods either
introduce a selection marker in the edited locus or require a
two-step process that includes a counter-selection system. More
recently, phage recombination proteins have been used for
recombineering, a technique that promotes homologuous recombination
of linear DNA or oligonucleotides. However, because there is no
selection of mutations, recombineering efficiency can be relatively
low (0.1-10% for point mutations down to 10.sup.-5-10.sup.-6 for
larger modifications), in many cases requiring the screening of a
large number of colonies. Therefore new technologies that are
affordable, easy to use and efficient are still in need for the
genetic engineering of both eukaryotic and prokaryotic
organisms.
[0240] Recent work on the CRISPR (clustered, regularly interspaced,
short palindromic repeats) adaptive immune system of prokaryotes
has led to the identification of nucleases whose sequence
specificity is programmed by small RNAs. CRISPR loci are composed
of a series of repeats separated by `spacer` sequences that match
the genomes of bacteriophages and other mobile genetic elements.
The repeat-spacer array is transcribed as a long precursor and
processed within repeat sequences to generate small crRNA that
specify the target sequences (also known as protospacers) cleaved
by CRISPR systems. Essential for cleavage is the presence of a
sequence motif immediately downstream of the target region, known
as the protospacer-adjacent motif (PAM). CRISPR-associated (cas)
genes usually flank the repeat-spacer array and encode the
enzymatic machinery responsible for crRNA biogenesis and targeting.
Cas9 is a dsDNA endonuclease that uses a crRNA guide to specify the
site of cleavage. Loading of the crRNA guide onto Cas9 occurs
during the processing of the crRNA precursor and requires a small
RNA antisense to the precursor, the tracrRNA, and RNAse III. In
contrast to genome editing with ZFNs or TALENs, changing Cas9
target specificity does not require protein engineering but only
the design of the short crRNA guide.
[0241] Applicants recently showed in S. pneumoniae that the
introduction of a CRISPR system targeting a chromosomal locus leads
to the killing of the transformed cells. It was observed that
occasional survivors contained mutations in the target region,
suggesting that Cas9 dsDNA endonuclease activity against endogenous
targets could be used for genome editing. Applicants showed that
marker-less mutations can be introduced through the transformation
of a template DNA fragment that will recombine in the genome and
eliminate Cas9 target recognition. Directing the specificity of
Cas9 with several different crRNAs allows for the introduction of
multiple mutations at the same time. Applicants also characterized
in detail the sequence requirements for Cas9 targeting and show
that the approach can be combined with recombineering for genome
editing in E. coli.
[0242] RESULTS: Genome editing by Cas9 cleavage of a chromosomal
target
[0243] S. pneumoniae strain crR6 contains a Cas9-based CRISPR
system that cleaves a target sequence present in the bacteriophage
.phi.8232.5. This target was integrated into the srtA chromosomal
locus of a second strain R6.sup.8232.5. An altered target sequence
containing a mutation in the PAM region was integrated into the
srtA locus of a third strain R6.sup.370.1, rendering this strain
`immune` to CRISPR cleavage (FIG. 28a). Applicants transformed
R6.sup.8232.5 and R6.sup.370.1 cells with genomic DNA from crR6
cells, expecting that successful transformation of R6.sup.8232.5
cells should lead to cleavage of the target locus and cell death.
Contrary to this expectation, Applicants isolated R6.sup.8232.5
transformants, albeit with approximately 10-fold less efficiency
than R6.sup.370.1 transformants (FIG. 28b). Genetic analysis of
eight R6.sup.8232.5 transformants (FIG. 28) revealed that the great
majority are the product of a double recombination event that
eliminates the toxicity of Cas9 targeting by replacing the
.phi.8232.5 target with the crR6 genome's wild-type srtA locus,
which does not contain the protospacer required for Cas9
recognition. These results were proof that the concurrent
introduction of a CRISPR system targeting a genomic locus (the
targeting construct) together with a template for recombination
into the targeted locus (the editing template) led to targeted
genome editing (FIG. 23a).
[0244] To create a simplified system for genome editing, Applicants
modified the CRISPR locus in strain crR6 by deleting cas1, cas2 and
csn2, genes which have been shown to be dispensable for CRISPR
targeting, yielding strain crR6M (FIG. 28a). This strain retained
the same properties of crR6 (FIG. 28b). To increase the efficiency
of Cas9-based editing and demonstrate that a template DNA of choice
can be used to control the mutation introduced, Applicants
co-transformed R6.sup.8232.5 cells with PCR products of the
wild-type srIA gene or the mutant R6.sup.370.1 target, either of
which should be resistant to cleavage by Cas9. This resulted in a
5- to 10-fold increase of the frequency of transformation compared
with genomic crR6 DNA alone (FIG. 23b). The efficiency of editing
was also substantially increased, with 8/8 transformants tested
containing a wild-type srtA copy and 7/8 containing the PAM
mutation present in the R6.sup.370.1 target (FIG. 23b and FIG.
29a). Taken together, these results showed the potential of genome
editing assisted by Cas9.
[0245] Analysis of Cas9 Target Requirements:
[0246] To introduce specific changes in the genome, one must use an
editing template carrying mutations that abolish Cas9-mediated
cleavage, thereby preventing cell death. This is easy to achieve
when the deletion of the target or its replacement by another
sequence (gene insertion) is sought. When the goal is to produce
gene fusions or to generate single-nucleotide mutations, the
abolishment of Cas9 nuclease activity will only be possible by
introducing mutations in the editing template that alter either the
PAM or the protospacer sequences. To determine the constraints of
CRISPR-mediated editing, Applicants performed an exhaustive
analysis of PAM and protospacer mutations that abrogate CRISPR
targeting.
[0247] Previous studies proposed that S. pyogenes Cas9 requires an
NGG PAM immediately downstream of the protospacer. However, because
only a very limited number of PAM-inactivating mutations have been
described so far, Applicants conducted a systematic analysis to
find all 5-nucleotide sequences following the protospacer that
eliminate CRISPR cleavage. Applicants used randomized
oligonucleotides to generate all possible 1,024 PAM sequences in a
heterogeneous PCR product that was transformed into crR6 or R6
cells. Constructs carrying functional PAMs were expected to be
recognized and destroyed by Cas9 in crR6 but not R6 cells (FIG.
24a). More than 2.times.10' colonies were pooled together to
extract DNA for use as template for the co-amplification of all
targets. PCR products were deep sequenced and found to contain all
1,024 sequences, with coverage ranging from 5 to 42,472 reads (See
section "Analysis of deep sequencing data"). The functionality of
each PAM was estimated by the relative proportion of its reads in
the crR6 sample over the R6 sample. Analysis of the first three
bases of the PAM, averaging over the two last bases, clearly showed
that the NGG pattern was under-represented in crR6 transformants
(FIG. 24b). Furthermore, the next two bases had no detectable
effect on the NGG PAM (See section "Analysis of deep sequencing
data"), demonstrating that the NGGNN sequence was sufficient to
license Cas9 activity. Partial targeting was observed for NAG PAM
sequences (FIG. 24b). Also the NNGGN pattern partially inactivated
CRISPR targeting (Table G), indicating that the NGG motif can still
be recognized by Cas9 with reduced efficiency when shifted by 1 bp.
These data shed light onto the molecular mechanism of Cas9 target
recognition, and they revealed that NGG (or CCN on the
complementary strand) sequences are sufficient for Cas9 targeting
and that NGG to NAG or NNGGN mutations in the editing template
should be avoided. Owing to the high frequency of these
tri-nucleotide sequences (once every 8 bp), this means that almost
any position of the genome can be edited. Indeed, Applicants tested
ten randomly chosen targets carrying various PAMs and all were
found to be functional (FIG. 30).
[0248] Another way to disrupt Cas9-mediated cleavage is to
introduce mutations in the protospacer region of the editing
template. It is known that point mutations within the `seed
sequence` (the 8 to 10 protospacer nucleotides immediately adjacent
to the PAM) can abolish cleavage by CRISPR nucleases. However, the
exact length of this region is not known, and it is unclear whether
mutations to any nucleotide in the seed can disrupt Cas9 target
recognition. Applicants followed the same deep sequencing approach
described above to randomize the entire protospacer sequence
involved in base pair contacts with the crRNA and to determine all
sequences that disrupt targeting. Each position of the 20 matching
nucleotides (14) in the spc1 target present in R6.sup.8232.5 cells
(FIG. 23a) was randomized and transformed into crR6 and R6 cells
(FIG. 24a). Consistent with the presence of a seed sequence, only
mutations in the 12 nucleotides immediately upstream of the PAM
abrogated cleavage by Cas9 (FIG. 24c). However, different mutations
displayed markedly different effects. The distal (from the PAM)
positions of the seed (12 to 7) tolerated most mutations and only
one particular base substitution abrogated targeting. In contrast,
mutations to any nucleotide in the proximal positions (6 to 1,
except 3) eliminated Cas9 activity, although at different levels
for each particular substitution. At position 3, only two
substitutions affected CRISPR activity and with different strength.
Applicants concluded that, although seed sequence mutations can
prevent CRISPR targeting, there are restrictions regarding the
nucleotide changes that can be made in each position of the seed.
Moreover, these restrictions can most likely vary for different
spacer sequences. Therefore Applicants believe that mutations in
the PAM sequence, if possible, should be the preferred editing
strategy. Alternatively, multiple mutations in the seed sequence
may be introduced to prevent Cas9 nuclease activity.
[0249] Cas9-Mediated Genome Editing in S. pneumonia:
[0250] To develop a rapid and efficient method for targeted genome
editing, Applicants engineered strain crR6Rk, a strain in which
spacers can be easily introduced by PCR (FIG. 33). Applicants
decided to edit the .beta.-galactosidase (bgaA) gene of S.
pneumoniae, whose activity can be easily measured. Applicants
introduced alanine substitutions of amino acids in the active site
of this enzyme: R481A (R-.A) and N563A,E564A (NE.fwdarw.AA)
mutations. To illustrate different editing strategies, Applicants
designed mutations of both the PAM sequence and the protospacer
seed. In both cases the same targeting construct with a crRNA
complementary to a region of the .beta.-galactosidase gene that is
adjacent to a TGG PAM sequence (CCA in the complementary strand,
FIG. 26) was used. The R.fwdarw.A editing template created a
three-nucleotide mismatch on the protospacer seed sequence (CGT to
GCA, also introducing a BtgZI restriction site). In the
NE.fwdarw.AA editing template Applicants simultaneously introduced
a synonymous mutation that created an inactive PAM (TGG to TTG)
along with mutations that are 218 nt downstream of the protospacer
region (AAT GAA to GCT GCA, also generating a TseI restriction
site). This last editing strategy demonstrated the possibility of
using a remote PAM to make mutations in places where a proper
target may be hard to choose. For example, although the S.
pneumoniae R6 genome, which has a 39.7% GC content, contains on
average one PAM motif every 12 bp, some PAM motifs are separated by
up to 194 bp (FIG. 33). In addition Applicants designed a
.DELTA.bgaA in-frame deletion of 6,664 bp. In all three cases,
co-transformation of the targeting and editing templates produced
10-times more kanamycin-resistant cells than co-transformation with
a control editing template containing wild-type bgaA sequences
(FIG. 25b). Applicants genotyped 24 transformants (8 for each
editing experiment) and found that all but one incorporated the
desired change (FIG. 25c). DNA sequencing also confirmed not only
the presence of the introduced mutations but also the absence of
secondary mutations in the target region (FIG. 29b,c). Finally,
Applicants measured .beta.-galactosidase activity to confirm that
all edited cells displayed the expected phenotype (FIG. 25d).
[0251] Cas9-mediated editing can also be used to generate multiple
mutations for the study of biological pathways. Applicants decided
to illustrate this for the sortase-dependent pathway that anchors
surface proteins to the envelope of Gram-positive bacteria.
Applicants introduced a sortase deletion by co-transformation of a
chloramphenicol-resistant targeting construct and a .DELTA.srtA
editing template (FIG. 33a,b), followed by a .DELTA.bgaA deletion
using a kanamycin-resistant targeting construct that replaced the
previous one. In S. pneumoniae, .beta.-galactosidase is covalently
linked to the cell wall by sortase. Therefore, deletion of srtA
results in the release of the surface protein into the supernatant,
whereas the double deletion has no detectable .beta.-galactosidase
activity (FIG. 34c). Such a sequential selection can be iterated as
many times as required to generate multiple mutations.
[0252] These two mutations may also be introduced at the same time.
Applicants designed a targeting construct containing two spacers,
one matching srtA and the other matching bgaA, and co-transformed
it with both editing templates at the same time (FIG. 25e). Genetic
analysis of transformants showed that editing occurred in 6/8 cases
(FIG. 25f). Notably, the remaining two clones each contained either
a .DELTA.srtA or a .DELTA.bgaA deletion, suggesting the possibility
of performing combinatorial mutagenesis using Cas9. Finally, to
eliminate the CRISPR sequences, Applicants introduced a plasmid
containing the bgaA target and a spectinomycin resistance gene
along with genomic DNA from the wild-type strain R6.
Spectinomycin-resistant transformants that retain the plasmid
eliminated the CRISPR sequences (FIG. 34a,d).
[0253] Mechanism and Efficiency of Editing:
[0254] To understand the mechanisms underlying genome editing with
Cas9, Applicants designed an experiment in which the editing
efficiency was measured independently of Cas9 cleavage. Applicants
integrated the ermAM erythromycin resistance gene in the srtA
locus, and introduced a premature stop codon using Cas9-mediated
editing (FIG. 33). The resulting strain (JEN53) contains an
ermAM(stop) allele and is sensitive to erythromycin. This strain
may be used to assess the efficiency at which the ermAM gene is
repaired by measuring the fraction of cells that restore antibiotic
resistance with or without the use of Cas9 cleavage. JEN53 was
transformed with an editing template that restores the wild-type
allele, together with either a kanamycin-resistant CRISPR construct
targeting the ermAM(stop) allele (CRISPR::ermAM(stop)) or a control
construct without a spacer (CRISPR::O) (FIG. 26a,b). In the absence
of kanamycin selection, the fraction of edited colonies was on the
order of 10.sup.-2 (erythromycin-resistant cfu/total cfu) (FIG.
26c), representing the baseline frequency of recombination without
Cas9-mediated selection against unedited cells. However, if
kanamycin selection was applied and the control CRISPR construct
was co-transformed, the fraction of edited colonies increased to
about 10.sup.-1 (kanamycin- and erythromycin-resistant
cfu/kanamycin-resistant cfu) (FIG. 26c). This result shows that
selection for the recombination of the CRISPR locus co-selected for
recombination in the ermAM locus independently of Cas9 cleavage of
the genome, suggesting that a subpopulation of cells is more prone
to transformation and/or recombination. Transformation of the
CRISPR::ermAM(stop) construct followed by kanamycin selection
resulted in an increase of the fraction of erythromycin-resistant,
edited cells to 99% (FIG. 26c). To determine if this increase is
caused by the killing of non-edited cells, Applicants compared the
kanamycin-resistant colony forming units (cfu) obtained after
co-transformation of JEN53 cells with the CRISPR::ermAM(stop) or
CRISPR::O constructs.
[0255] Applicants counted 5.3 times less kanamycin-resistant
colonies after transformation of the ermAM(stop) construct
(2.5.times.10.sup.4/4.7.times.10.sup.3, FIG. 35a), a result that
suggests that indeed targeting of a chromosomal locus by Cas9 leads
to the killing of non-edited cells. Finally, because the
introduction of dsDNA breaks in the bacterial chromosome is known
to trigger repair mechanisms that increase the rate of
recombination of the damaged DNA, Applicants investigated whether
cleavage by Cas9 induces recombination of the editing template.
Applicants counted 2.2 times more colonies after co-transformation
with the CRISPR::erm(stop) construct than with the CRISPR::O
construct (FIG. 26d), indicating that there was a modest induction
of recombination. Taken together, these results showed that
co-selection of transformable cells, induction of recombination by
Cas9-mediated cleavage and selection against non-edited cells, each
contributed to the high efficiency of genome editing in S.
pneumoniae.
[0256] As cleavage of the genome by Cas9 should kill non-edited
cells, one would not expect to recover any cells that received the
kanamycin resistance-containing Cas9 cassette but not the editing
template. However, in the absence of the editing template
Applicants recovered many kanamycin-resistant colonies after
transformation of the CRISPR::ermAM(stop) construct (FIG. 35a).
These cells that `escape` CRISPR-induced death produced a
background that determined a limit of the method. This background
frequency may be calculated as the ratio of
CRISPR::ermAM(stop)/CRISPR::O cfu, 2.6.times.10.sup.-1
(7.1.times.10.sup.1/2.7.times.10.sup.4) in this experiment, meaning
that if the recombination frequency of the editing template is less
than this value, CRISPR selection may not efficiently recover the
desired mutants above the background. To understand the origin of
these cells, Applicants genotyped 8 background colonies and found
that 7 contained deletions of the targeting spacer (FIG. 35b) and
one harbored a presumably inactivating mutation in Cas9 (FIG.
35c).
[0257] Genome Editing with Cas9 in E. coli:
[0258] The activation of Cas9 targeting through the chromosomal
integration of a CRISPR-Cas system is only possible in organisms
that are highly recombinogenic. To develop a more general method
that is applicable to other microbes, Applicants decided to perform
genome editing in E. coli using a plasmid-based CRISPR-Cas system.
Two plasmids were constructed: a pCas9 plasmid carrying the
tracrRNA, Cas9 and a chloramphenicol resistance cassette (FIG. 36),
and a pCRISPR kanamycin-resistant plasmid carrying the array of
CRISPR spacers. To measure the efficiency of editing independently
of CRISPR selection, Applicants sought to introduce an A to C
transversion in the rpsL gene that confers streptomycin resistance.
Applicants constructed a pCRISPR::rpsL plasmid harboring a spacer
that would guide Cas9 cleavage of the wild-type, but not the mutant
rpsL allele (FIG. 27b). The pCas9 plasmid was first introduced into
E. coli MG1655 and the resulting strain was co-transformed with the
pCRISPR::rpsL plasmid and W542, an editing oligonucleotide
containing the A to C mutation. streptomycin-resistant colonies
after transformation of the pCRISPR::rpsL plasmid were only
recovered, suggesting that Cas9 cleavage induces recombination of
the oligonucleotide (FIG. 37). However, the number of
streptomycin-resistant colonies was two orders of magnitude lower
than the number of kanamycin-resistant colonies, which are
presumably cells that escape cleavage by Cas9. Therefore, in these
conditions, cleavage by Cas9 facilitated the introduction of the
mutation, but with an efficiency that was not enough to select the
mutant cells above the background of `escapers`.
[0259] To improve the efficiency of genome editing in E. coli,
Applicants applied their CRISPR system with recombineering, using
Cas9-induced cell death to select for the desired mutations. The
pCas9 plasmid was introduced into the recombineering strain HME63
(31), which contains the Gam, Exo and Beta functions of the
.quadrature.-red phage. The resulting strain was co-transformed
with the pCRISPR::rpsL plasmid (or a pCRISPR::O control) and the
W542 oligonucleotide (FIG. 27a). The recombineering efficiency was
5.3.times.10.sup.-5, calculated as the fraction of total cells that
become streptomycin-resistant when the control plasmid was used
(FIG. 27c). In contrast, transformation with the pCRISPR::rpsL
plasmid increased the percentage of mutant cells to 65.+-.14%
(FIGS. 27c and 29f). Applicants observed that the number of cfu was
reduced by about three orders of magnitude after transformation of
the pCRISPR::rpsL plasmid than the control plasmid
(4.8.times.10.sup.5/5.3.times.10.sup.2, FIG. 38a), suggesting that
selection results from CRISPR-induced death of non-edited cells. To
measure the rate at which Cas9 cleavage was inactivated, an
important parameter of Applicants' method, Applicants transformed
cells with either pCRISPR::rpsL or the control plasmid without the
W542 editing oligonucleotide (FIG. 38a). This background of CRISPR
`escapers`, measured as the ratio of pCRISPR::rpsL/pCRISPR::O cfu,
was 2.5.times.10.sup.-4 (1.2.times.10.sup.2/4.8.times.10.sup.5).
Genotyping eight of these escapers revealed that in all cases there
was a deletion of the targeting spacer (FIG. 38b). This background
was higher than the recombineering efficiency of the rpsL mutation,
5.3.times.10'5, which suggested that to obtain 65% of edited cells,
Cas9 cleavage must induce oligonucleotide recombination. To confirm
this, Applicants compared the number of kanamycin- and
streptomycin-resistant cfu after transformation of pCRISPR::rpsL or
pCRISPR::O (FIG. 27d). As in the case for S. pneumoniae, Applicants
observed a modest induction of recombination, about 6.7 fold
(2.0.times.10.sup.-4/3.0.times.10.sup.-5). Taken together, these
results indicated that the CRISPR system provided a method for
selecting mutations introduced by recombineering.
[0260] Applicants showed that CRISPR-Cas systems may be used for
targeted genome editing in bacteria by the co-introduction of a
targeting construct that killed wild-type cells and an editing
template that both eliminated CRISPR cleavage and introduced the
desired mutations. Different types of mutations (insertions,
deletions or scar-less single-nucleotide substitutions) may be
generated. Multiple mutations may be introduced at the same time.
The specificity and versatility of editing using the CRISPR system
relied on several unique properties of the Cas9 endonuclease: (i)
its target specificity may be programmed with a small RNA, without
the need for enzyme engineering, (ii) target specificity was very
high, determined by a 20 bp RNA-DNA interaction with low
probability of non-target recognition, (iii) almost any sequence
may be targeted, the only requirement being the presence of an
adjacent NGG sequence, (iv) almost any mutation in the NGG
sequence, as well as mutations in the seed sequence of the
protospacer, eliminates targeting.
[0261] Applicants showed that genome engineering using the CRISPR
system worked not only in highly recombinogenic bacteria such as S.
pneumoniae, but also in E. coli. Results in E. coli suggested that
the method may be applicable to other microorganisms for which
plasmids may be introduced. In E. coli, the approach complements
recombineering of mutagenic oligonucleotides. To use this
methodology in microbes where recombineering is not a possible, the
host homologous recombination machinery may be used by providing
the editing template on a plasmid. In addition, because accumulated
evidence indicates that CRISPR-mediated cleavage of the chromosome
leads to cell death in many bacteria and archaea, it is possible to
envision the use of endogenous CRISPR-Cas systems for editing
purposes.
[0262] In both S. pneumoniae and E. coli, Applicants observed that
although editing was facilitated by a co-selection of transformable
cells and a small induction of recombination at the target site by
Cas9 cleavage, the mechanism that contributed the most to editing
was the selection against non-edited cells. Therefore the major
limitation of the method was the presence of a background of cells
that escape CRISPR-induced cell death and lack the desired
mutation. Applicants showed that these `escapers` arose primarily
through the deletion of the targeting spacer, presumably after the
recombination of the repeat sequences that flank the targeting
spacer. Future improvements may focus on the engineering of
flanking sequences that can still support the biogenesis of
functional crRNAs but that are sufficiently different from one
another to eliminate recombination. Alternatively, the direct
transformation of chimeric crRNAs may be explored. In the
particular case of E. coli, the construction of the CRISPR-Cas
system was not possible if this organism was also used as a cloning
host. Applicants solved this issue by placing Cas9 and the tracrRNA
on a different plasmid than the CRISPR array. The engineering of an
inducible system may also circumvent this limitation.
[0263] Although new DNA synthesis technologies provide the ability
to cost-effectively create any sequence with a high throughput, it
remains a challenge to integrate synthetic DNA in living cells to
create functional genomes. Recently, the co-selection MAGE strategy
was shown to improve the mutation efficiency of recombineering by
selecting a subpopulation of cells that has an increased
probability to achieve recombination at or around a given locus. In
this method, the introduction of selectable mutations is used to
increase the chances of generating nearby non-selectable mutations.
As opposed to the indirect selection provided by this strategy, the
use of the CRISPR system makes it possible to directly select for
the desired mutation and to recover it with a high efficiency.
These technologies add to the toolbox of genetic engineers, and
together with DNA synthesis, they may substantially advance both
the ability to decipher gene function and to manipulate organisms
for biotechnological purposes. Two other studies also relate to
CRISPR-assisted engineering of mammalian genomes. It is expected
that these crRNA-directed genome editing technologies may be
broadly useful in the basic and medical sciences.
[0264] Strains and Culture Conditions.
[0265] S. pneumoniae strain R6 was provided by Dr. Alexander
Tomasz. Strain crR6 was generated in a previous study. Liquid
cultures of S. pneumoniae were grown in THYE medium (30 g/l
Todd-Hewitt agar, 5 g/l yeast extract). Cells were plated on
tryptic soy agar (TSA) supplemented with 5% defibrinated sheep
blood. When appropriate, antibiotics were added as followings:
kanamycin (400 .mu.g/ml), chloramphenicol (5 .mu.g/ml),
erythromycin (1 .mu.g/ml) streptomycin (100 .mu.g/ml) or
spectinomycin (100 .mu.g/ml). Measurements of .beta.-galactosidase
activity were made using the Miller assay as previously
described.
[0266] E. coli strains MG1655 and HME63 (derived from MG1655,
.DELTA.(argF-lac) U169.lamda. c1857 .DELTA.cro-bioA galK tyr 145
UAG mutS< >amp) (31) were provided by Jeff Roberts and Donald
Court, respectively. Liquid cultures of E. coli were grown in LB
medium (Difco). When appropriate, antibiotics were added as
followings: chloramphenicol (25 .mu.g/ml), kanamycin (25 .mu.g/ml)
and streptomycin (50 .mu.g/ml).
[0267] S. pneunmoniae Transformation.
[0268] Competent cells were prepared as described previously (23).
For all genome editing transformations, cells were gently thawed on
ice and resuspended in 10 volumes of M2 medium supplemented with
100 ng/ml of competence-stimulating peptide CSP1(40), and followed
by addition of editing constructs (editing constructs were added to
cells at a final concentration between 0.7 ng/.mu.l to 2.5
.mu.g/ul). Cells were incubated 20 min at 37.degree. C. before the
addition of 2 .mu.l of targeting constructs and then incubated 40
min at 37 .mu.C. Serial dilutions of cells were plated on the
appropriate medium to determine the colony forming units (cfu)
count.
[0269] E. coli Lambda-Red Recombineering.
[0270] Strain HME63 was used for all recombineering experiments.
Recombineering cells were prepared and handled according to a
previously published protocol (6). Briefly, a 2 ml overnight
culture (LB medium) inoculated from a single colony obtained from a
plate was grown at 30.degree. C. The overnight culture was diluted
100-fold and grown at 30.degree. C. with shaking (200 rpm) until
the OD.sub.600 is from 0.4-0.5 (approximately 3 hrs). For
Lambda-red induction, the culture was transferred to a 42.degree.
C. water bath to shake at 200 rpm for 15 min. Immediately after
induction, the culture was swirled in an ice-water slurry and
chilled on ice for 5-10 min. Cells were then washed and aliquoted
according to the protocol. For electro-transformation, 50 .mu.l of
cells were mixed with 1mM of salt-free oligos (IDT) or 100-150 ng
of plasmid DNA (prepared by QIAprep Spin Miniprep Kit, Qiagen).
Cells were electroporated using 1 mm Gene Pulser cuvette (Bio-rad)
at 1.8 kV and were immediately resuspended in 1 ml of room
temperature LB medium. Cells were recovered at 30.degree. C. for
1-2 hrs before being plated on LB agar with appropriate antibiotic
resistance and incubated at 32.degree. C. overnight.
[0271] Preparation of S. pneumoniae Genomic DNA.
[0272] For transformation purposes, S. pneumoniae genomic DNA was
extracted using the Wizard Genomic DNA Purification Kit, following
instructions provided by the manufacturer (Promega). For genotyping
purposes, 700 ul of overnight S. pneumoniae cultures were pelleted,
resuspended in 60 ul of lysozyme solution (2 mg/ml) and incubated
30 min at 37.degree. C. The genomic DNA was extracted using QIAprep
Spin Miniprep Kit (Qiagen).
[0273] Strain Construction.
[0274] All primers used in this study are provided in Table G. To
generate S. pneumoniae crR6M, an intermediate strain, LAM226, was
made. In this strain the alphA-3 gene (providing kanamycin
resistance) adjacent to the CRISPR array of S. pneumoniae crR6
strain was replaced by a cat gene (providing chloramphenicol
resistance). Briefly, crR6 genomic DNA was amplified using primers
L448/L444 and L447/L481, respectively. The cat gene was amplified
from plasmid pC194 using primers L445/L446. Each PCR product was
gel-purified and all three were fused by SOEing PCR with primers
L448/L481. The resulting PCR product was transformed into competent
S. pneumoniae crR6 cells and chloramphenicol-resistant
transformants were selected. To generate S. pneumoniae crR6M, S.
pneumoniae crR6 genomic DNA was amplified by PCR using primers
L409/L488 and L448/L481, respectively. Each PCR product was
gel-purified and they were fused by SOEing PCR with primers
L409/L481. The resulting PCR product was transformed into competent
S. pneumoniae LAM226 cells and kanamycin-resistant transformants
were selected.
[0275] To generate S. pneumoniae crR6Rc, S. pneumoniae crR6M
genomic DNA was amplified by PCR using primers L430/W286, and S.
pneumoniae LAM226 genomic DNA was amplified by PCR using primers
W288/L481. Each PCR product was gel-purified and they were fused by
SOEing PCR with primers L430/L481. The resulting PCR product was
transformed into competent S. pneumoniae crR6M cells and
chloramphenicol-resistant transformants were selected.
[0276] To generate S. pneumoniae crR6Rk, S. pneumoniae crR6M
genomic DNA was amplified by PCR using primers L430/W286 and
W287/L481, respectively. Each PCR product was gel-purified and they
were fused by SOEing PCR with primers L430/L481. The resulting PCR
product was transformed into competent S. pneumoniae crR6Rc cells
and kanamycin-resistant transformants were selected.
[0277] To generate JEN37, S. pneumoniae crR6Rk genomic DNA was
amplified by PCR using primers L430/W356 and W357/L481,
respectively. Each PCR product was gel-purified and they were fused
by SOEing PCR with primers L430/L481. The resulting PCR product was
transformed into competent S. pneumoniae crR6Rc cells and
kanamycin-resistant transformants were selected.
[0278] To generate JEN38, R6 genomic DNA was amplified using
primers L422/L461 and L459/L426, respectively. The ermAM gene
(specifying erythromycin resistance) was amplified from plasmid
pFW15.sup.43 using primers L457/L458. Each PCR product was
gel-purified and all three were fused by SOEing PCR with primers
L422/L426. The resulting PCR product was transformed into competent
S. pneumoniae crR6Rc cells and erythromycin-resistant transformants
were selected.
[0279] S. pneumoniae JEN53 was generated in two steps. First JEN43
was constructed as illustrated in FIG. 33. JEN53 was generated by
transforming genomic DNA of JEN25 into competent JEN43 cells and
selecting on both chloramphenicol and erythromycin.
[0280] To generate S. pneumoniae JEN62, S. pneumoniae crR6Rk
genomic DNA was amplified by PCR using primers W256/W365 and
W366/L403, respectively. Each PCR product was purified and ligated
by Gibson assembly. The assembly product was transformed into
competent S. pneumoniae crR6Rc cells and kanamycin-resistant
transformants were selected.
[0281] Plasmid Construction.
[0282] pDB97 was constructed through phosphorylation and annealing
of oligonucleotides B296/B297, followed by ligation in pLZ12spec
digested by EcoRI/BamHI. Applicants fully sequenced pLZ12spec and
deposited its sequence in genebank (accession: KC 112384).
[0283] pDB98 was obtained after cloning the CRISPR leader sequence
was cloned together with a repeat-spacer-repeat unit into
pLZ12spec. This was achieved through amplification of crR6Rc DNA
with primers B298/B320 and B299/B321, followed by SOEing PCR of
both products and cloning in pLZ12spec with restriction sites
BamHI/EcoRI. In this way the spacer sequence in pDB98 was
engineered to contain two BsaI restriction sites in opposite
directions that allow for the scar-less cloning of new spacers.
[0284] pDB99 to pDB108 were constructed by annealing of
oligonucleotides B300/B301 (pDB99), B302/B303 (pDB100), B304/B305
(pDB01), B306/B307 (pDB102), B308/B309 (pDB103), B310/B311
(pDB104), B312/B313 (pDB105), B314/B315 (pDB106), B315/B317
(pDB107), B318/B319 (pDB108), followed by ligation in pDB98 cut by
BsaI.
[0285] The pCas9 plasmid was constructed as follow. Essential
CRISPR elements were amplified from Streptococcos pyogenes SF370
genomic DNA with flanking homology arms for Gibson Assembly. The
tracrRNA and Cas9 were amplified with oligos HC008 and HCO10. The
leader and CRISPR sequences were amplified HC011/HC014 and
HC015/HC009, so that two BsaI type IIS sites were introduced in
between two direct repeats to facilitate easy insertion of
spacers.
[0286] pCRISPR was constructed by subcloning the pCas9 CRISPR array
in pZE21-MCSI through amplification with oligos B298+B299 and
restriction with EcoRI and BamHI. The rpsL targeting spacer was
cloned by annealing of oligos B352+B353 and cloning in the BsaI cut
pCRISPR giving pCRISPR::rpsL.
[0287] Generation of Targeting and Editing Constructs.
[0288] Targeting constructs used for genome editing were made by
Gibson assembly of Left PCRs and Right PCRs (Table G). Editing
constructs were made by SOEing PCR fusing PCR products A (PCR A),
PCR products B (PCR B) and PCR products C (PCR C) when applicable
(Table G). The CRISPR::O and CRISPR::ermAM(stop) targeting
constructs were generated by PCR amplification of JEN62 and crR6
genomic DNA respectively, with oligos L409 and L481.
[0289] Generation of Targets with Randomized PAM or Protospacer
Sequences.
[0290] The 5 nucleotides following the spacer 1 target were
randomized through amplification of R6.sup.8232.5 genomic DNA with
primers W377/L426. This PCR product was then assembled with the cat
gene and the srtA upstream region that were amplified from the same
template with primers L422/W376. 80 ng of the assembled DNA was
used to transform strains R6 and crR6. Samples for the randomized
targets were prepared using the following primers: B280-B290/L426
to randomize bases 1-10 of the target and B269-B278/L426 to
randomize bases 10-20. Primers L422/B268 and L422/B279 were used to
amplify the cat gene and srtA upstream region to be assembled with
the first and last 10 PCR products respectively. The assembled
constructs were pooled together and 30 ng was transformed in R6 and
crR6. After transformation, cells were plated on chloramphenicol
selection. For each sample more than 2.times.10.sup.5 cells were
pooled together in 1 ml of THYE and genomic DNA was extracted with
the Promega Wizard kit. Primers B250/B251 were used to amplify the
target region. PCR products were tagged and run on one Illumina
MiSeq paired-end lane using 300 cycles.
[0291] Analysis of Deep Sequencing Data.
[0292] Randomized PAM: For the randomized PAM experiment 3,429,406
reads were obtained for crR6 and 3,253,998 for R6. It is expected
that only half of them will correspond to the PAM-target while the
other half will sequence the other end of the PCR product.
1,623,008 of the crR6 reads and 1,537,131 of the R6 reads carried
an error-free target sequence. The occurrence of each possible PAM
among these reads is shown in supplementary file. To estimate the
functionality of a PAM, its relative proportion in the crR6 sample
over the R6 sample was computed and is denoted r.sub.ijklm where
are one of the 4 possible bases. The following statistical model
was constructed:
log(r.sub.ijklm)=.mu.b2.sub.i+b3.sub.j+b4.sub.k+b2b3.sub.i,j+b3b4.sub.j,-
k+.epsilon..sub.ijklm,
[0293] where .epsilon. is the residual error, b2 is the effect of
the 2.sup.nd base of the PAM, b3 of the third, b4 of the fourth,
b2b3 is the interaction between the second and third bases, b3b4
between the third and fourth bases. An analysis of variance was
performed:
TABLE-US-00007 Anova table Df Sum Sq Mean Sq F value Pr (>F) b3
3 151.693 50.564 601.8450 <2.2e-16 *** b2 3 90.521 30.174
359.1454 <2.2e-16 *** b4 3 1.881 0.627 7.4623 6.070e-05 ***
b3:b2 9 228.940 25.438 302.7738 <2.2e-16 *** b3:b4 9 3.010 0.334
3.9809 5.227e-05 *** Residuals 996 83.680 0.084
[0294] When added to this model, b1 or b5 do not appear to be
significant and other interactions than the ones included can also
be discarded. The model choice was made through successive
comparisons of more or less complete models using the anova method
in R. Tukey's honest significance test was used to determine if
pairwise differences between effects are significant.
[0295] NGGNN patterns are significantly different from all other
patterns and carry the strongest effect (see table below)
[0296] In order to show that positions 1, 4 or 5 do not affect the
NGGNN pattern Applicants looked at theses sequences only. Their
effect appears to be normally distributed (see QQ plot in FIG. 71),
and model comparisons using the anova method in R shows that the
null model is the best one, i.e. there is no significant role of
b1, b4 and b5.
TABLE-US-00008 Model comparison using the anova method in R for the
NGGNN sequences Model 1: ratio.log~1 Model 2: ratio.log~b1 / b4 +
b5 Res. Df RSS Df Sum of Sq F Pr (>F) 1 63 14.579 2 54 11.295 9
3.2336 1.7443 0.1013
[0297] Partial interference of NAGNN and NNGGN patterns
[0298] NAGNN patterns are significantly different from all other
patterns but carry a much smaller effect than NGGNN (see Tukey's
honest significance test below).
[0299] Finally, NTGGN and NCGGN patterns are similar and show
significantly more CRISPR interference than NTGHN and NCGHN
patterns (where H is A, T or C), as shown by a bonferroni adjusted
pairwi se student-test.
TABLE-US-00009 Pairwise comparisons of the effect of b4 on NYGNN
sequences using t tests with pooled SD Data: b4 A C G C 1.00 -- --
G 9.2e-05 2.4e-06 -- T 0.31 1.00 1.2e-08
[0300] Taken together, these results allow concluding that NNGGN
patterns in general produce either a complete interference in the
case of NGGGN, or a partial interference in the case of NAGGN,
NTGGN or NCGGN.
[0301] Tukey multiple comparisons of means: 95% family-wise
confidence level
TABLE-US-00010 diff lwr upr p adj $b2:b3 G:G-A:A -2.76475 -2.94075
-2.58875 <1E-07 G:G-C:A -2.79911 -2.97511 -2.62311 <1E-07
G:G-T:A -2.7809 -2.9569 -2.6049 <1E-07 G:G-A:C -2.81643 -2.99244
-2.64043 <1E-07 G:G-C:C -2.77903 -2.95504 -2.60303 <1E-07
G:G-G:C -2.64867 -2.82468 -2.47267 <1E-07 G:G-T:C -2.79718
-2.97319 -2.62118 <1E-07 G:G-A:G -2.67068 -2.84668 -2.49468
<1E-07 G:G-C:G -2.73525 -2.91125 -2.55925 <1E-07 G:G-T:G
-2.7976 -2.62159 -2.9736 <1E-07 G:G-A:T -2.76727 -2.59127
-2.94328 <1E-07 G:G-C:T -2.84114 -2.66513 -3.01714 <1E-07
G:G-G:T -2.76409 -2.58809 -2.94009 <1E-07 G:G-T:T -2.76781
-2.59181 -2.94381 <1E-07 G:G-G:A -2.13964 -2.31565 -1.96364
<1E-07 G:A-A:A -0.62511 -0.80111 -0.4491 <1E-07 G:A-C:A
-0.65947 -0.83547 -0.48346 <1E-07 G:A-T:A -0.64126 -0.46525
-0.81726 <1E-07 G:A-A:C -0.67679 -0.50078 -0.85279 <1E-07
G:A-C:C -0.63939 -0.46339 -0.81539 <1E-07 G:A-G:C -0.50903
-0.33303 -0.68503 <1E-07 G:A-T:C -0.65754 -0.48154 -0.83354
<1E-07 G:A-A:G -0.53104 -0.35503 -0.70704 <1E-07 G:A-C:G
-0.59561 -0.4196 -0.77161 <1E-07 G:A-T:G -0.65795 -0.48195
-0.83396 <1E-07 G:A-A:T -0.62763 -0.45163 -0.80363 <1E-07
G:A-C:T -0.70149 -0.52549 -0.8775 <1E-07 G:A-G:T -0.62445
-0.44844 -0.80045 <1E-07 G:A-T:T -0.62817 -0.45216 -0.80417
<1E-07 $b3:b4 G:G-G:A -0.33532 -0.51133 -0.15932 <1E-07
G:G-G:C -0.18118 -0.35719 -0.00518 0.036087 G:G-G:T -0.31626
-0.14026 -0.49226 <1E-07
[0302] Randomized Target
[0303] For the randomized target experiment 540,726 reads were
obtained for crR6 and 753,570 for R6. As before, only half of the
reads are expected to sequence the interesting end of the PCR
product. After filtering for reads that carry a target that is
error-free or with a single point mutation, 217,656 and 353,141
reads remained for crR6 and R6 respectively. The relative
proportion of each mutant in the crR6 sample over the R6 sample was
computed (FIG. 24c). All mutations outside of the seed sequence
(13-20 bases away from the PAM) show full interference. Those
sequences were used as a reference to determine if other mutations
inside the seed sequence can be said to significantly disrupt
interference. A normal distribution was fitted to theses sequences
using the fitdistr function of the MASS R package. The 0.99
quantile of the fitted distribution is shown as a dotted line in
FIG. 24c. FIG. 72 shows a histogram of the data density with fitted
normal distribution (black line) and 0.99 quantile (dotted
line).
TABLE-US-00011 TABLE F Relative abundance of PAM sequences in the
crR6/R6 samples averaged over bases 1 and 5. 3rd 2nd position 4th
position A C G T position A AAA 1.04 ACA 1.12 AGA 0.73 ATA 1.10 A
AAC 1.07 ACC 1.04 AGC 0.64 ATC 0.97 C AAG 1.00 ACG 1.09 AGG 0.61
ATG 1.07 G AAT 0.98 ACT 1.02 AGT 0.65 ATT 1.01 T C CAA 1.05 CCA
1.05 CGA 0.99 CTA 1.07 A CAC 1.04 CCC 1.02 CGC 1.08 CTC 1.04 C CAG
1.08 CCG 1.08 CGG 0.81 CTG 1.05 G CAT 1.13 CCT 1.05 CGT 1.07 CTT
1.08 T G GAA 0.97 GCA 1.05 GGA 0.08 GTA 0.99 A GAC 0.92 GCC 1.00
GGC 0.05 GTC 1.15 C GAG 0.96 GCG 0.98 GGG 0.07 GTG 0.98 G GAT 0.98
GCT 0.99 GGT 0.06 GTT 1.05 T T TAA 1.08 TCA 1.16 TGA 1.05 TTA 1.14
A TAC 1.00 TCC 1.08 TGC 1.06 TTA 1.05 C TAG 1.02 TCG 1.11 TGG 0.77
TTG 1.01 G TAT 1.01 TCT 1.12 TGT 1.21 TTT 1.02 T
TABLE-US-00012 TABLE G Primers used in this study (SEQ ID NOS
68-183, respectively, in order of appearance). Primer Sequence
5'-3' B217 TCCTAGCAGGATTTCTGATATTACTGTCACGTTTT AGAGCTATGCTGTTTTGA
B218 GTGACAGTAATATCAGAAATCCTGCTAGGAGTTTT GGGACCATTCAAAACAGC B229
GGGTTTCAAGTCTTTGTAGCAAGAG B230 GCCAATGAACGGGAACCCTTGGTC B250
NNNNGACGAGGCAATGGCTGAAATC B251 NNNNTTATTTGGCTCATATTTGCTG B255
CTTTACACCAATCGCTGCAACAGAC B256 CAAAATTTCTAGTCTTCTTTGCCTTTCCCCATAAA
ACCCTCCTTA B257 AGGGTTTTATGGGGAAAGGCAAAGAAGACTAGAAA TTTTGATACC B258
CTTACGGTGCATAAAGTCAATTTCC B269 TGGCTCGATTTCAGCCATTGC B270
CTTTGACGAGGCAATGGCTGAAATCGAGCCAANAA AGCGCAAG B271
CTTTGACGAGGCAATGGCTGAAATCGAGCCAAANA AGCGCAAG B272
CTTTGACGAGGCAATGGCTGAAATCGAGCCAAAAN AGCGCAAG B273
CTTTGACGAGGCAATGGCTGAAATCGAGCCAAAAA NGCGCAAG B274
CTTTGACGAGGCAATGGCTGAAATCGAGCCAAAAA ANCGCAAG B275
CTTTGACGAGGCAATGGCTGAAATCGAGCCAAAAA AGNGCAAG B276
CTTTGACGAGGCAATGGCTGAAATCGAGCCAAAAA AGCNCAAGAAG B277
CTTTGACGAGGCAATGGCTGAAATCGAGCCAAAAA AGCGNAAGAAG B278
CTTTGACGAGGCAATGGCTGAAATCGAGCCAAAAA AGCGCNAGAAG B279
GCGCTTTTTTGGCTCGATTTCAG B280 CAATGGCTGAAATCGAGCCAAAAAAGCGCANGAAG
AAATC B281 CAATGGCTGAAATCGAGCCAAAAAAGCGCAANAAG AAATC B282
CAATGGCTGAAATCGAGCCAAAAAAGCGCAAGNAG AAATC B283
CAATGGCTGAAATCGAGCCAAAAAAGCGCAAGANG AAATC B284
CAATGGCTGAAATCGAGCCAAAAAAGCGCAAGAAN AAATC B285
CAATGGCTGAAATCGAGCCAAAAAAGCGCAAGAAG NAATCAACC B286
CAATGGCTGAAATCGAGCCAAAAAAGCGCAAGAAG ANATCAACC B287
CAATGGCTGAAATCGAGCCAAAAAAGCGCAAGAAG AANTCAACC B288
CAATGGCTGAAATCGAGCCAAAAAAGCGCAAGAAG AAANCAACC B289
CAATGGCTGAAATCGAGCCAAAAAAGCGCAAGAAG AAATNAACCAGC B290
CAATGGCTGAAATCGAGCCAAAAAAGCGCAAGAAG AAATCNACCAGC B296
gatccTCCATCCGTACAACCCACAACCCTGg B297
aattcCAGGGTTGTGGGTTGTACGGATGGAg B298
CATGGATCCTATTTCTTAATAACTAAAAATATGG B299
CATGAATTCAACTCAACAAGTCTCAGTGTGCTG B300
AAACATTTTTTCTCCATTTAGGAAAAAGGATGCTG B301
AAAACAGCATCCTTTTTCCTAAATGGAGAAAAAAT B302
AAACCTTAAATCAGTCACAAATAGCAGCAAAATTG B303
AAAACAATTTTGCTGCTATTTGTGACTGATTTAAG B304
AAACTTTTCATCATACGACCAATCTGCTTTATTTG B305
AAAACAAATAAAGCAGATTGGTCGTATGATGAAAA B306
AAACTCGTCCAGAAGTTATCGTAAAAGAAATCGAG B307
AAAACTCGATTTCTTTTACGATAACTTCTGGACGA B308
AAACAATCTCTCCAAGGTTTCCTTAAAAATCTCTG B309
AAAACAGAGATTTTTAAGGAAACCTTGGAGAGATT B310
AAACGCCATCGTCAGGAAGAAGCTATGCTTGAGTG B311
AAAACACTCAAGCATAGCTTCTTCCTGACGATGGC B312
AAACATCTCTATACTTATTGAAATTTCTTTGTATG B313
AAAACATACAAAGAAATTTCAATAAGTATAGAGAT B314
AAACTAGCTGTGATAGTCCGCAAAACCAGCCTTCG B315
AAAACGAAGGCTGGTTTTGCGGACTATCACAGCTA B316
AAACATCGGAAGGTCGAGCAAGTAATTATCTTTTG B317
AAAACAAAAGATAATTACTTGCTCGACCTTCCGAT B318
AAACAAGATGGTATCGCAAAGTAAGTGACAATAAG B319
AAAACTTATTGTCACTTACTTTGCGATACCATCTT B320
GAGACCTTTGAGCTTCCGAGACTGGTCTCAGTTTT GGGACCATTCAAAACAG B321
TGAGACCAGTCTCGGAAGCTCAAAGGTCTCGTTTT AGAGCTATGCTGTTTTG B352
aaacTACTTTACGCAGCGCGGAGTTCGGTTTTTTg B353
aaaacAAAAAACCGAACTCCGCGCTGCGTAAAGTA HC008_SP
ATGCCGGTACTGCCGGGCCTCTTGCGGGATTACGA AATCATCCTG HC009_SP
GTGACTGGCGATGCTGTCGGAATGGACGATCACAC TACTCTTCTT HC010_SP
TTAAGAAATAATCTTCATCTAAAATATACTTCAGT CACCTCCTAGCTGAC HC011_SP
ATTGATTTGAGTCAGCTAGGAGGTGACTGAAGTAT ATTTTAGATGAAG HC014_SP
GAGACCTTTGAGCTTCCGAGACTGGTCTCAGTTTT
GGGACCATTCAAAACAGCATAGCTCTAAAACCTCG TAGACTATTTTTGTC HC015_SP
GAGACCAGTCTCGGAAGCTCAAAGGTCTCGTTTTA
GAGCTATGCTGTTTTGAATGGTCCCAAAACTTCAG CACACTGAGACTTG L403
AGTCATCCCAGCAACAAATGG L409 CGTGGTAAATCGGATAACGTTCCAAGTGAAG L422
Tgctcttcttcacaaacaaggg L426 AAGCCAAAGTTTGGCACCACC L430
GTAGCTTATTCAGTCCTAGTGG L444 CGTTTGTTGAACTAATGGGTGCAAATTACGAATCT
TCTCCTGACG L445 CGTCAGGAGAAGATTCGTAATTTGCACCCATTAGT TCAACAAACG L446
GATATTATGGAGCCTATTTTTGTGGGTTTTTAGGC ATAAAACTATATG L447
CATATAGTTTTATGCCTAAAAACCcACAAAAATAG GCTCCATAATATC L448
ATTATTTCTTAATAACTAAAAATATGG L457 CGTgtacaattgctagcgtacggc L458
GCACCGGTGATCACTAGTCCTAGG L459 cctaggactagtgatcaccggtGCAAATATGAGCC
AAATAAATATAT L461 GCCGTACGCTAGCAATTGTACACGTTTGTTGAACT AATGGGTGC
L481 TTCAAATTTTCCCATTTGATTCTCC L488
CCATATTTTTAGTTATTAAGAAATAATACCAGCCA TCAGTCACCTCC W256
AGACGATTCAATAGACAATAAGG W286 GTTTTGGGACCATTCAAAACAGCATAGCTCTAAAA
CCTCGTAGAC W287 GCTATGCTGTTTTGAATGGTCCCAAAACcattatt ttaacacacgaggtg
W288 GCTATGCTGTTTTGAATGGTCCCAAAACGCACCCA TTAGTTCAACAAACG W326
AATTCTTTTCTTCATCATCGGTC W327 AAGAAAGAATGAAGATTGTTCATG W341
GGTACTAATCAAAATAGTGAGGAGG W354 GTTTTTCAAAATCTGCGGTTGCG W355
AAAAATTGAAAAAATGGTGGAAACAC W356 ATTTCGTAAACGGTATCGGTTTCTTTTAAAGTTTT
GGGACCATTCAAAACAGC W357 TTTAAAAGAAACCGATACCGTTTACGAAATGTTTT
AGAGCTATGCTGTTTTGA W365 AAACGGTATCGGTTTCTTTTAAATTCAATTGTTTT
GGGACCATTCAAAACAGC W366 AATTCAATTTAAAAGAAACCGATACCGTTTGTTTT
AGAGCTATGCTGTTTTGA W370 GTTCCTTAAACCAAAACGGTATCGGTTTCTTTTAA ATTC
W371 GAAACCGATACCGTTTTGGTTTAAGGAACAGGTAA AGGGCATTTAAC
W376 CGATTTCAGCCATTGCCTCGTC W377
GCCTTTGACGAGGCAATGGCTGAAATCGNNNNNAA AAAGCGCAAGAAGAAATCAAC W391
TCCGTACAACCCACAACCCTGCTAGTGAGCGTTTT GGGACCATTCAAAACAGC W392
GCTCACTAGCAGGGTTGTGGGTTGTACGGAGTTTT AGAGCTATGCTGTTTTGA W393
TTGTTGCCACTCTTCCTTCTTTC W397 CAGGGTTGTGGGTTGTTGCGATGGAGTTAACTCCC
ATCTCC W398 GGGAGTTAACTCCATCGCAACAACCCACAACCCTG CTAGTG W403
GTGGTATCTATCGTGATGTGAC W404 TTACCGAAACGGAATTTATCTGC W405
AAAGCTAGAGTTCCGCAATTGG W431 GTGGGTTGTACGGATTGAGTTAACTCCCATCTCCT TC
W432 GATGGGAGTTAACTCAATCCGTACAACCCACAACC CTG W433
GCTTCACCTATTGCAGCACCAATTGACCACATGAA GATAG W434
GTGGTCAATTGGTGCTGCAATAGGTGAAGCTAATG GTGATG W463
CTGATTTGTATTAATTTTGAGACATTATGCTTCAC CTTC W464
GCATAATGTCTCAAAATTAATACAAATCAGTGAAA TCATG W465
GTTTTGGGACCATTCAAAACAGCATAGCTCTAAAA CGTGACAGTAATATCAG W466
GTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAA CGCTCACTAGCAGGGTTG W542
ATACTTTACGCAGCGCGGAGTTCGGTTTTgTAGGA GTGGTAGTATATACACGAGTACAT
TABLE-US-00013 TABLE H Design of targeting and editing constructs
used in this study (SEQ ID NOS 184, 184, 184, 185, and 186,
respectively, in order of appearance). Targeting Constructs Edition
Template DNA Left PCR Right PCR Spacer sequence PAM bgaA R > A
crR6Rk W256/W391 W392/L403 GCTCACTAGCAGGGT TGG TGTGGGTTGTACGGA bgaA
NE > AA crR6Rk W256/W391 W392/L403 GCTCACTAGCAGGGT TGG
TGTGGGTTGTACGGA .DELTA.bgaA crR6Rk W256/W391 W392/L403
GCTCACTAGCAGGGT TGG TGTGGGTTGTACGGA .DELTA.srtA crR6Rc W256/B218
B217/L403 TCCTAGCAGGATTTC TGG TGATATTACTGTCAC ermB Stop crR6Rk
W256/W356 W357/L403 TTTAAAAGAAACCGA TGG TACCGTTTACGAAAT .DELTA.srtA
.DELTA.bgaA JEN51 W256/W465 W466/W403 same as the TGG (for Left
PCR) ones used for and .DELTA.srtA and .DELTA.bgaA JEN52 (for Right
PCR) Editing Constructs Primers used Name of to verify Template
SOEing resulting edited Edition DNA PCR A PCR B PCR C PCR strains
genotype bgaA R > A R6 W403/W397 W398/W404 N/A W403/W404 JEN55
W403/W404 bgaA NE > AA R6 W403/W431 W432/W433 W434/W404
W403/W404 JEN60 W403/W404 .DELTA.bgaA R6 B255/B256 B257/B258 N/A
B255/B258 JEN52 W393/W405 .DELTA.srtA R6 B230/W463 W464/B229 N/A
B230/B229 JEN51 W422/W426 ermB Stop JEN38 L122/W370 W371/L426 N/A
L422/L426 JEN43 L457/L458 .DELTA.srtA .DELTA.bgaA same as the JEN64
same as the ones used ones used for .DELTA.srtA for .DELTA.srtA and
.DELTA.bgaA and .DELTA.bgaA
Example 6
Optimization of the Guide RNA for Streptococcus pyogenes Cas9
(Referred to as SpCas9)
[0304] Applicants mutated the tracrRNA and direct repeat sequences,
or mutated the chimeric guide RNA to enhance the RNAs in cells.
[0305] The optimization is based on the observation that there were
stretches of thymines (Ts) in the tracrRNA and guide RNA, which
might lead to early transcription termination by the pol 3
promoter. Therefore Applicants generated the following optimized
sequences. Optimized tracrRNA and corresponding optimized direct
repeat are presented in pairs.
TABLE-US-00014 Optimized tracrRNA 1 (mutation underlined): (SEQ ID
NO: 187) GGAACCATTCAtAACAGCATAGCAAGTTAtAATAAGGCTAGTCCGTTA
TCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTT Optimized direct repeat 1
(mutation underlined): (SEQ ID NO: 188)
GTTaTAGAGCTATGCTGTTaTGAATGGTCCCAAAAC Optimized tracrRNA 2 (mutation
underlined): (SEQ ID NO: 189)
GGAACCATTCAAtACAGCATACGCAAGTTAAtATAAGGCTAGTCCGTT
ATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTT Optimized direct repeat 2
(mutation underlined): (SEQ ID NO: 190)
GTaTTAGAGCTATGCTGTaTTGAATGGTCCCAAAAC
[0306] Applicants also optimized the chimetic guideRNA for optimal
activity in eukaryotic cells.
TABLE-US-00015 Original guide RNA: (SEQ ID NO: 191)
NNNNNNNNNNNNNNNNNNNNGTTTTAGAGCTAGAAATAGC
AAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGT GGCACCGAGTCGGTGCTTTTTTT
Optimized chimeric guide RNA sequence 1: (SEQ ID NO: 192)
NNNNNNNNNNNNNNNNNNNNGTATTAGAGCTAGAAATAGC
AAGTTAATATAAGGCTAGTCCGTTATCAACTTGAAAAAGT GGCACCGAGTCGGTGCTTTTTTT
Optimized chimeric guide RNA sequence 2: (SEQ ID NO: 193)
NNNNNNNNNNNNNNNNNNNNGTTTTAGAGCTATGGTGTTT
TGGAAACAAAACAGCATAGCAAGTTAAAATAAGGCTAGTC
CGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTT TTT Optimized chimeric
guide RNA sequence 3: (SEQ ID NO: 194)
NNNNNNNNNNNNNNNNNNNNGTATTAGAGCTATGCTGTAT
TGGAAACAATACAGCATAGCAAGTTAATATAAGGCTAGTC
CGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTT TTT
[0307] Applicants showed that optimized chimeric guide RNA works
better as indicated in FIG. 3. The experiment was conducted by
co-transfecting 293FT cells with Cas9 and a U6-guide RNA DNA
cassette to express one of the four RNA forms shown above. The
target of the guide RNA is the same target site in the human Emx1
locus: "GTCACCTCCAATGACTAGGG (SEQ ID NO: 195)"
Example 7
Optimization of Streptococcus thermophiles LMD-9 CRISPR1 Cas9
(Referred to as StlCas9)
[0308] Applicants designed guide chimeric RNAs as shown in FIG.
4.
[0309] The StlCas9 guide RNAs can undergo the same type of
optimization as for SpCas9 guide RNAs, by breaking the stretches of
poly thymines (Ts)
Example 8
Cas9 Diversity and Mutations
[0310] The CRISPR-Cas system is an adaptive immune mechanism
against invading exogenous DNA employed by diverse species across
bacteria and archaea. The type II CRISPR-Cas9 system consists of a
set of genes encoding proteins responsible for the "acquisition" of
foreign DNA into the CRISPR locus, as well as a set of genes
encoding the "execution" of the DNA cleavage mechanism; these
include the DNA nuclease (Cas9), a non-coding transactivating
cr-RNA (tracrRNA), and an array of foreign DNA-derived spacers
flanked by direct repeats (crRNAs). Upon maturation by Cas9, the
tracRNA and crRNA duplex guide the Cas9 nuclease to a target DNA
sequence specified by the spacer guide sequences, and mediates
double-stranded breaks in the DNA near a short sequence motif in
the target DNA that is required for cleavage and specific to each
CRISPR-Cas system. The type II CRISPR-Cas systems are found
throughout the bacterial kingdom and highly diverse in in Cas9
protein sequence and size, tracrRNA and crRNA direct repeat
sequence, genome organization of these elements, and the motif
requirement for target cleavage. One species may have multiple
distinct CRISPR-Cas systems.
[0311] Applicants evaluated 207 putative Cas9s from bacterial
species identified based on sequence homology to known Cas9s and
structures orthologous to known subdomains, including the HNH
endonuclease domain and the RuvC endonuclease domains [information
from the Eugene Koonin and Kira Makarova]. Phylogenetic analysis
based on the protein sequence conservation of this set revealed
five families of Cas9s, including three groups of large Cas9s
(.about.1400 amino acids) and two of small Cas9s (.about.1100 amino
acids) (FIGS. 39 and 40A-F).
[0312] In this example, Applicants show that the following
mutations can convert SpCas9 into a nicking enzyme: D10A, E762A,
H840A, N854A, N863A, D986A.
[0313] Applicants provide sequences showing where the mutation
points are located within the SpCas9 gene (FIG. 41). Applicants
also show that the nickases are still able to mediate homologous
recombination (Assay indicated in FIG. 2). Furthermore, Applicants
show that SpCas9 with these mutations (individually) do not induce
double strand break (FIG. 47).
Example 9
Supplement to DNA Targeting Specificity of the RNA-Guided Cas9
Nuclease
[0314] Cell Culture and Transfection
[0315] Human embryonic kidney (HEK) cell line 293FT (Life
Technologies) was maintained in Dulbecco's modified Eagle's Medium
(DMEM) supplemented with 10% fetal bovine serum (HyClone), 2 mM
GlutaMAX (Life Technologies), 100 U/mL penicillin, and 100 U/mL
streptomycin at 37.degree. C. with 5% CO2 incubation.
[0316] 293FT cells were seeded either onto 6-well plates, 24-well
plates, or 96-well plates (Corning) 24 hours prior to transfection.
Cells were transfected using Lipofectamine 2000 (Life Technologies)
at 80-90% confluence following the manufacturer's recommended
protocol. For each well of a 6-well plate, a total of 1 ug of
Cas9+sgRNA plasmid was used. For each well of a 24-well plate, a
total of 500 ng Cas9+sgRNA plasmid was used unless otherwise
indicated. For each well of a 96-well plate, 65 ng of Cas9 plasmid
was used at a 1:1 molar ratio to the U6-sgRNA PCR product.
[0317] Human embryonic stem cell line HUES9 (Harvard Stem Cell
Institute core) was maintained in feeder-free conditions on GelTrex
(Life Technologies) in mTesR medium (Stemcell Technologies)
supplemented with 100 ug/ml Normocin (InvivoGen). HUES9 cells were
transfected with Amaxa P3 Primary Cell 4-D Nucleofector Kit (Lonza)
following the manufacturer's protocol.
[0318] SURVEYOR Nuclease Assay for Genome Modification
[0319] 293FT cells were transfected with plasmid DNA as described
above. Cells were incubated at 37.degree. C. for 72 hours
post-transfection prior to genomic DNA extraction. Genomic DNA was
extracted using the QuickExtract DNA Extraction Solution
(Epicentre) following the manufacturer's protocol. Briefly,
pelleted cells were resuspended in QuickExtract solution and
incubated at 65.degree. C. for 15 minutes and 98.degree. C. for 10
minutes.
[0320] The genomic region flanking the CRISPR target site for each
gene was PCR amplified (primers listed in Tables J and K), and
products were purified using QiaQuick Spin Column (Qiagen)
following the manufacturer's protocol. 400 ng total of the purified
PCR products were mixed with 2 .mu.l 10.times.Taq DNA Polymerase
PCR buffer (Enzymatics) and ultrapure water to a final volume of
2011, and subjected to a re-annealing process to enable
heteroduplex formation: 95.degree. C. for 10 min, 95.degree. C. to
85.degree. C. ramping at -2.degree. C./s, 85.degree. C. to
25.degree. C. at -0.25.degree. C./s, and 25.degree. C. hold for 1
minute. After re-annealing, products were treated with SURVEYOR
nuclease and SURVEYOR enhancer S (Transgenomics) following the
manufacturer's recommended protocol, and analyzed on 4-20% Novex
TBE poly-acrylamide gels (Life Technologies). Gels were stained
with SYBR Gold DNA stain (Life Technologies) for 30 minutes and
imaged with a Gel Doc gel imaging system (Bio-rad). Quantification
was based on relative band intensities.
[0321] Northern Blot Analysis of tracrRNA Expression in Human
Cells
[0322] Northern blots were performed as previously described 1.
Briefly, RNAs were heated to 95.degree. C. for 5 min before loading
on 8% denaturing polyacrylamide gels (SequaGel, National
Diagnostics). Afterwards, RNA was transferred to a pre-hybridized
Hybond N+ membrane (GE Healthcare) and crosslinked with Stratagene
UV Crosslinker (Stratagene). Probes were labeled with
[gamma-32P]ATP (Perkin Elmer) with T4 polynucleotide kinase (New
England Biolabs). After washing, membrane was exposed to phosphor
screen for one hour and scanned with phosphorimager (Typhoon).
[0323] Bisulfite Sequencing to Assess DNA Methylation Status
[0324] HEK 293FT cells were transfected with Cas9 as described
above. Genomic DNA was isolated with the DNeasy Blood & Tissue
Kit (Qiagen) and bisulfite converted with EZ DNA
Methylation-Lightning Kit (Zymo Research). Bisulfite PCR was
conducted using KAPA2G Robust HotStart DNA Polymerase (KAPA
Biosystems) with primers designed using the Bisulfite Primer Seeker
(Zymo Research, Tables J and K). Resulting PCR amplicons were
gel-purified, digested with EcoRI and HindII, and ligated into a
pUC19 backbone prior to transformation. Individual clones were then
Sanger sequenced to assess DNA methylation status.
[0325] In Vitro Transcription and Cleavage Assay
[0326] HEK 293FT cells were transfected with Cas9 as described
above. Whole cell lysates were then prepared with a lysis buffer
(20 mM HEPES, 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 5% glycerol, 0.1%
Triton X-100) supplemented with Protease Inhibitor Cocktail
(Roche). T7-driven sgRNA was in vitro transcribed using custom
oligos (Example 10) and HiScribe T7 In Vitro Transcription Kit
(NEB), following the manufacturer's recommended protocol. To
prepare methylated target sites, pUC19 plasmid was methylated by
M.SssI and then linearized by NheI. The in vitro cleavage assay was
performed as follows: for a 20 uL cleavage reaction, 10 uL of cell
lysate with incubated with 2 uL cleavage buffer (100 mM HEPES, 500
mM KCl, 25 mM MgCl2, 5 mM DTT, 25% glycerol), the in vitro
transcribed RNA, and 300 ng pUC19 plasmid DNA.
[0327] Deep Sequencing to Assess Targeting Specificity
[0328] HEK 293FT cells plated in 96-well plates were transfected
with Cas9 plasmid DNA and single guide RNA (sgRNA) PCR cassette 72
hours prior to genomic DNA extraction (FIG. 72). The genomic region
flanking the CRISPR target site for each gene was amplified (FIG.
74, FIG. 80, (Example 10) by a fusion PCR method to attach the
Illumina P5 adapters as well as unique sample-specific barcodes to
the target amplicons (schematic described in FIG. 73). PCR products
were purified using EconoSpin 96-well Filter Plates (Epoch Life
Sciences) following the manufacturer's recommended protocol.
[0329] Barcoded and purified DNA samples were quantified by
Quant-iT PicoGreen dsDNA Assay Kit or Qubit 2.0 Fluorometer (Life
Technologies) and pooled in an equimolar ratio. Sequencing
libraries were then deep sequenced with the Illumina MiSeq Personal
Sequencer (Life Technologies).
[0330] Sequencing Data Analysis and Indel Detection
[0331] MiSeq reads were filtered by requiring an average Phred
quality (Q score) of at least 23, as well as perfect sequence
matches to barcodes and amplicon forward primers. Reads from on-
and off-target loci were analyzed by first performing
Smith-Waterman alignments against amplicon sequences that included
50 nucleotides upstream and downstream of the target site (a total
of 120 bp). Alignments, meanwhile, were analyzed for indels from 5
nucleotides upstream to 5 nucleotides downstream of the target site
(a total of 30 bp). Analyzed target regions were discarded if part
of their alignment fell outside the MiSeq read itself, or if
matched base-pairs comprised less than 85% of their total
length.
[0332] Negative controls for each sample provided a gauge for the
inclusion or exclusion of indels as putative cutting events. For
each sample, an indel was counted only if its quality score
exceeded .mu.-.sigma., where .mu. was the mean quality-score of the
negative control corresponding to that sample and .sigma. was the
standard deviation of same. This yielded whole target-region indel
rates for both negative controls and their corresponding samples.
Using the negative control's per-target-region-per-read error rate,
q, the sample's observed indel count n, and its read-count R, a
maximum-likelihood estimate for the fraction of reads having
target-regions with true-indel s, P, was derived by applying a
binomial error model, as follows.
[0333] Letting the (unknown) number of reads in a sample having
target regions incorrectly counted as having at least 1 indel be E,
we can write without making any assumptions about the number of
true indels)
Prob ( E p ) = ( R ( 1 - p ) E ) q E ( 1 - q ) R ( 1 - p ) - E
##EQU00001##
[0334] since R(1-p) is the number of reads having target-regions
with no true indels. Meanwhile, because the number of reads
observed to have indels is n, n=E+Rp, in other words the number of
reads having target-regions with errors but no true indels plus the
number of reads whose target-regions correctly have indels. We can
then re-write the above
Prob ( E p ) = Prob ( n = E + Rp p ) = ( R ( 1 - p ) n - Rp ) q n -
Rp ( 1 - q ) R - n ##EQU00002##
[0335] Taking all values of the frequency of target-regions with
true-indels P to be equally probable a priori,
Prob(n|P).varies.Prob(p|n). The maximum-likelihood estimate (MLE)
for the frequency of target regions with true-indels was therefore
set as the value of P that maximized Prob(n|p). This was evaluated
numerically.
[0336] In order to place error bounds on the true-indel read
frequencies in the sequencing libraries themselves, Wilson score
intervals (2) were calculated for each sample, given the
MLE-estimate for true-indel target-regions, Rp, and the number of
reads R. Explicitly, the lower bound l and upper bound u were
calculated as
l = ( Rp + z 2 2 - z Rp ( 1 - p ) + z 2 / 4 ) / ( R + z 2 )
##EQU00003## u = ( Rp + z 2 2 + z Rp ( 1 - p ) + z 2 / 4 ) / ( R +
z 2 ) ##EQU00003.2##
[0337] where z, the standard score for the confidence required in
normal distribution of variance 1, was set to 1.96, meaning a
confidence of 95%. The maximum upper bounds and minimum lower
bounds for each biological replicate are listed in FIGS. 80-83.
[0338] qRT-PCR Analysis of Relative Cas9 and sgRNA Expression
[0339] 293FT cells plated in 24-well plates were transfected as
described above. 72 hours post-transfection, total RNA was
harvested with miRNeasy Micro Kit (Qiagen). Reverse-strand.
synthesis for sgRNAs was performed with qScript Flex cDNA kit (MR)
and custom first-strand synthesis primers (Tables J and K). qPCR
analysis was performed with Fast SYBR Green Master Mix (Life
Technologies) and custom primers (Tables J and K), using GAPDH as
an endogenous control. Relative quantification was calculated by
the .DELTA..DELTA.CT method.
TABLE-US-00016 TABLE I Target site sequences. Tested target sites
for S. pyogenes type II CRISPR system with the requisite PAM. Cells
were transfected with Cas9 and either crRNA-tracrRNA or chimeric
sgRNA for each target. Target genomic Target site site ID target
sequence (5' to 3') PAM strand 1 EMX1 GTCACCTCCAATGACTAGGG TGG +
(SEQ ID NO: 319) 2 EMX1 GACATCGATGTCCTCCCCAT TGG - (SEQ ID NO: 196)
3 EMX1 GAGTCCGAGCAGAAGAAGAA GGG + (SEQ ID NO: 197) 6 EMX1
GCGCCACCGGTTGATGTGAT GGG - (SEQ ID NO: 198) 10 EMX1
GGGGCACAGATGAGAAACTC AGG - (SEQ ID NO: 199) 11 EMX1
GTACAAACGGCAGAAGCTGG AGG + (SEQ ID NO: 200) 12 EMX1
GGCAGAAGCTGGAGGAGGAA GGG + (SEQ ID NO: 201) 13 EMX1
GGAGCCCTTCTTCTTCTGCT CGG - (SEQ ID NO: 202) 14 EMX1
GGGCAACCACAAACCCACGA GGG + (SEQ ID NO: 203) 15 EMX1
GCTCCCATCACATCAACCGG TGG + (SEQ ID NO: 204) 16 EMX1
GTGGCGCATTGCCACGAAGC AGG + (SEQ ID NO: 205) 17 EMX1
GGCAGAGTGCTGCTTGCTGC TGG + (SEQ ID NO: 206) 18 EMX1
GCCCCTGCGTGGGCCCAAGC TGG + (SEQ ID NO: 207) 19 EMX1
GAGTGGCCAGAGTCCAGCTT GGG - (SEQ ID NO: 208) 20 EMX1
GGCCTCCCCAAAGCCTGGCC AGG - (SEQ ID NO: 209) 4 PVALB
GGGGCCGAGATTGGGTGTTC AGG + (SEQ ID NO: 210) 5 PVALB
GTGGCGAGAGGGGCCGAGAT TGG + (SEQ ID NO: 211) 1 SERPINB5
GAGTGCCGCCGAGGCGGGGC GGG + (SEQ ID NO: 212) 2 SERPINB5
GGAGTGCCGCCGAGGCGGGG CGG + (SEQ ID NO: 213) 3 SERPINB5
GGAGAGGAGTGCCGCCGAGG CGG + (SEQ ID NO: 214)
TABLE-US-00017 TABLE J Primer sequences SURVEYOR assay primer
genomic primer sequence name target (5' to 3') Sp-EMX1-F1 EMX1
AAAACCACCCTTCTCTCTGGC (SEQ ID NO: 36) Sp-EMX1-R1 EMX1
GGAGATTGGAGACACGGAGAG (SEQ ID NO: 37) Sp-EMX1-F2 EMX1
CCATCCCCTTCTGTGAATGT (SEQ ID NO: 215) Sp-EMX1-R2 EMX1
GGAGATTGGAGACACGGAGA (SEQ ID NO: 216) Sp-PVALB-F PVALB
CTGGAAAGCCAATGCCTGAC (SEQ ID NO: 38) Sp-PVALB-R PVALB
GGCAGCAAACTCCTTGTCCT (SEQ ID NO: 39) qRT-PCR for Cas9 and sgRNA
expression primer primer sequence name (5' to 3') sgRNA reverse-
AAGCACCGACTCGGTGCCAC strand synthesis (SEQ ID NO: 217) EXM1.1 sgRNA
TCACCTCCAATGACTAGGGG qPCR F (SEQ ID NO: 218) EXM1.1 sgRNA
CAAGTTGATAACGGACTAGCCT qPCR R (SEQ ID NO: 219) EXM1.3 sgRNA
AGTCCGAGCAGAAGAAGAAGTTT qPCR F (SEQ ID NO: 220) EXM1.3 sgRNA
TTTCAAGTTGATAACGGACTAGCCT qPCR R (SEQ ID NO: 221) Cas9 qPCR F
AAACAGCAGATTCGCCTGGA (SEQ ID NO: 222) Cas9 qPCR R
TCATCCGCTCGATGAAGCTC (SEQ ID NO: 223) GAPDH qPCR F
TCCAAAATCAAGTGGGGCGA (SEQ ID NO: 224) GAPDH qPCR R
TGATGACCCTTTTGGCTCCC (SEQ ID NO: 225) Bisulfate PCR and sequencing
primer primer sequence name (5' to 3') Bisulfate PCR F
GAGGAATTCTTTTTTTGTTYGAATA (SERPINB5 locus) TGTTGGAGGTTTTTTGGAAG
(SEQ ID NO: 226) Bisulfate PCR R GAGAAGCTTAAATAAAAAACRACAA
(SERPINB5 locus) TACTCAACCCAACAACC (SEQ ID NO: 227) pUC19
sequencing CAGGAAACAGCTATGAC (SEQ ID NO: 228)
TABLE-US-00018 TABLE K Sequences for primers to test sgRNA
architecture. Primers hybridize to the reverse strand of the U6
promoter unless otherwise indicated. The U6 priming site is in
italics, the guide sequence is indicated as a stretch of Ns, the
direct repeat sequence is highlighted in bold, and the tracrRNA
sequence underlined. The secondary structure of each sgRNA
architecture is shown in FIG. 43. primer name primer sequence (5'
to 3') U6-Forward GCCTCTAGAGGTACCTGAGGGCCTAT TTCCCATGATTCC (SEQ ID
NO: 229) I: sgRNA(DR +12, ACCTCTAGAAAAAAAGCACCGACTCG tracrRNA +85)
GTGCCACTTTTTCAAGTTGATAACGG ACTAGCCTTATTTTAACTTGCTATTT
CTAGCTCTAAAACNNNNNNNNNNNNN NNNNNNNGGTGTTTTCGTCCTTTCCA CAAG (SEQ ID
NO: 230) II: sgRNA(DR +12, ACCTCTAGAAAAAAAGCACCGACTCG tracrRNA +85)
GTGCCACTTTTTCAAGTTGATAACGG mut2 ACTAGCCTTATATTAACTTGCTATTT
CTAGCTCTAATACNNNNNNNNNNNNN NNNNNNNGGTGTTTCGTCCTTTCCAC AAG (SEQ ID
NO: 231) III: sgRNA(DR +22, ACCTCTAGAAAAAAAGCACCGACTTC tracrRNA
+85) GGTGCCACTTTTTCAAGTTGATAACG GACTAGCCTTATTTTAACTTGCTATG
CTGTTTTGTTTCCAAAACAGCATAGC TCTAAAACNNNNNNNNNNNNNNNNNN
NNGGTGTTTCGTCCTTTCCACAAG (SEQ ID NO: 232) IV: sgRNA(DR +22,
ACCTCTAGAAAAAAAGCACCGACTTC tracrRNA +85) GGTGCCACTTTTTCAAGTTGATAACG
mut4 GACTAGCCTTATATTAACTTGCTATG CTGTATTGTTTCCAATACAGCATAGC
TCTAATACNNNNNNNNNNNNNNNNNN NNGGTGTTTCGTCCTTTCCACAAG (SEQ ID NO:
233)
TABLE-US-00019 TABLE L Target sites with alternate PAMs for testing
PAM specificity of Cas9, All target sites for PAM specificity
testing are found within the human EMX1 locus. Target site sequence
(5' to 3') PAM AGGCCCCAGTGGCTGCTCT (SEQ ID NO: 234) NAA
ACATCAACCGGTGGCGCAT (SEQ ID NO: 235) NAT AAGGTGTGGTTCCAGAACC (SEQ
ID NO: 236) NAC CCATCACATCAACCGGTGG (SEQ ID NO: 237) NAG
AAACGGCAGAAGCTGGAGG (SEQ ID NO: 238) NTA GGCAGAAGCTGGAGGAGGA (SEQ
ID NO: 239) NTT GGTGTGGTTCCAGAACCGG (SEQ ID NO: 240) NTC
AACCGGAGGACAAAGTACA (SEQ ID NO: 241) NTG TTCCAGAACCGGAGGACAA (SEQ
ID NO: 242) NCA GTGTGGTTCCAGAACCGGA (SEQ ID NO: 243) NCT
TCCAGAACCGGAGGACAAA (SEQ ID NO: 244) NCC CAGAAGCTGGAGGAGGAAG (SEQ
ID NO: 245) NCG CATCAACCGGTGGCGCATT (SEQ ID NO: 246) NGA
GCAGAAGCTGGAGGAGGAA (SEQ ID NO: 247) NGT CCTCCCTCCCTGGCCCAGG (SEQ
ID NO: 248) NGC TCATCTGTGCCCCTCCCTC (SEQ ID NO: 249) NAA
GGGAGGACATCGATGTCAC (SEQ ID NO: 250) NAT CAAACGGCAGAAGCTGGAG (SEQ
ID NO: 251) NAC GGGTGGGCAACCACAAACC (SEQ ID NO: 252) NAG
GGTGGGCAACCACAAACCC (SEQ ID NO: 253) NTA GGCTCCCATCACATCAACC (SEQ
ID NO: 254) NTT GAAGGGCCTGAGTCCGAGC (SEQ ID NO: 255) NTC
CAACCGGTGGCGCATTGCC (SEQ ID NO: 256) NTG AGGAGGAAGGGCCTGAGTC (SEQ
ID NO: 257) NCA AGCTGGAGGAGGAAGGGCC (SEQ ID NO: 258) NCT
GCATTGCCACGAAGCAGGC (SEQ ID NO: 259) NCC ATTGCCACGAAGCAGGCCA (SEQ
ID NO: 260) NCG AGAACCGGAGGACAAAGTA (SEQ ID NO: 261) NGA
TCAACCGGTGGCGCATTGC (SEQ ID NO: 262) NGT GAAGCTGGAGGAGGAAGGG (SEQ
ID NO: 263) NGC
Example 10
Supplementary Sequences
[0340] All sequences are in the 5' to 3' direction. For U6
transcription, the string of underlined Ts serve as the
transcriptional terminator.
TABLE-US-00020 > U6-short tracrRNA (Streptococcus pyogenes
SF370) (SEQ ID NO: 40)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattggaattaa-
tttgactgtaaa
cacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagttttaaaattat-
gttttaaaatggactatcatatgc
ttaccgtaacttgaaagtatttcgatttcttggctttatatatcttgtggaaaggacgaaacaccGGAACCATT-
CAAAACAGC ATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGA
GTCGGTGCTTTTTTT (tracrRNA sequence in bold) >U6-DR-guide
sequence-DR (Streptococcus pyogenes SF370) (SEQ ID NO: 54)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattggaattaa-
tttgactgtaaa
cacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtagcagtataaaattatga-
ttaaaatggactatcatatgc ##STR00001## ##STR00002## TTTTTT ##STR00003##
> sgRNA containing +48 tracrRNA (Streptococcus pyogenes SF370)
(SEQ ID NO: 55)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattggaattaa-
tttgactgtaaa
cacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagttttaaaattat-
gtataaaatggactatcatatgc
ttaccgtaacttgaaagtatttcgatttcttggctttatatatcttgtggaaaggacgaaacaccNNNNNNNNN-
NNNNNNNNN ##STR00004## (guide sequence is in bold Ns and the
tracrRNA fragment is in bold) > sgRNA containing +54 tracrRNA
(Streptococcus pyogenes SF370) (SEQ ID NO: 56)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgnagagagataattggaataatt-
tgactgtaaa
cacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagttttaaaattat-
gtataaaatggactatcatatgc
ttaccgtaacttgaaagtatttcgatttcttggctttatatatcttgtggaaaggacgaaacaccNNNNNNNNN-
NNNNNNNNN ##STR00005## (guide sequence is in bold Ns and the
tracrRNA fragment is in bold) > sgRNA containing +67 tracrRNA
(Streptococcus pyogenes SF370) (SEQ ID NO: 57)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattggaattaa-
tttgactgtaaa
cacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtagcagtataaaattatgt-
ataaaatggactatcatatgc
ttaccgtaacttgaaagtatttcgatttcttggctttatatatcttgtggaaaggacgaaacaccNNNNNNNNN-
NNNNNNNNN ##STR00006## (guide sequence is in bold Ns and the
tracrRNA fragment is in bold) > sgRNA containing +85 tracrRNA
(Streptococcus pyogenes SF370) (SEQ ID NO: 58)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattggaattaa-
tttgactgtaaa
cacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtagcagtataaaattatga-
ttaaaatggactatcatatgc
ttaccgtaacttgaaagtatttcgatttcttggattatatatcttgtggaaaggacgaaacaccNNNNNNNNNN-
NNNNNNNN ##STR00007## T (guide sequence is in bold Ns and the
tracrRNA fragment is in bold) > CBh-NLS-SpCas9-NLS (SEQ ID NO:
59) CGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCAACGACC
CCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGACTT
TCCATTGACGTCAATGGGTGGAGTATTTACGGTAAACTGCCCACTTGGCAGTACATC
AAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCG
CCTGGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTA
CGTATTAGTCATCGCTATTACCATGGTCGAGGTGAGCCCCACGTTCTGCTTCACTCTC
CCCATCTCCCCCCCCTCCCCACCCCCAATTTTGTATTTATTTATTTTTTAATTATTTTG
TGCAGCGATGGGGGCGGGGGGGGGGGGGGGGCGCGCGCCAGGCGGGGCGGGGCGG
GGCGAGGGGCGGGGCGGGGCGAGGCGGAGAGGTGCGGCGGCAGCCAATCAGAGCG
GCGCGCTCCGAAAGTTTCCTTCTTATGGCGAGGCGGCGGCGGCGGCGGCCCTATAAA
AAGCGAAGCGCGCGGCGGGCGGGAGTCGCTGCGACGCTGCCTTCGCCCCGTGCCCC
GCTCCGCCGCCGCCTCGCGCCGCCCGCCCCGGCTCTGACTGACCGCGTTACTCCCAC
AGGTGAGCGGGCGGGACGGCCCTTCTCCTCCGGGCTGTAATTAGCTGAGCAAGAGG
TAAGGGTTTAAGGGATGGTTGGTTGGTGGGGTATTAATGTTTAATTACCTGGAGCAC
CTGCCTGAAATCACTTTTTTTCAGGTTGGaccggtgccaccATGGACTATAAGGACCACG
ACGGAGACTACAAGGATCATGATATTGATTACAAAGACGATGACGATAAGATG
GCCCCAAAGAAGAAGCGGAAGGTVGGTATCCACGGAGTCCCAGCAGCCGACAA
GAAGTACAGCATCGGCCTGGACATCGGCACCAACTCTGTGGGCTGGGCCGTGA
TCACCGACGAGTACAAGGTGCCCAGCAAGAAATTCAAGGTGCTGGGCAACACC
GACCGGCACAGCATCAAGAAGAACCTGATCGGAGCCCTGCTGTTCGACAGCGG
CGAAACAGCCGAGGCCACCCGGCTGAAGAGAACCGCCAGAAGAAGATACACCA
GACGGAAGAACCGGATCTGCTATCTGCAAGAGATCTTCAGCAACGAGATGGCC
AAGGTGGACGACAGCTTCTTCCACAGACTGGAAGAGTCCTTCCTGGTGGAAGA
GGATAAGAAGCACGAGCGGCACCCCATCTTCGGCAACATCGTGGACGAGGTGG
CCTACCACGAGAAGTACCCCACCATCTACCACCTGAGAAAGAAACTGGTGGAC
AGCACCGACAAGGCCGACCTGCGGCTGATCTATCTGGCCCTGGCCCACATGAT
CAAGTTCCGGGGCCACTTCCTGATCGAGGGCGACCTGAACCCCGACAACAGCG
ACGTGGACAAGCTGTTCATCCAGGTGGTGCAGACCTACAACCAGCTGTTCGAG
GAAAACCCCATCAACGCCAGCGGCGTGGACGCCAAGGCCATCCTGTCTGCCAG
ACTGAGCAAGAGCAGACGGCTGGAAAATCTGATCGCCCAGCTGCCCGGCGAGA
AGAAGAATGGCCTGTTCGGCAACCTGATTGCCCTGAGCCTGGGCCTGACCCCC
AACTTCAAGAGCAACTTCGACCTGGCCGAGGATGCCAAACTGCAGCTGAGCAA
GGACACCTACGACGACGACCTGGACAACCTGCTGGCCCAGATCGGCGACCAGT
ACGCCGACCTGTTTCTGGCCGCCAAGAACCTGTCCGACGCCATCCTGCTGAGC
GACATCCTGAGAGTGAACACCGAGATCACCAAGGCCCCCCTGAGCGCCTCTAT
GATCAAGAGATACGACGAGCACCACCAGGACCTGACCCTGCTGAAAGCTCTCG
TGCGGCAGCAGCTGCCTGAGAAGTACAAAGAGATTTTCTTCGACCAGAGCAAG
AACGGCTACGCCGGCTACATTGACGGCGGAGCCAGCCAGGAAGAGTTCTACAA
GTTCATCAAGCCCATCCTGGAAAAGATGGACGGCACCGAGGAACTGCTCGTGA
AGCTGAACAGAGAGGACCTGCTGCGGAAGCAGCGGACCTTCGACAACGGCAG
CATCCCCCACCAGATCCACCTGGGAGAGCTGCACGCCATTCTGCGGCGGCAGG
AAGATTTTTACCCATTCCTGAAGGACAACCGGGAAAAGATCGAGAAGATCCTG
ACCTTCCGCATCCCCTACTACGTGGGCCCTCTGGCCAGGGGAAACAGCAGATT
CGCCTGGATGACCAGAAAGAGCGAGGAAACCATCACCCCCTGGAACTTCGAGG
AAGTGGTGGACAAGGCCGCTTCCGCCCAGAGCTTCATCGAGCGGATGACCAAC
TTCGATAAGAACCTGCCCAACGAGAAGGTGCTGCCCAAGCACAGCCTGCTGTA
CGAGTACTTCACCGTGTATAACGAGCTGACCAAAGTGAAATACGTGACCGAGG
GAATGAGAAAGCCCGCCTTCCTGAGCGGCGAGCAGAAAAAGGCCATCGTGGAC
CTGCTGTTCAAGACCAACCGGAAAGTGACCGTGAAGCAGCTGAAAGAGGACTA
CTTCAAGAAAATCGAGTGCTTCGACTCCGTGGAAATCTCCGGCGTGGAAGATC
GGTTCAACGCCTCCCTGGGCACATACCACGATCTGCTGAAAATTATCAAGGAC
AAGGACTTCCTGGACAATGAGGAAAACGAGGACATTCTGGAAGATATCGTGCT
GACCCTGACACTGTTTGAGGACAGAGAGATGATCGAGGAACGGCTGAAAACCT
ATGCCCACCTGTTCGACGACAAAGTGATGAAGCAGCTGAAGCGGCGGAGATAC
ACCGGCTGGGGCAGGCTGAGCCGGAAGCTGATCAACGGCATCCGGGACAAGC
AGTCCGGCAAGACAATCCTGGATTTCCTGAAGTCCGACGGCTTCGCCAACAGA
AACTTCATGCAGCTGATCCACGACGACAGCCTGACCTTTAAAGAGGACATCCA
GAAAGCCCAGGTGTCCGGCCAGGGCGATAGCCTGCACGAGCACATTGCCAATC
TGGCCGGCAGCCCCGCCATTAAGAAGGGCATCCTGCAGACACTGAAGGTGGTG
GACGAGCTCGTGAAAGTGATGGGCCGGCACAAGCCCGAGAACATCGTGATCGA
AATGGCCAGAGAGAACCAGACCACCCAGAAGGGACAGAAGAACAGCCGCGAG
AGAATGAAGCGGATCGAAGAGGGCATCAAAGAGCTGGGCAGCCAGATCCTGAA
AGAACACCCCGTGGAAAACACCCAGCTGCAGAACGAGAAGCTGTACCTGTACT
ACCTGCAGAATGGGCGGGATATGTACGTGGACCAGGAACTGGACATCAACCGG
CTGTCCGACTACGATGTGGACCATATCGTGCCTCAGAGCTTTCTGAAGGACGA
CTCCATCGACAACAAGGTGCTGACCAGAAGCGACAAGAACCGGGGCAAGAGCG
ACAACGTGCCCTCCGAAGAGGTCGTGAAGAAGATGAAGAACTACTGGCGGCAG
CTGCTGAACGCCAAGCTGATTACCCAGAGAAAGTTCGACAATCTGACCAAGGC
CGAGAGAGGCGGCCTGAGCGAACTGGATAAGGCCGGCTTCATCAAGAGACAG
CTGGTGGAAACCCGGCAGATCACAAAGCACGTGGCACAGATCCTGGACTCCCG
GATGAACACTAAGTACGACGAGAATGACAAGCTGATCCGGGAAGTGAAAGTGA
TCACCCTGAAGTCCAAGCTGGTGTCCGATTTCCGGAAGGATTTCCAGTTTTACA
AAGTGCGCGAGATCAACAACTACCACCACGCCCACGACGCCTACCTGAACGCC
GTCGTGGGAACCGCCCTGATCAAAAAGTACCCTAAGCTGGAAAGCGAGTTCGT
GTACGGCGACTACAAGGTGTACGACGTGCGGAAGATGATCGCCAAGAGCGAGC
AGGAAATCGGCAAGCCTACCGCCAAGTACTTCTTCTACAGCAACATCATGAACT
TTTTCAAGACCGAGATTACCCTGGCCAACGGCGAGATCCGGAAGCGGCCTCTG
ATCGAGACAAACGGCGAAACCGGGGAGATCGTGTGGGATAAGGGCCGGGATT
TTGCCACCGTGCGGAAAGTGCTGAGCATGCCCCAAGTGAATATCGTGAAAAAG
ACCGAGGTGCAGACAGGCGGCTTCAGCAAAGAGTCTATCCTGCCCAAGAGGAA
CAGCGATAAGCTGATCGCCAGAAAGAAGGACTGGGACCCTAAGAAGTACGGCG
GCTTCGACAGCCCCACCGTGGCCTATTCTGTGCTGGTGGTGGCCAAAGTGGAA
AAGGGCAAGTCCAAGAAACTGAAGAGTGTGANAGAGCTGCTGGGGATCACCAT
CATGGAAAGAAGCAGCTTCGAGAAGAATCCCATCGACTTTCTGGAAGCCAAGG
GCTACAAAGAAGTGAAAAAGGACCTGATCATCAAGCTGCCTAAGTACTCCCTG
TTCGAGCTGGAAAACGGCCGGAAGAGAATGCTGGCCTCTGCCGGCGAACTGCA
GAAGGGAAACGAACTGGCCCTGCCCTCCAAATATGTGAACTTCCTGTACCTGG
CCAGCCACTATGAGAAGCTGAAGGGCTCCCCCGAGGATAATGAGCAGAAACAG
CTGTTTGTGGAACAGCACAAGCACTACCTGGACGAGATCATCGAGCAGATCAG
CGAGTTCTCCAAGAGAGTGATCCTGGCCGACGCTAATCTGGACAAAGTGCTGT
CCGCCTACAACAAGCACCGGGATAAGCCCATCAGAGAGCAGGCCGAGAATATC
ATCCACCTGTTTACCCTGACCAATCTGGGAGCCCCTGCCGCCTTCAAGTACTTT
GACACCACCATCGACCGGAAGAGGTACACCAGCACCAAAGAGGTGCTGGACGC
CACCCTGATCCACCAGAGCATCACCGGCCTGTACGAGACACGGATCGACCTGT
CTCAGCTGGGAGGCGACTTTCTTTTTCTTAGCTTGACCAGCTTTCTTAGTAGCA
GCAGGACGCTTTAA (NLS-hSpCas9-NLS is highlighted in bold) >
Sequencing amplicon for EMX1 guides 1.1, 1.14, 1.17 (SEQ ID NO:
264) CCAATGGGGAGGACATCGATGTCACCTCCAATGACTAGGGTGGGCAACC
ACAAACCCACGAGGGCAGAGTGCTGCTTGCTGCTGGCCAGGCCCCTGCGTGGGCCC
AAGCTGGACTCTGGCCAC > Sequencing amplicon for EMX1 guides 1.2,
1.16 (SEQ ID NO: 265)
CGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCC
ACGAAGCAGGCCAATGGGGAGGACATCGATGTCACCTCCAATGACTAGGGTGGGCA
ACCACAAACCCACGAG > Sequencing amplicon for EMX1 guides 1.3,
1.13, 1,15 (SEQ ID NO: 266)
GGAGGACAAAGTACAAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTC
CGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGC
AGGCCAATGGGGAGGACATCGAT > Sequencing amplicon for EMX1 guides
1.6 (SEQ ID NO: 267)
AGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTC
CCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATGGGGAGGACATCG
ATGTCACCTCCAATGACTAGGGTGG > Sequencing amplicon for EMX1 guides
1.10 (SEQ ID NO: 268)
CCTCAGTCTTCCCATCAGGCTCTCAGCTCAGCCTGAGTGTTGAGGCCCCAG
TGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGG
TGAAGGTGTGGTTCCA > Sequencing amplicon for EMX1 guides 1.11,
1.12 (SEQ ID NO: 269)
TCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACC
GGAGGACAAAGTACAAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCA
GAAGAAGAAGGGCTCCCATCACA > Sequencing amplicon for EMX1 guides
1.18, 1.19 (SEQ ID NO: 270)
CTCCAATGACTAGGGTGGGCAACCACAAACCCACGAGGGCAGAGTGCTG
CTTGCTGCTGGCCAGGCCCCTGCGTGGGCCCAAGCTGGACTCTGGCCACTCCCTGGC
CAGGCTTTGGGGAGGCCTTGGAGT > Sequencing amplicon for EMX1 guides
1.20 (SEQ ID NO: 271)
CTGCTTGCTGCTGGCCAGGCCCCTGCGTGGGCCCAAGCTGGACTCTGGCC
ACTCCCTGGCCAGGCTTTGGGGAGGCCTGGAGTCATGGCCCCACAGGGCTTGAAGC
CCGGGGCCGCCATTGACAGAG >T7 promoter F primer for annealing with
target strand (SEQ ID NO: 272) GAAATTAATACGACTCACTATAGGG >oligo
containing pUC19 target site 1 for methylation (T7 reverse) (SEQ ID
NO: 273) AAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCC
TTATTTTAACTTGCTATTTCTAGCTCTAAAACAACGACGAGCGTGACACCACCCTAT
AGTGAGTCGTATTAATTTC >oligo containing pUC19 target site 2 for
methylation (T7 reverse) (SEQ ID NO: 274)
AAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCC
TTATTTTAACTTGCTATTTCTAGCTCTAAAACGCAACAATTAATAGACTGGACCTATA
GTGAGTCGTATTAATTTC
Example 11
Oligo-Mediated Cas9-Induced Homologous Recombination
[0341] The oligo homologous recombination test is a comparison of
efficiency across different Cas9 variants and different HR template
(oligo vs. plasmid).
[0342] 293FT cells were used. SpCas9=Wildtype Cas9 and
SpCas9n=nickase Cas9 (D10A). The chimeric RNA target is the same
EMAI Protospacer Target 1 as in Examples 5, 9 and 10 and oligos
synthesized by IDT using PAGE purification.
[0343] FIG. 44 depicts a design of the oligo DNA used as Homologous
Recombination (HR) template in this experiment. Long oligos contain
100 bp homology to the EMX1 locus and a HindIII restriction site.
293FT cells were co-transfected with: first, a plasmid containing a
chimeric RNA targeting human EMX1 locus and wild-type cas9 protein,
and second, the oligo DNA as HR template. Samples are from 293FT
cells collected 96 hours post transfection with Lipofectamine 2000.
All products were amplified with an EMX1 HR Primer, gel purified,
followed by digestion with HindIII to detect the efficiency of
integration of HR template into the human genome.
[0344] FIGS. 45 and 46 depict a comparison of HR efficiency induced
by different combination of Cas9 protein and HR template. The Cas9
construct used were either wild-type Cas9 or the nickase version of
Cas9 (Cas9n). The HR template used were: antisense oligo DNA
(Antisense-Oligo in above figure), or sense oligo DNA (Sense-Oligo
in above figure), or plasmid HR template (HR template in above
figure). The sense/anti-sense definition is that the
actively-transcribed strand with sequence corresponding to the
transcribed mRNA is defined as the sense strand of genome. HR
Efficiency is shown as percentage of HindIII digestion band as
against all genomic PCR amplified product (bottom numbers).
Example 12
Autistic Alouse
[0345] Recent large-scale sequencing initiatives have produced a
large number of genes associated with disease. Discovering the
genes is only the beginning in understanding what the gene does and
how it leads to a diseased phenotype. Current technologies and
approaches to study candidate genes are slow and laborious. The
gold standards, gene targeting and genetic knockouts, require a
significant investment in time and resources, both monetary and in
terms of research personnel. Applicants set out to utilize the
hSpCas9 nuclease to target many genes and do so with higher
efficiency and lower turnaround compared to any other technology.
Because of the high efficiency of hSpCas9 Applicants can do RNA
injection into mouse zygotes and immediately get genome-modified
animals without the need to do any preliminary gene targeting in
mESCs.
[0346] Chromodomain helicase DNA binding protein 8 (CHD8) is a
pivotal gene in involved in early vertebrate development and
morphogenesis. Mice lacking CHD8 die during embryonic development.
Mutations in the CHD8 gene have been associated with autism
spectrum disorder in humans. This association was made in three
different papers published simultaneously in Nature. The same three
studies identified a plethora of genes associated with autism
spectrum disorder. Applicants' aim was to create knockout mice for
the four genes that were found in all papers, Chd8, Katna12,
Kctd13, and Scn2a. In addition, Applicants chose two other genes
associated with autism spectrum disorder, schizophrenia, and ADHD,
GIT1, CACNA1C, and CACNB2. And finally, as a positive control
Applicants decide to target MeCP2.
[0347] For each gene Applicants designed three gRNAs that would
likely knockout the gene. A knockout would occur after the hSpCas9
nuclease makes a double strand break and the error prone DNA repair
pathway, non-homologous end joining, corrects the break, creating a
mutation. The most likely result is a frameshift mutation that
would knockout the gene. The targeting strategy involved finding
proto-spacers in the exons of the gene that had a PAM sequence,
NGG, and was unique in the genome. Preference was given to
proto-spacers in the first exon, which would be most deleterious to
the gene.
[0348] Each gRNA was validated in the mouse cell line, Neuro-N2a,
by liposomal transient co-transfection with hSpCas9. 72 hours
post-transfection genomic DNA was purified using QuickExtract DNA
from Epicentre. PCR was performed to amplify the locus of interest.
Subsequently the SURVEYOR Mutation Detection Kit from Transgenomics
was followed. The SURVEYOR results for each gRNA and respective
controls are shown in Figure A1. A positive SURVEYOR result is one
large band corresponding to the genomic PCR and two smaller bands
that are the product of the SURVEYOR nuclease making a
double-strand break at the site of a mutation. The average cutting
efficiency of each gRNA was also determined for each gRNA. The gRNA
that was chosen for injection was the highest efficiency gRNA that
was the most unique within the genome.
[0349] RNA (hSpCas9+gRNA RNA) was injected into the pronucleus of a
zygote and later transplanted into a foster mother. Mothers were
allowed to go full term and pups were sampled by tail snip 10 days
postnatal. DNA was extracted and used as a template for PCR, which
was then processed by SURVEYOR. Additionally, PCR products were
sent for sequencing. Animals that were detected as being positive
in either the SURVEYOR assay or PCR sequencing would have their
genomic PCR products cloned into a pUC19 vector and sequenced to
determine putative mutations from each allele.
[0350] So far, mice pups from the Chd8 targeting experiment have
been fully processed up to the point of allele sequencing. The
Surveyor results for 38 live pups (lanes 1-38) 1 dead pup (lane 39)
and 1 wild-type pup for comparison (lane 40) are shown in Figure
A2. Pups 1-19 were injected with gRNA Chd8.2 and pups 20-38 were
injected with gRNA Chd8.3. Of the 38 live pups, 13 were positive
for a mutation. The one dead pup also had a mutation. There was no
mutation detected in the wild-type sample. Genomic PCR sequencing
was consistent with the SURVEYOR assay findings.
Example 13
CRISPR/Cas-Mediated Transcriptional Modulation
[0351] FIG. 67 depicts a design of the CRISPR-TF (Transcription
Factor) with transcriptional activation activity. The chimeric RNA
is expressed by U6 promoter, while a human-codon-optimized,
double-mutant version of the Cas9 protein (hSpCas9m), operably
linked to triple NLS and a VP64 functional domain is expressed by a
EF1.alpha. promoter. The double mutations, D10A and H840A, renders
the cas9 protein unable to introduce any cleavage but maintained
its capacity to bind to target DNA when guided by the chimeric
RNA.
[0352] FIG. 68 depicts transcriptional activation of the human SOX2
gene with CRISPR-TF system (Chimeric RNA and the Cas9-NLS-VP64
fusion protein). 293FT cells were transfected with plasmids bearing
two components: (1) U6-driven different chimeric RNAs targeting
20-bp sequences within or around the human SOX2 genomic locus, and
(2) EF1a-driven hSpCas9m (double mutant)-NLS-VP64 fusion protein.
96 hours post transfection, 293FT cells were harvested and the
level of activation is measured by the induction of mRNA expression
using a qRT-PCR assay. All expression levels are normalized against
the control group (grey bar), which represents results from cells
transfected with the CRISPR-TF backbone plasmid without chimeric
RNA. The qRT-PCR probes used for detecting the SOX2 mRNA is Taqman
Human Gene Expression Assay (Life Technologies). All experiments
represents data from 3 biological replicates, n=3, error bars show
s.e.m.
Example 14
NLS: Cas9 NLS
[0353] 293FT cells were transfected with plasmid containing two
components: (1) EF1.alpha. promoter driving the expression of Cas9
(wild-type human-codon-optimized Sp Cas9) with different NLS
designs (2) U6 promoter driving the same chimeric RNA targeting
human EMX1 locus.
[0354] Cells were collect at 72 h time point post transfection, and
then extracted with 50 .mu.l of the QuickExtract genomic DNA
extraction solution following manufacturer's protocol. Target EMX1
genomic DNA were PCR amplified and then Gel-purify with 1% agarose
gel. Genomic PCR product were re-anneal and subjected to the
Surveyor assay following manufacturer's protocol. The genomic
cleavage efficiency of different constructs were measured using
SDS-PAGE on a 4-12%0 TBE-PAGE gel (Life Technologies), analyzed and
quantified with ImageLab (Bio-rad) software, all following
manufacturer's protocol.
[0355] FIG. 69 depicts a design of different Cas9 NLS constructs.
All Cas9 were the human-codon-optimized version of the Sp Cas9. NLS
sequences are linked to the cas9 gene at either N-terminus or
C-terminus. All Cas9 variants with different NLS designs were
cloned into a backbone vector containing so it is driven by EF1a
promoter. On the same vector there is a chimeric RNA targeting
human EMX1 locus driven by U6 promoter, together forming a
two-component system.
TABLE-US-00021 TABLE M Cas9 NLS Design Test Results. Quantification
of genomic cleavage of different cas9-nls constructs by surveyor
assay. Percentage Error Genome Biological Biological Biological
(S.E.M., Cleavage as Replicate Replicate Replicate standard
measured by 1 2 3 Average error of Surveyor assay (%) (%) (%) (%)
the mean) Cas9 (No NLS) 2.50 3.30 2.73 2.84 0.24 Cas9 with N- term
7.61 6.29 5.46 6.45 0.63 NLS Cas9 with C-term 5.75 4.86 4.70 5.10
0.33 NLS Cas9 with Double 9.08 9.85 7.78 8.90 0.60 (N-term and
C-term) NLS
[0356] FIG. 70 depicts the efficiency of genomic cleavage induced
by Cas9 variants bearing different NLS designs. The percentage
indicate the portion of human EMX1 genomic DNA that were cleaved by
each construct. All experiments are from 3 biological replicates.
n=3, error indicates S.E.M.
Example 15
Engineering of a Microalgae Using Cas9
[0357] Methods of Delivering Cas9
[0358] Method 1: Applicants deliver Cas9 and guide RNA using a
vector that expresses Cas9 under the control of a constitutive
promoter such as Hsp70A-Rbc S2 or Beta2-tubulin.
[0359] Method 2: Applicants deliver Cas9 and T7 polymerase using
vectors that expresses Cas9 and T7 polymerase under the control of
a constitutive promoter such as Hsp70A-Rbc S2 or Beta2-tubulin.
Guide RNA will be delivered using a vector containing T7 promoter
driving the guide RNA.
[0360] Method 3: Applicants deliver Cas9 mRNA and in vitro
transcribed guide RNA to algae cells. RNA can be in vitro
transcribed. Cas9 mRNA will consist of the coding region for Cas9
as well as 3'UTR from Cop1 to ensure stabilization of the Cas9
mRNA.
[0361] For Homologous recombination, Applicants provide an
additional homology directed repair template,
[0362] Sequence for a cassette driving the expression of Cas9 under
the control of beta-2 tubulin promoter, followed by the 3' UTR. of
Cop1.
TABLE-US-00022 (SEQ ID NO: 275)
TCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTAGGGCGGGCTG
CGAGACGGCTTCCCGGCGCTGCATGCAACACCGATGATGCTTCGA
CCCCCCGAAGCTCCTTCGGGGCTGCATGGGCGCTCCGATGCCGCT
CCAGGGCGAGCGCTGTTTAAATAGCCAGGCCCCCGATTGCAAAGA
CATTATAGCGAGCTACCAAAGCCATATTCAAACACCTAGATCACT
ACCACTTCTACACAGGCCACTCGAGCTTGTGATCGCACTCCGCTA
AGGGGGCGCCTCTTCCTCTTCGTTTCAGTCACAACCCGCAAACAT
GTACCCATACGATGTTCCAGATTACGCTTCGCCGAAGAAAAAGCG
CAAGGTCGAAGCGTCCGACAAGAAGTACAGCATCGGCCTGGACAT
CGGCACCAACTCTGTGGGCTGGGCCGTGATCACCGACGAGTACAA
GGTGCCCAGCAAGAAATTCAAGGTGCTGGGCAACACCGACCGGCA
CAGCATCAAGAAGAACCTGATCGGAGCCCTGCTGTTCGACAGCGG
CGAAACAGCCGAGGCCACCCGGCTGAAGAGAACCGCCAGAAGAAG
ATACACCAGACGGAAGAACCGGATCTGCTATCTGCAAGAGATCTT
CAGCAACGAGATGGCCAAGGTGGACGACAGCTTCTTCCACAGACT
GGAAGAGTCCTTCCTGGTGGAAGAGGATAAGAAGCACGAGCGGCA
CCCCATCTTCGGCAACATCGTGGACGAGGTGGCCTACCACGAGAA
GTACCCCACCATCTACCACCTGAGAAAGAAACTGGTGGACAGCAC
CGACAAGGCCGACCTGCGGCTGATCTATCTGGCCCTGGCCCACAT
GATCAAGTTCCGGGGCCACTTCCTGATCGAGGGCGACCTGAACCC
CGACAACAGCGACGTGGACAAGCTGTTCATCCAGCTGGTGCAGAC
CTACAACCAGCTGTTCGAGGAAAACCCCATCAACGCCAGCGGCGT
GGACGCCAAGGCCATCCTGTCTGCCAGACTGAGCAAGAGCAGACG
GCTGGAAAATCTGATCGCCCAGCTGCCCGGCGAGAAGAAGAATGG
CCTGTTCGGCAACCTGATTGCCCTGAGCCTGGGCCTGACCCCCAA
CTTCAAGAGCAACTTCGACCTGGCCGAGGATGCCAAACTGCAGCT
GAGCAAGGACACCTACGACGACGACCTGGACAACCTGCTGGCCCA
GATCGGCGACCAGTACGCCGACCTGTTTCTGGCCGCCAAGAACCT
GTCCGACGCCATCCTGCTGAGCGACATCCTGAGAGTGAACACCGA
GATCACCAAGGCCCCCCTGAGCGCCTCTATGATCAAGAGATACGA
CGAGCACCACCAGGACCTGACCCTGCTGAAAGCTCTCGTGCGGCA
GCAGCTGCCTGAGAAGTACAAAGAGATTTTCTTCGACCAGAGCAA
GAACGGCTACGCCGGCTACATTGACGGCGGAGCCAGCCAGGAAGA
GTTCTACAAGTTCATCAAGCCCATCCTGGAAAAGATGGACGGCAC
CGAGGAACTGCTCGTGAAGCTGAACAGAGAGGACCTGCTGCGGAA
GCAGCGGACCTTCGACAACGGCAGCATCCCCCACCAGATCCACCT
GGGAGAGCTGCACGCCATTCTGCGGCGGCAGGAAGATTTTTACCC
ATTCCTGAAGGACAACCGGGAAAAGATCGAGAAGATCCTGACCTT
CCGCATCCCCTACTACGTGGGCCCTCTGGCCAGGGGAAACAGCAG
ATTCGCCTGGATGACCAGAAAGAGCGAGGAAACCATCACCCCCTG
GAACTTCGAGGAAGTGGTGGACAAGGGCGCTTCCGCCCAGAGCTT
CATCGAGCGGATGACCAACTTCGATAAGAACCTGCCCAACGAGAA
GGTGCTGCCCAAGCACAGCCTGCTGTACGAGTACTTCACCGTGTA
TAACGAGCTGACCAAAGTGAAATACGTGACCGAGGGAATGAGAAA
GCCCGCCTTCCTGAGCGGCGAGCAGAAAAAGGCCATCGTGGACCT
GCTGTTCAAGACCAACCGGAAAGTGACCGTGAAGCAGCTGAAAGA
GGACTACTTCAAGAAAATCGAGTGCTTCGACTCCGTGGAAATCTC
CGGCGTGGAAGATCGGTTCAACGCCTCCCTGGGCACATACCACGA
TCTGCTGAAAATTATCAAGGACAAGGACTTCCTGGACAATGAGGA
AAACGAGGACATTCTGGAAGATATCGTGCTGACCCTGACACTGTT
TGAGGACAGAGAGATGATCGAGGAACGGCTGAAAACCTATGCCCA
CCTGTTCGACGACAAAGTGATGAAGCAGCTGAAGCGGCGGAGATA
CACCGGCTGGGGCAGGCTGAGCCGGAAGCTGATCAACGGCATCCG
GGACAAGCAGTCCGGCAAGACAATCCTGGATTTCCTGAAGTCCGA
CGGCTTCGCCAACAGAAACTTCATGCAGCTGATCCACGACGACAG
CCTGACCTTTAAAGAGGACATCCAGAAAGCCCAGGTGTCCGGCCA
GGGCGATAGCCTGCACGAGCACATTGCCAATCTGGCCGGCAGCCC
CGCCATTAAGAAGGGCATCCTGCAGACAGTGAAGGTGGTGGACGA
GCTCGTGAAAGTGATGGGCCGGCACAAGCCCGAGAACATCGTGAT
CGAAATGGCCAGAGAGAACCAGACCACCCAGAAGGGACAGAAGAA
CAGCCGCGAGAGAATGAAGCGGATCGAAGAGGGCATCAAAGAGCT
GGGCAGCCAGATCCTGAAAGAACACCCCGTGGAAAACACCCAGCT
GCAGAACGAGAAGCTGTACCTGTACTACCTGCAGAATGGGCGGGA
TATGTACGTGGACCAGGAACTGGACATCAACCGGCTGTCCGACTA
CGATGTGGACCATATCGTGCCTCAGAGCTTTCTGAAGGACGACTC
CATCGACAACAAGGTGCTGACCAGAAGCGACAAGAACCGGGGCAA
GAGCGACAACGTGCCCTCCGAAGAGGTCGTGAAGAAGATGAAGAA
CTACTGGCGGCAGCTGCTGAACGCCAAGCTGATTACCCAGAGAAA
GTTCGACAATCTGACCAAGGCCGAGAGAGGCGGCCTGAGCGAACT
GGATAAGGCCGGCTTCATCAAGAGACAGCTGGTGGAAACCCGGCA
GATCACAAAGCACGTGGCACAGATCCTGGACTCCCGGATGAACAC
TAAGTACGACGAGAATGACAAGCTGATCCGGGAAGTGAAAGTGAT
CACCCTGAAGTCCAAGCTGGTGTCCGATTTCCGGAAGGATTTCCA
GTTTTACAAAGTGCGCGAGATCAACAACTACCACCACGCCCACGA
CGCCTACCTGAACGCCGTCGTGGGAACCGCCCTGATCAAAAAGTA
CCCTAAGCTGGAAAGCGAGTTCGTGTACGGCGACTACAAGGTGTA
CGACGTGCGGAAGATGATCGCCAAGAGCGAGCAGGAAATCGGCAA
GGCTACCGCCAAGTACTTCTTCTACAGCAACATCATGAACTTTTT
CAAGACCGAGATTACCCTGGCCAACGGCGAGATCCGGAAGCGGCC
TCTGATCGAGACAAACGGCGAAACCGGGGAGATCGTGTGGGATAA
GGGCCGGGATTTTGCCACCGTGCGGAAAGTGCTGAGCATGCCCCA
AGTGAATATCGTGAAAAAGACCGAGGTGCAGACAGGCGGCTTCAG
CAAAGAGTCTATCCTGCCCAAGAGGAACAGCGATAAGCTGATCGC
CAGAAAGAAGGACTGGGACCCTAAGAAGTACGGCGGCTTCGACAG
CCCCACCGTGGCCTATTCTGTGCTGGTGGTGGCCAAAGTGGAAAA
GGGCAAGTCCAAGAAACTGAAGAGTGTGAAAGAGCTGCTGGGGAT
CACCATCATGGAAAGAAGCAGCTTCGAGAAGAATCCCATCGACTT
TCTGGAAGCCAAGGGCTACAAAGAAGTGAAAAAGGACCTGATCAT
CAAGCTGCCTAAGTACTCCCTGTTCGAGCTGGAAAACGGCCGGAA
GAGAATGCTGGCCTCTGCCGGCGAACTGCAGAAGGGAAACGAACT
GGCCCTGCCCTCCAAATATGTGAACTTCCTGTACCTGGCCAGCCA
CTATGAGAAGCTGAAGGGCTCCCCCGAGGATAATGAGCAGAAACA
GCTGTTTGTGGAACAGCACAAGCACTACCTGGACGAGATCATCGA
GCAGATCAGCGAGTTCTCCAAGAGAGTGATCCTGGCCGACGCTAA
TCTGGACAAAGTGCTGTCCGCCTACAACAAGCACCGGGATAAGCC
CATCAGAGAGCAGGCCGAGAATATCATCCACCTGTTTACCCTGAC
CAATCTGGGAGCCCCTGCCGCCTTCAAGTACTTTGACACCACCAT
CGACCGGAAGAGGTACACCAGCACCAAAGAGGTGCTGGACGCCAC
CCTGATCCACCAGAGCATCACCGGCCTGTACGAGACACGGATCGA
CCTGTCTCAGCTGGGAGGCGACAGCCCCAAGAAGAAGAGAAAGGT
GGAGGCCAGCTAAGGATCCGGCAAGACTGGCCCCGCTTGGCAACG
CAACAGTGAGCCCCTCCCTAGTGTGTTTGGGGATGTGACTATGTA
TTCGTGTGTTGGCCAACGGGTCAACCCGAACAGATTGATACCCGC
CTTGGCATTTCCTGTCAGAATGTAACGTCAGTTGATGGTACT
[0363] Sequence for a cassette driving the expression of 17
polymerase under the control of beta-2 tubulin promoter, followed
by the 3' UTR of Cop1:
TABLE-US-00023 (SEQ ID NO: 276)
TCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTAGGGCGGGCTG
CGAGACGGCTTCCCGGCGCTGCATGCAACACCGATGATGCTTCGA
CCCCCCGAAGCTCCTTCGGGGCTGCATGGGCGCTCCGATGCCGCT
CCAGGGCGAGCGCTGTTTAAATAGCCAGGCCCCCGATTGCAAAGA
CATTATAGCGAGCTACCAAAGCCATATTCAAACACCTAGATCACT
ACCACTTCTACACAGGCCACTCGAGCTTGTGATCGCACTCCGCTA
AGGGGGCGCCTCTTCCTCTTCGTTTCAGTCACAACCCGCAAACat
gcctaagaagaagaggaaggttaacacgattaacatcgctaagaa
cgacttctctgacatcgaactggctgctatcccgttcaacactct
ggctgaccattacggtgagcgtttagctcgcgaacagttggccct
tgagcatgagtcttacgagatgggtgaagcacgcttccgcaagat
gtttgagcgtcaacttaaagctggtgaggttgcggataacgctgc
cgccaagcctctcatcactaccctactccctaagatgattgcacg
catcaacgactggtttgaggaagtgaaagctaagcgcggcaagcg
cccgacagccttccagttcctgcaagaaatcaagccggaagccgt
agcgtacatcaccattaagaccactctggcttgcctaaccagtgc
tgacaatacaaccgttcaggctgtagcaagcgcaatcggtcgggc
cattgaggacgaggctcgcttcggtcgtatccgtgaccttgaagc
taagcacttcaagaaaaacgttgaggaacaactcaacaagcgcgt
agggcacgtctacaagaaagcatttatgcaagttgtcgaggctga
catgctctctaagggtctactcggtggcgaggcgtggtcttcgtg
gcataaggaagactctattcatgtaggagtacgctgcatcgagat
gctcattgagtcaaccggaatggttagcttacaccgccaaaatgc
tggcgtagtaggtcaagactctgagactatcgaactcgcacctga
atacgctgaggctatcgcaacccgtgcaggtgcgctggctggcat
ctctccgatgttccaaccttgcgtagttcctcctaagccgtggac
tggcattactggtggtggctattgggctaacggtcgtcgtcctct
ggcgctggtgcgtactcacagtaagaaagcactgatgcgctacga
agacgtttacatgcctgaggtgtacaaagcgattaacattgcgca
aaacaccgcatggaaaatcaacaagaaagtcctagcggtcgccaa
cgtaatcaccaagtggaagcattgtccggtcgaggacatccctgc
gattgagcgtgaagaactcccgatgaaaccggaagacatcgacat
gaatcctgaggctctcaccgcgtggaaacgtgctgccgctgctgt
gtaccgcaaggacaaggctcgcaagtctcgccgtatcagccttga
gttcatgcttgagcaagccaataagtttgctaaccataaggccat
ctggttcccttacaacatggactggcgcggtcgtgtttacgctgt
gtcaatgttcaacccgcaaggtaacgatatgaccaaaggactgct
tacgctggcgaaaggtaaaccaatcggtaaggaaggttactactg
gctgaaaatccacggtgcaaactgtgcgggtgtcgacaaggttcc
gttccctgagcgcatcaagttcattgaggaaaaccacgagaacat
catggcttgcgctaagtctccactggagaacacttggtgggctga
gcaagattctccgttctgcttccttgcgttctgctttgagtacgc
tggggtacagcaccacggcctgagctataactgctcccttccgct
ggcgtttgacgggtcttgctctggcatccagcacttctccgcgat
gctccgagatgaggtaggtggtcgcgcggttaacttgcttcctag
tgaaaccgttcaggacatctacgggattgttgctaagaaagtcaa
cgagattctacaagcagacgcaatcaatgggaccgataacgaagt
agttaccgtgaccgatgagaacactggtgaaatctctgagaaagt
caagctgggcactaaggcactggctggtcaatggctggcttacgg
tgttactcgcagtgtgactaagcgttcagtcatgacgctggctta
cgggtccaaagagttcggcttccgtcaacaagtgctggaagatac
cattcagccagctattgattccggcaagggtctgatgttcactca
gccgaatcaggctgctggatacatggctaagctgatttgggaatc
tgtgagcgtgacggtggtagctgcggttgaagcaatgaactggct
taagtctgctgctaagctgctggctgctgaggtcaaagataagaa
gactggagagattcttcgcaagcgttgcgctgtgcattgggtaac
tcctgatggtttccctgtgtggcaggaatacaagaagcctattca
gacgcgcttgaacctgatgttcctcggtcagttccgcttacagcc
taccattaacaccaacaaagatagcgagattgatgcacacaaaca
ggagtctggtatcgctcctaacttgtacacagccaagacggtagc
caccttcgtaagactgtagtgtgggcacacgagaagtacggaatc
gaatcttttgcactgattcacgactccttcggtacgattccggct
gacgctgcgaacctgttcaaagcagtgcgcgaaactatggttgac
acatatgagtcttgtgatgtactggctgatttctacgaccagttc
gctgaccagttgcacgagtctcaattggacaaaatgccagcactt
ccggctaaaggtaacttgaacctccgtgacatcttagagtcggac
ttcgcgttcgcgtaaGGATCCGGCAAGACTGGCCCCGCTTGGCAA
CGCAACAGTGAGCCCCTCCCTAGTGTGTTTGGGGATGTGACTATG
TATTCGTGTGTTGGCCAACGGGTCAACCCGAACAGATTGATACCC
GCCTTGGCATTTCCTGTCAGAATGTAACGTCAGTTGATGGTACT
[0364] Sequence of guide RNA driven In 7 promoter (T7 promoter, Ns
represent targeting sequence):
TABLE-US-00024 (SEQ ID NO: 277)
gaaatTAATACGACTCACTATANNNNNNNNNNNNNNNNNNNNgtt
ttagagctaGAAAtagcaagttaaaataaggctagtccgttatca
acttgaaaaagtggcaccgagtcggtgcttttttt
[0365] Gene Delivery:
[0366] Chlamydomonas reinhardtii strain CC-124 and CC-125 from the
Chlamydomonas Resource Center will be used for electroporation.
Electroporation protocol follows standard recommended protocol from
the GeneArt Chlamydomonas Engineering kit.
[0367] Also, Applicants generate a line of Chlamydomonas
reinhardtii that expresses Cas9 constitutively. This can be done by
using pChlamyl (linearized using PvuI) and selecting for hygromycin
resistant colonies. Sequence for pChlamyl containing Cas9 is below.
In this way to achieve gene knockout one simply needs to deliver
RNA for the guideRNA. For homologous recombination Applicants
deliver guideRNA as well as a linearized homologous recombination
template.
TABLE-US-00025 pChlamy1-Cas9: (SEQ ID NO: 278)
TGCGGTATTTCACACCGCATCAGGTGGCACTTTTCGGGGAAATGT
GCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATAT
GTATCCGCTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCT
TTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGA
GTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACC
TATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACT
CCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGG
CCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCC
AGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAG
AAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTG
TTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCG
CAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTC
GTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCG
AGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTT
CGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATC
ACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCC
ATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTC
ATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGC
GTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGT
GCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGAT
CTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACC
CAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTG
AGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGC
GACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTA
TTGAAGCATTTATCAGGGTTATTGTCTCATGACCAAAATCCCTTA
ACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGAT
CAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTG
CTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCC
GGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAG
CAGAGCGCAGATACCAAATACTGTTCTTCTAGTGTAGCCGTAGTT
AGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGC
TCTGCTAATCCTGTTACCAGTGGCTGTTGCCAGTGGCGATAAGTC
GTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGC
GCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTT
GGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCT
ATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTA
TCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCT
TCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCG
CCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGG
GCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTT
CCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTT
ATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGC
TGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGT
GAGCGAGGAAGCGGTCGCTGAGGCTTGACATGATTGGTGCGTATG
TTTGTATGAAGCTACAGGACTGATTTGGCGGGCTATGAGGGCGGG
GGAAGCTCTGGAAGGGCCGCGATGGGGCGCGCGGCGTCCAGAAGG
CGCCATACGGCCCGCTGGCGGCACCCATCCGGTATAAAAGCCCGC
GACCCCGAACGGTGACCTCCACTTTCAGCGACAAACGAGCACTTA
TACATACGCGACTATTCTGCCGCTATACATAACCACTCAGCTAGC
TTAAGATCCCATCAAGCTTGCATGCCGGGCGCGCCAGAAGGAGCG
CAGCCAAACCAGGATGATGTTTGATGGGGTATTTGAGCACTTGCA
ACCCTTATCCGGAAGCCCCCTGGCCCACAAAGGCTAGGCGCCAAT
GCAAGCAGTTCGCATGCAGCCCCTGGAGCGGTGCCCTCCTGATAA
ACCGGCCAGGGGGCCTATGTTCTTTACTTTTTTACAAGAGAAGTC
ACTCAACATCTTAAAATGGCCAGGTGAGTCGACGAGCAAGCCCGG
CGGATCAGGCAGCGTGCTTGCAGATTTGACTTGCAACGCCCGCAT
TGTGTCGACGAAGGCTTTTGGCTCCTCTGTCGCTGTCTCAAGCAG
CATCTAACCCTGCGTCGCCGTTTCCATTTGCAGGAGATTCGAGGT
ACCATGTACCCATACGATGTTCCAGATTACGCTTCGCCGAAGAAA
AAGCGCAAGGTCGAAGCGTCCGACAAGAAGTACAGCATCGGCCTG
GACATCGGCACCAACTCTGTGGGCTGGGCCGTGATCACCGACGAG
TACAAGGTGCCCAGCAAGAAATTCAAGGTGCTGGGCAACACCGAC
CGGCACAGCATCAAGAAGAACCTGATCGGAGCCCTGCTGTTCGAC
AGCGGCGAAACAGCCGAGGCCACCCGGCTGAAGAGAACCGCCAGA
AGAAGATACACCAGACGGAAGAACCGGATCTGCTATCTGCAAGAG
ATCTTCAGCAACGAGATGGCCAAGGTGGACGACAGCTTCTTCCAC
AGACTGGAAGAGTCCTTCCTGGTGGAAGAGGATAAGAAGCACGAG
CGGCACCCCATCTTCGGCAACATCGTGGACGAGGTGGCCTACCAC
GAGAAGTACCCCACCATCTACCACCTGAGAAAGAAACTGGTGGAC
AGCACCGACAAGGCCGACCTGCGGCTGATCTATCTGGCCCTGGCC
CACATGATCAAGTTCCGGGGCCACTTCCTGATCGAGGGCGACCTG
AACCCCGACAACAGCGACGTGGACAAGCTGTTCATCCAGCTGGTG
CAGACCTACAACCAGCTGTTCGAGGAAAACCCCATCAACGCCAGC
GGCGTGGACGCCAAGGCCATCCTGTCTGCCAGACTGAGCAAGAGC
AGACGGCTGGAAAATCTGATCGCCCAGCTGCCCGGCGAGAAGAAG
AATGGCCTGTTCGGCAACCTGATTGCCCTGAGCCTGGGCCTGACC
CCCAACTTCAAGAGCAACTTCGACCTGGCCGAGGATGCCAAACTG
CAGCTGAGCAAGGACACCTACGACGACGACCTGGACAACCTGCTG
GCCCAGATCGGCGACCAGTACGCCGACCTGTTTCTGGCCGCCAAG
AACCTGTCCGACGCCATCCTGCTGAGCGACATCCTGAGAGTGAAC
ACCGAGATCACCAAGGCCCCCCTGAGCGCCTCTATGATCAAGAGA
TACGACGAGCACCACCAGGACCTGACCCTGCTGAAAATCTGATCG
CCCAGCTGCCCGGCGAGAAGAAGAATGGCCTGTTCGGCAACCTGA
TTGCCCTGAGCCTGGGCCTGACCCCCAACTTCAAGAGCAACTTCG
ACCTGGCCGAGGATGCCAAACTGCAGCTGAGCAAGGACACCTACG
ACGACGACCTGGACAACCTGCTGGCCCAGATCGGCGACCAGTACG
CCGACCTGTTTCTGGCCGCCAAGAACCTGTCCGACGCCATCCTGC
TGAGCGACATCCTGAGAGTGAACACCGAGATCACCAAGGCCCCCC
TGAGCGCCTCTATGATCAAGAGATACGACGAGCACCACCAGGACC
TGACCCTGCTGAAAGCTCTCGTGCGGCAGCAGCTGCCTGAGAAGT
ACAAAGAGATTTTCTTCGACCAGAGCAAGAACGGCTACGCCGGCT
ACATTGACGGCGGAGCCAGCCAGGAAGAGTTCTACAAGTTCATCA
AGCCCATCCTGGAAAAGATGGACGGCACCGAGGAACTGCTCGTGA
AGCTGAACAGAGAGGACCTGCTGCGGAAGCAGCGGACCTTCGACA
ACGGCAGCATCCCCCACCAGATCCACCTGGGAGAGCTGCACGCCA
TTCTGCGGCGGCAGGAAGATTTTTACCCATTCCTGAAGGACAACC
GGGAAAAGATCGAGAAGATCCTGACCTTCCGCATCCCCTACTACG
TGGGCCCTCTGGCCAGGGGAAACAGCAGATTCGCCTGGATGACCA
GAAAGAGCGAGGAAACCATCACCCCCTGGAACTTCGAGGAAGTGG
TGGACAAGGGCGCTTCCGCCCAGAGCTTCATCGAGCGGATGACCA
ACTTCGATAAGAACCTGCCCAACGAGAAGGTGCTGCCCAAGCACA
GCCTGCTGTACGAGTACTTCACCGTGTATAACGAGCTGACCAAAG
TGAAATACGTGACCGAGGGAATGAGAAAGCCCGCCTTCCTGAGCG
GCGAGCAGAAAAAGGCCATCGTGGACCTGCTGTTCAAGACCAACC
GGAAAGTGACCGTGAAGCAGCTGAAAGAGGACTACTTCAAGAAAA
TCGAGTGCTTCGACTCCGTGGAAATCTCCGGCGTGGAAGATCGGT
TCAACGCCTCCCTGGGCACATACCACGATCTGCTGAAAATTATCA
AGGACAAGGACTTCCTGGACAATGAGGAAAACGAGGACATTCTGG
AAGATATCGTGCTGACCCTGACACTGTTTGAGGACAGAGAGATGA
TCGAGGAACGGCTGAAAACCTATGCCCACCTGTTCGACGACAAAG
TGATGAAGCAGCTGAAGCGGCGGAGATACACCGGCTGGGGCAGGC
TGAGCCGGAAGCTGATCAACGGCATCCGGGACAAGCAGTCCGGCA
AGACAATCCTGGATTTCCTGAAGTCCGACGGCTTCGCCAACAGAA
ACTTCATGCAGCTGATCCACGACGACAGCCTGACCTTTAAAGAGG
ACATCCAGAAAGCCCAGGTGTCCGGCCAGGGCGATAGCCTGCACG
AGCACATTGCCAATCTGGCCGGCAGCCCCGCCATTAAGAAGGGCA
TCCTGCAGACAGTGAAGGTGGTGGACGAGCTCGTGAAAGTGATGG
GCCGGCACAACTCCCGAGAACATCGTGATCGAAATGGCCAGAGAG
AACCAGACCACCCAGAAGGGACAGAAGAACAGCCGCGAGAGAATG
AAGCGGATCGAAGAGGGCATCAAAGAGCTGGGCAGCCAGATCCTG
AAAGAACACCCCGTGGAAAACACCCAGCTGCAGAACGAGAAGCTG
TACCTGTACTACCTGCAGAATGGGCGGGATATGTACGTGGACCAG
GAACTGGACATCAACCGGCTGTCCGACTACGATGTGGACCATATC
GTGCCTCAGAGCTTTCTGAAGGACGACTCCATCGACAACAAGGTG
CTGACCAGAAGCGACAAGAACCGGGGCAAGAGCGACAACGTGCCC
TCCGAAGAGGTCGTGAAGAAGATGAAGAACTACTGGCGGCAGCTG
CTGAACGCCAAGCTGATTACCCAGAGAAAGTTCGACAATCTGACC
AAGGCCGAGAGAGGCGGCCTGAGCGAACTGGATAAGGCCGGCTTC
ATCAAGAGACAGCTGGTGGAAACCCGGCAGATCACAAAGCACGTG
GCACAGATCCTGGACTCCCGGATGAACACTAAGTACGACGAGAAT
GACAAGCTGATCCGGGAAGTGAAAGTGATCACCCTGAAGTCCAAG
CTGGTGTCCGATTTCCGGAAGGATTTCCAGTTTTACAAAGTGCGC
GAGATCAACAACTACCACCACGCCCACGACGCCTACCTGAACGCC
GTCGTGGGAACCGCCCTGATCAAAAAGTACCCTAAGCTGGAAAGC
GAGTTCGTGTACGGCGACTACAAGGTGTACGACGTGCGGAAGATG
ATCGCCAAGAGCGAGCAGGAAATCGGCAAGGCTACCGCCAAGTAC
TTCTTCTACAGCAACATCATGAACTTTTTCAAGACCGAGATTACC
CTGGCCAACGGCGAGATCCGGAAGCGGCCTCTGATCGAGACAAAC
GGCGAAACCGGGGAGATCGTGTGGGATAAGGGCCGGGATTTTGCC
ACCGTGCGGAAAGTGCTGAGCATGCCCCAAGTGAATATCGTGAAA
AAGACCGAGGTGCAGACAGGCGGCTTCAGCAAAGAGTCTATCCTG
CCCAAGAGGAACAGCGATAAGCTGATCGCCAGAAAGAAGGACTGG
GACCCTAAGAAGTACGGCGGCTTCGACAGCCCCACCGTGGCCTAT
TCTGTGCTGGTGGTGGCCAAAGTGGAAAAGGGCAAGTCCAAGAAA
CTGAAGAGTGTGAAAGAGCTGCTGGGGATCACCATCATGGAAAGA
AGCAGCTTCGAGAAGAATCCCATCGACTTTCTGGAAGCCAAGGGC
TACAAAGAAGTGAAAAAGGACCTGATCATCAAGCTGCCTAAGTAC
TCCCTGTTCGAGCTGGAAAACGGCCGGAAGAGAATGCTGGCCTCT
GCCGGCGAACTGCAGAAGGGAAACGAACTGGCCCTGCCCTCCAAA
TATGTGAACTTCCTGTACCTGGCCAGCCACTATGAGAAGCTGAAG
GGCTCCCCCGAGGATAATGAGCAGAAACAGCTGTTTGTGGAACAG
CACAAGCACTACCTGGACGAGATCATCGAGCAGATCAGCGAGTTC
TCCAAGAGAGTGATCCTGGCCGACGCTAATCTGGACAAAGTGCTG
TCCGCCTACAACAAGCACCGGGATAAGCCCATCAGAGAGCAGGCC
GAGAATATCATCCACCTGTTTACCCTGACCAATCTGGGAGCCCCT
GCCGCCTTCAAGTACTTTGACACCACCATCGACCGGAAGAGGTAC
ACCAGCACCAAAGAGGTGCTGGACGCCACCCTGATCCACCAGAGC
ATCACCGGCCTGTACGAGACACGGATCGACCTGTCTCAGCTGGGA
GGCGACAGCCCCAAGAAGAAGAGAAAGGTGGAGGCCAGCTAACAT
ATGATTCGAATGTCTTTCTTGCGCTATGACACTTCCAGCAAAAGG
TAGGGCGGGCTGCGAGACGGCTTCCCGGCGCTGCATGCAACACCG
ATGATGCTTCGACCCCCCGAAGCTCCTTCGGGGCTGCATGGGCGC
TCCGATGCCGCTCCAGGGCGAGCGCTGTTTAAATAGCCAGGCCCC
CGATTGCAAAGACATTATAGCGAGCTACCAAAGCCATATTCAAAC
ACCTAGATCACTACCACTTCTACACAGGCCACTCGAGCTTGTGAT
CGCACTCCGCTAAGGGGGCGCCTCTTCCTCTTCGTTTCAGTCACA
ACCCGCAAACATGACACAAGAATCCCTGTTACTTCTCGACCGTAT
TGATTCGGATGATTCCTACGCGAGCCTGCGGAACGACCAGGAATT
CTGGGAGGTGAGTCGACGAGCAAGCCCGGCGGATCAGGCAGCGTG
CTTGCAGATTTGACTTGCAACGCCCGCATTGTGTCGACGAAGGCT
TTTGGCTCCTCTGTCGCTGTCTCAAGCAGCATCTAACCCTGCGTC
GCCGTTTCCATTTGCAGCCGCTGGCCCGCCGAGCCCTGGAGGAGC
TCGGGCTGCCGGTGCCGCCGGTGCTGCGGGTGCCCGGCGAGAGCA
CCAACCCCGTACTGGTCGGCGAGCCCGGCCCGGTGATCAAGCTGT
TCGGCGAGCACTGGTGCGGTCCGGAGAGCCTCGCGTCGGAGTCGG
AGGCGTACGCGGTCCTGGCGGACGCCCCGGTGCCGGTGCCCCGCC
TCCTCGGCCGCGGCGAGCTGCGGCCCGGCACCGGAGCCTGGCCGT
GGCCCTACCTGGTGATGAGCCGGATGACCGGCACCACCTGGCGGT
CCGCGATGGACGGCACGACCGACCGGAACGCGCTGCTCGCCCTGG
CCCGCGAACTCGGCCGGGTGCTCGGCCGGCTGCACAGGGTGCCGC
TGACCGGGAACACCGTGCTCACCCCCCATTCCGAGGTCTTCCCGG
AACTGCTGCGGGAACGCCGCGCGGCGACCGTCGAGGACCACCGCG
GGTGGGGCTACCTCTCGCCCCGGCTGCTGGACCGCCTGGAGGACT
GGCTGCCGGACGTGGACACGCTGCTGGCCGGCCGCGAACCCCGGT
TCGTCCACGGCGACCTGCACGGGACCAACATCTTCGTGGACCTGG
CCGCGACCGAGGTCACCGGGATCGTCGACTTCACCGACGTCTATG
CGGGAGACTCCCGCTACAGCCTGGTGCAACTGCATCTCAACGCCT
TCCGGGGCGACCGCGAGATCCTGGCCGCGCTGCTCGACGGGGCGC
AGTGGAAGCGGACCGAGGACTTCGCCCGCGAACTGCTCGCCTTCA
CCTTCCTGCACGACTTCGAGGTGTTCGAGGAGACCCCGCTGGATC
TCTCCGGCTTCACCGATCCGGAGGAACTGGCGCAGTTCCTCTGGG
GGCCGCCGGACACCGCCCCCGGCGCCTGATAAGGATCCGGCAAGA
CTGGCCCCGCTTGGCAACGCAACAGTGAGCCCCTCCCTAGTGTGT
TTGGGGATGTGACTATGTATTCGTGTGTTGGCCAACGGGTCAACC
CGAACAGATTGATACCCGCCTTGGCATTTCCTGTCAGAATGTAAC GTCAGTTGATGGTACT
[0368] For all modified Chlatnydomonas reinhardtii cells,
Applicants used PCR, SURVEYOR nuclease assay, and DNA sequencing to
verify successful modification.
Example 16
Use of Cas9 as a Transcriptional Repressor in Bacteria
[0369] The ability to artificially control transcription is
essential both to the study of gene function and to the
construction of synthetic gene networks with desired properties.
Applicants describe here the use of the RNA-guided Cas9 protein as
a programmable transcriptional repressor.
[0370] Applicants have previously demonstrated how the Cas9 protein
of Streptococcus pyogenes SF370 can be used to direct genome
editing in Streptococcus pneumoniae. In this study Applicants
engineered the crR6Rk strain containing a minimal CRISPR system,
consisting of cas9, the tracrRNA and a repeat. The DIOA-H840
mutations were introduced into cas9 in this strain, giving strain
crR6Rk**. Four spacers targeting different positions of the bga4
P3-galactosidase gene promoter were cloned in the CRISPR array
carried by the previously described pDB98 plasmid. Applicants
observed a X to Y fold reduction in j3-galactosidase activity
depending on the targeted position, demonstrating the potential of
Cas9 as a programmable repressor (FIG. 73).
[0371] To achieve Cas9** repression in Escherichia coli a green
fluorescence protein (GFP) reporter plasimd (pDB127) was
constructred to express the gfpmu12 gene from a constituitive
promoter. The promoter was designed to carry several NPP PAMs on
both strands, to measure the effect of Cas9** binding at various
positions. Applicants introduced the D10A-H840 mutations into
pCas9, a plasmid described carrying the tracrRNA, cas9 and a
minimal CRISPR array designed for the easy cloning of new spacers.
Twenty-two different spacers were designed to target different
regions of the gfpmut2 promoter and open reading frame. An
approximately 20-fold reduction of fluorescence of was observed
upon targeting regions overlapping or adjacent to the -35 and -10
promoter elements and to the Shine-Dalgarno sequence. Targets on
both strands showed similar repression levels. These results
suggest that the binding of Cas9** to any position of the promoter
region prevents transcription initiation, presumably through steric
inhibition of RNAP binding.
[0372] To determine whether Cas9** could prevent transcription
elongation, Applicants directed it to the reading frame of gpfmut2.
A reduction in fluorescence was observed both when the coding and
non-coding strands where targeted, suggesting that Cas9 binding is
actually strong enough to represent an obstacle to the running
RNAP. However, while a 40% reduction in expression was observed
when the coding strand was the target, a 20-fold reduction was
observed for the non-coding strand (FIG. 21b, compare T9, T10 and
T11 to B9, B10 and B11). To directly determine the effects of
Cas9** binding on transcription, Applicants extracted RNA from
strains carrying either the T5, T10, B10 or a control construct
that does not target pDB127 and subjected it to Northern blot
analysis using either a probe binding before (B477) or after (B510)
the B10 and T10 target sites. Consistent with Applicants'
fluorescence methods, no g4)mut2 transcription was detected when
Cas9** was directed to the promoter region (T5 target) and a
transcription was observed after the targeting of the T10 region.
Interestingly, a smaller transcript was observed with the B477
probe. This band corresponds to the expected size of a transcript
that would be interrupted by Cas9**, and is a direct indication of
a transcriptional termination caused by dgRNA::Cas9** binding to
the coding strand. Surprisingly, Applicants detected no transcript
when the non-coding strand was targeted (B10). Since Cas9** binding
to the B10 region is unlikely to interfere with transcription
initiation, this result suggests that the mRNA was degraded.
DgRNA::Cas9 was shown to bind ssRNA in vitro. Applicants speculate
that binding may trigger degradation of the mRNA by host nucleases.
Indeed, ribosome stalling can induce cleavage on the translated
mRNA in E. coli.
[0373] Some applications require a precise tuning gene expression
rather than its complete repression. Applicants sought to achieve
intermediate repression levels through the introduction of
mismatches that will weaken the crRNA/target interactions.
Applicants created a series of spacers based on the B1, T5 and B10
constructs with increasing numbers of mutations in the 5' end of
the crRNA. Up to 8 mutations in B1 and T5 did not affect the
repression level, and a progressive increased in fluorescence was
observed for additional mutations.
[0374] The observed repression with only an 8 nt match between the
crRNA and its target raises the question of off-targeting effects
of the use of Cas9** as a transcriptional regulator. Since a good
PAM (NGG) is also required for Cas9 binding, the number of
nucleotides to match to obtain some level of respiration is 10. A
10 nt match occurs randomly once every .about.1 Mbp, and such sites
are thus likely to be found even in small bacterial genomes.
However, to effectively repress transcription, such site needs to
be in the promoter region of gene, which makes off-targeting much
less likely. Applicants also showed that gene expression can be
affected if the non-coding strand of a gene is targeted. For this
to happen, a random target would have to be in the right
orientation, but such events relatively more likely to happen. As a
matter of fact, during the course of this study Applicants were
unable to construct one of the designed spacer on pCas9**.
Applicants later found this spacer showed a 12 bp match next to a
good PAM in the essential murC gene. Such off-targeting could
easily be avoided by a systematic blast of the designed
spacers.
[0375] Aspects of the invention are further described in the
following numbered paragraphs:
[0376] 1. A vector system comprising one or more vectors, wherein
the system comprises
[0377] a. a first regulatory element operably linked to a traer
mate sequence and one or more insertion sites for inserting a guide
sequence upstream of the traer mate sequence, wherein when
expressed, the guide sequence directs sequence-specific binding of
a CRISPR complex to a target sequence in a eukaryotic cell, wherein
the CRISPR complex comprises a CRISPR enzyme complexed with (1) the
guide sequence that is hybridized to the target sequence, and (2)
the traer mate sequence that is hybridized to the traer sequence;
and
[0378] b. a second regulatory element operably linked to an
enzyme-coding sequence encoding said CRISPR enzyme comprising a
nuclear localization sequence;
[0379] wherein components (a) and (b) are located on the same or
different vectors of the system.
[0380] 2. The vector system of paragraph 1, wherein component (a)
further comprises the traer sequence downstream of the traer mate
sequence under the control of the first regulatory element.
[0381] 3. The vector system of paragraph 1, wherein component (a)
further comprises two or more guide sequences operably linked to
the first regulatory element, wherein when expressed, each of the
two or more guide sequences direct sequence specific binding of a
CRISPR complex to a different target sequence in a eukaryotic
cell.
[0382] 4. The vector system of paragraph 1, wherein the system
comprises the traer sequence under the control of a third
regulatory element.
[0383] 5. The vector system of paragraph 1, wherein the traer
sequence exhibits at least 50% of sequence complementarity along
the length of the traer mate sequence when optimally aligned.
[0384] 6. The vector system of paragraph 1, wherein the CRISPR
enzyme comprises one or more nuclear localization sequences of
sufficient strength to drive accumulation of said CRISPR enzyme in
a detectable amount in the nucleus of a eukaryotic cell.
[0385] 7. The vector system of paragraph 1, wherein the CRISPR
enzyme is a type II CRISPR system enzyme.
[0386] 8. The vector system of paragraph 1, wherein the CRISPR
enzyme is a Cas9 enzyme.
[0387] 9. The vector system of paragraph 1, wherein the CRISPR
enzyme is codon-optimized for expression in a eukaryotic cell.
[0388] 10. The vector system of paragraph 1, wherein the CRISPR
enzyme directs cleavage of one or two strands at the location of
the target sequence.
[0389] 11. The vector system of paragraph 1, wherein the CRISPR
enzyme lacks DNA strand cleavage activity.
[0390] 12. The vector system of paragraph 1, wherein the first
regulatory element is a polymerase III promoter.
[0391] 13. The vector system of paragraph 1, wherein the second
regulatory element is a polymerase II promoter.
[0392] 14. The vector system of paragraph 4, wherein the third
regulatory element is a polymerase III promoter.
[0393] 15. The vector system of paragraph 1, wherein the guide
sequence is at least 15 nucleotides in length.
[0394] 16. The vector system of paragraph 1, wherein fewer than 50%
of the nucleotides of the guide sequence participate in
self-complementary base-pairing when optimally folded.
[0395] 17. A vector comprising a regulatory element operably linked
to an enzyme-coding sequence encoding a CRISPR enzyme comprising
one or more nuclear localization sequences, wherein said regulatory
element drives transcription of the CRISPR enzyme in a eukaryotic
cell such that said CRISPR enzyme accumulates in a detectable
amount in the nucleus of the eukaryotic cell.
[0396] 18. The vector of paragraph 17, wherein said regulatory
element is a polymerase II promoter.
[0397] 19. The vector of paragraph 17, wherein said CRISPR enzyme
is a type IICRISPR system enzyme.
[0398] 20. The vector of paragraph 17, wherein said CRISPR enzyme
is a Cas9 enzyme.
[0399] 21. The vector of paragraph 17, wherein said CRISPR enzyme
lacks the ability to cleave one or more strands of a target
sequence to which it binds.
[0400] 22. A CRISPR enzyme comprising one or more nuclear
localization sequences of sufficient strength to drive accumulation
of said CRISPR enzyme in a detectable amount in the nucleus of a
eukaryotic cell.
[0401] 23. The CRISPR enzyme of paragraph 22, wherein said CRISPR
enzyme is a type IICRISPR system enzyme.
[0402] 24. The CRISPR enzyme of paragraph 22, wherein said CRISPR
enzyme is a Cas9 enzyme.
[0403] 25. The CRISPR enzyme of paragraph 22, wherein said CRISPR
enzyme lacks the ability to cleave one or more strands of a target
sequence to which it binds.
[0404] 26. A eukaryotic host cell comprising:
[0405] a. a first regulatory element operably linked to a traer
mate sequence and one or more insertion sites for inserting a guide
sequence upstream of the traer mate sequence, wherein when
expressed, the guide sequence directs sequence-specific binding of
a CRISPR complex to a target sequence in a eukaryotic cell, wherein
the CRISPR complex comprises a CRISPR enzyme complexed with (1) the
guide sequence that is hybridized to the target sequence, and (2)
the traer mate sequence that is hybridized to the traer sequence;
and/or
[0406] b. a second regulatory element operably linked to an
enzyme-coding sequence encoding said CRISPR enzyme comprising a
nuclear localization sequence.
[0407] 27. The eukaryotic host cell of paragraph 26, wherein said
host cell comprises components (a) and (b).
[0408] 28. The eukaryotic host cell of paragraph 26, wherein
component (a), component (b), or components (a) and (b) are stably
integrated into a genome of the host eukaryotic cell.
[0409] 29. The eukaryotic host cell of paragraph 26, wherein
component (a) further comprises the traer sequence downstream of
the traer mate sequence under the control of the first regulatory
element.
[0410] 30. The eukaryotic host cell of paragraph 26, wherein
component (a) further comprises two or more guide sequences
operably linked to the first regulatory element, wherein when
expressed, each of the two or more guide sequences direct sequence
specific binding of a CRISPR complex to a different target sequence
in a eukaryotic cell.
[0411] 31. The eukaryotic host cell of paragraph 26, further
comprising a third regulatory element operably linked to said traer
sequence.
[0412] 32. The eukaryotic host cell of paragraph 26, wherein the
traer sequence exhibits at least 50% of sequence complementarity
along the length of the traer mate sequence when optimally
aligned.
[0413] 33. The eukaryotic host cell of paragraph 26, wherein the
CRISPR enzyme comprises one or more nuclear localization sequences
of sufficient strength to drive accumulation of said CRISPR enzyme
in a detectable mount in the nucleus of a eukaryotic cell.
[0414] 34. The eukaryotic host cell of paragraph 26, wherein the
CRISPR enzyme is a type II CRISPR system enzyme.
[0415] 35. The eukaryotic host cell of paragraph 26, wherein the
CRISPR enzyme is a Cas9 enzyme.
[0416] 36. The eukaryotic host cell of paragraph 26, wherein the
CRISPR enzyme is codon-optimized for expression in a eukaryotic
cell.
[0417] 37. The eukaryotic host cell of paragraph 26, wherein the
CRISPR enzyme directs cleavage of one or two strands at the
location of the target sequence.
[0418] 38. The eukaryotic host cell of paragraph 26, wherein the
CRISPR enzyme lacks DNA strand cleavage activity.
[0419] 39. The eukaryotic host cell of paragraph 26, wherein the
first regulatory element is a polymerase III promoter.
[0420] 40. The eukaryotic host cell of paragraph 26, wherein the
second regulatory element is a polymerase II promoter.
[0421] 41. The eukaryotic host cell of paragraph 31, wherein the
third regulatory element is a polymerase III promoter.
[0422] 42. The eukaryotic host cell of paragraph 26, wherein the
guide sequence is at least 15 nucleotides in length.
[0423] 43. The eukaryotic host cell of paragraph 26, wherein fewer
than 50% of the nucleotides of the guide sequence participate in
self-complementary base-pairing when optimally folded.
[0424] 44. A non-human animal comprising a eukaryotic host cell of
any one of paragraphs 26-43.
[0425] 45. A kit comprising a vector system and instructions for
using said kit, the vector system comprising:
[0426] a. a first regulatory element operably linked to a traer
mate sequence and one or more insertion sites for inserting a guide
sequence upstream of the traer mate sequence, wherein when
expressed, the guide sequence directs sequence-specific binding of
a CRISPR complex to a target sequence in a eukaryotic cell, wherein
the CRISPR complex comprises a CRISPR enzyme complexed with (1) the
guide sequence that is hybridized to the target sequence, and (2)
the traer mate sequence that is hybridized to the traer sequence;
and/or
[0427] b. a second regulatory element operably linked to an
enzyme-coding sequence encoding said CRISPR enzyme comprising a
nuclear localization sequence.
[0428] 46. The kit of paragraph 45, wherein said kit comprises
components (a) and (b) located on the same or different vectors of
the system.
[0429] 47. The kit of paragraph 45, wherein component (a) further
comprises the traer sequence downstream of the traer mate sequence
under the control of the first regulatory element.
[0430] 48. The kit of paragraph 45, wherein component (a) further
comprises two or more guide sequences operably linked to the first
regulatory element, wherein when expressed, each of the two or more
guide sequences direct sequence specific binding of a CRISPR
complex to a different target sequence in a eukaryotic cell.
[0431] 49. The kit of paragraph 45, wherein the system comprises
the traer sequence under the control of a third regulatory
element.
[0432] 50. The kit of paragraph 45, wherein the traer sequence
exhibits at least 50% of sequence complementarity along the length
of the traer mate sequence when optimally aligned.
[0433] 51. The kit of paragraph 45, wherein the CRISPR enzyme
comprises one or more nuclear localization sequences of sufficient
strength to drive accumulation of said CRISPR enzyme in a
detectable mount in the nucleus of a eukaryotic cell.
[0434] 52. The kit of paragraph 45, wherein the CRISPR enzyme is a
type II CRISPR system enzyme.
[0435] 53. The kit of paragraph 45, wherein the CRISPR enzyme is a
Cas9 enzyme.
[0436] 54. The kit of paragraph 45, wherein the CRISPR enzyme is
codon-optimized for expression in a eukaryotic cell.
[0437] 55. The kit of paragraph 45, wherein the CRISPR enzyme
directs cleavage of one or two strands at the location of the
target sequence.
[0438] 56. The kit of paragraph 45, wherein the CRISPR enzyme lacks
DNA strand cleavage activity.
[0439] 57. The kit of paragraph 45, wherein the first regulatory
element is a polymerase III promoter.
[0440] 58. The kit of paragraph 45, wherein the second regulatory
element is a polymerase II promoter.
[0441] 59. The kit of paragraph 49, wherein the third regulatory
element is a polymerase III promoter.
[0442] 60. The kit of paragraph 45, wherein the guide sequence is
at least 15 nucleotides in length.
[0443] 61. The kit of paragraph 45, wherein fewer than 50% of the
nucleotides of the guide sequence participate in self-complementary
base-pairing when optimally folded.
[0444] 62. A computer system for selecting a candidate target
sequence within a nucleic acid sequence in a eukaryotic cell for
targeting by a CRISPR complex, the system comprising:
[0445] a. a memory unit configured to receive and/or store said
nucleic acid sequence; and
[0446] b. one or more processors alone or in combination programmed
to (i) locate a CRISPR motif sequence within said nucleic acid
sequence, and (ii) select a sequence adjacent to said located
CRISPR motif sequence as the candidate target sequence to which the
CRISPR complex binds.
[0447] 63. The computer system of paragraph 62, wherein said
locating step comprises identifying a CRISPR motif sequence located
less than about 500 nucleotides away from said target sequence.
[0448] 64. The computer system of paragraph 62, wherein said
candidate target sequence is at least 10 nucleotides in length.
[0449] 65. The computer system of paragraph 62, wherein the
nucleotide at the 3' end of the candidate target sequence is
located no more than about 10 nucleotides upstream of the CRISPR
motif sequence.
[0450] 66. The computer system of paragraph 62, wherein the nucleic
acid sequence in the eukaryotic cell is endogenous to the
eukaryotic genome.
[0451] 67. The computer system of claim 62, wherein the nucleic
acid sequence in the eukaryotic cell is exogenous to the eukaryotic
genome.
[0452] 68. A computer-readable medium comprising codes that, upon
execution by one or more processors, implements a method of
selecting a candidate target sequence within a nucleic acid
sequence in a eukaryotic cell for targeting by a CRISPR complex,
said method comprising: (a) locating a CRISPR motif sequence within
said nucleic acid sequence, and (b) selecting a sequence adjacent
to said located CRISPR motif sequence as the candidate target
sequence to which the CRISPR complex binds.
[0453] 69. The computer-readable medium of paragraph 68, wherein
said locating comprises locating a CRISPR motif sequence that is
less than about 500 nucleotides away from said target sequence.
[0454] 70. The computer-readable of paragraph 68, wherein said
candidate target sequence is at least 10 nucleotides in length.
[0455] 71. The computer-readable of paragraph 68, wherein the
nucleotide at the 3' end of the candidate target sequence is
located no more than about 10 nucleotides upstream of the CRISPR
motif sequence.
[0456] 72. The computer-readable of paragraph 68, wherein the
nucleic acid sequence in the eukaryotic cell is endogenous the
eukaryotic genome.
[0457] 73. The computer-readable of paragraph 68, wherein the
nucleic acid sequence in the eukaryotic cell is exogenous to the
eukaryotic genome.
[0458] 74. A method of modifying a target polynucleotide in a
eukaryotic cell, the method comprising allowing a CRISPR complex to
bind to the target polynucleotide to effect cleavage of said target
polynucleotide thereby modifying the target polynucleotide, wherein
the CRISPR complex comprises a CRISPR enzyme complexed with a guide
sequence hybridized to a target sequence within said target
polynucleotide, wherein said guide sequence is linked to a traer
mate sequence which in tum hybridizes to a traer sequence.
[0459] 75. The method of paragraph 74, wherein said cleavage
comprises cleaving one or two strands at the location of the target
sequence by said CRISPR enzyme.
[0460] 76. The method of paragraph 74, wherein said cleavage
results in decreased transcription of a target gene.
[0461] 77. The method of paragraph 74, further comprising repairing
said cleaved target polynucleotide by homologous recombination with
an exogenous template polynucleotide, wherein said repair results
in a mutation comprising an insertion, deletion, or substitution of
one or more nucleotides of said target polynucleotide.
[0462] 78. The method of paragraph 77, wherein said mutation
results in one or more amino acid changes in a protein expressed
from a gene comprising the target sequence.
[0463] 79. The method of paragraph 74, further comprising
delivering one or more vectors to said eukaryotic cell, wherein the
one or more vectors drive expression of one or more of: the CRISPR
enzyme, the guide sequence linked to the traer mate sequence, and
the traer sequence.
[0464] 80. The method of paragraph 79, wherein said vectors are
delivered to the eukaryotic cell in a subject.
[0465] 81. The method of paragraph 74, wherein said modifying takes
place in said eukaryotic cell in a cell culture.
[0466] 82. The method of paragraph 74, further comprising isolating
said eukaryotic cell from a subject prior to said modifying.
[0467] 83. The method of paragraph 82, further comprising returning
said eukaryotic cell and/or cells derived therefrom to said
subject.
[0468] 84. A method of modifying expression of a polynucleotide in
a eukaryotic cell, the method comprising: allowing a CRISPR complex
to bind to the polynucleotide such that said binding results in
increased or decreased expression of said polynucleotide; wherein
the CRISPR complex comprises a CRISPR enzyme complexed with a guide
sequence hybridized to a target sequence within said
polynucleotide, wherein said guide sequence is linked to a traer
mate sequence which in tum hybridizes to a traer sequence.
[0469] 85. The method of paragraph 74, further comprising
delivering one or more vectors to said eukaryotic cells, wherein
the one or more vectors drive expression of one or more of: the
CRISPR enzyme, the guide sequence linked to the traer mate
sequence, and the traer sequence.
[0470] 86. A method of generating a model eukaryotic cell
comprising a mutated disease gene, the method comprising:
[0471] a. introducing one or more vectors into a eukaryotic cell,
wherein the one or more vectors drive expression of one or more of:
a CRISPR enzyme, a guide sequence linked to a traer mate sequence,
and a traer sequence; and
[0472] b. allowing a CRISPR complex to bind to a target
polynucleotide to effect cleavage of the target polynucleotide
within said disease gene, wherein the CRISPR complex comprises the
CRISPR enzyme complexed with (1) the guide sequence that is
hybridized to the target sequence within the target polynucleotide,
and (2) the traer mate sequence that is hybridized to the traer
sequence, thereby generating a model eukaryotic cell comprising a
mutated disease gene.
[0473] 87. The method of paragraph 86, wherein said cleavage
comprises cleaving one or two strands at the location of the target
sequence by said CRISPR enzyme.
[0474] 88. The method of paragraph 86, wherein said cleavage
results in decreased transcription of a target gene.
[0475] 89. The method of paragraph 86, further comprising repairing
said cleaved target polynucleotide by homologous recombination with
an exogenous template polynucleotide, wherein said repair results
in a mutation comprising an insertion, deletion, or substitution of
one or more nucleotides of said target polynucleotide.
[0476] 90. The method of paragraph 89, wherein said mutation
results in one or more amino acid changes in a protein expressed
from a gene comprising the target sequence.
[0477] 91. A method of developing a biologically active agent that
modulates a cell signaling event associated with a disease gene,
comprising:
[0478] a. contacting a test compound with a model cell of any one
of paragraphs 86-90; and
[0479] b. detecting a change in a readout that is indicative of a
reduction or an augmentation of a cell signaling event associated
with said mutation in said disease gene, thereby developing said
biologically active agent that modulates said cell signaling event
associated with said disease gene.
[0480] 92. A recombinant polynucleotide comprising a guide sequence
upstream of a traer mate sequence, wherein the guide sequence when
expressed directs sequence-specific binding of a CRISPR complex to
a corresponding target sequence present in a eukaryotic cell.
[0481] 93. The recombinant polynucleotide of paragraph 89, wherein
the target sequence is a viral sequence present in a eukaryotic
cell.
[0482] 94. The recombinant polynucleotide of paragraph 89, wherein
the target sequence is a proto-oncogene or an oncogene.
[0483] While preferred embodiments of the present invention have
been shown and described herein, it will be obvious to those
skilled in the art that such embodiments are provided by way of
example only. Numerous variations, changes, and substitutions will
now occur to those skilled in the art without departing from the
invention. It should be understood that various alternatives to the
embodiments of the invention described herein may be employed in
practicing the invention. It is intended that the following claims
define the scope of the invention and that methods and structures
within the scope of these claims and their equivalents be covered
thereby.
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Sequence CWU 1
1
53717PRTSimian virus 40 1Pro Lys Lys Lys Arg Lys Val 1 5
216PRTUnknownDescription of Unknown Nucleoplasmin bipartite NLS
sequence 2Lys Arg Pro Ala Ala Thr Lys Lys Ala Gly Gln Ala Lys Lys
Lys Lys 1 5 10 15 39PRTUnknownDescription of Unknown C-myc NLS
sequence 3Pro Ala Ala Lys Arg Val Lys Leu Asp 1 5
411PRTUnknownDescription of Unknown C-myc NLS sequence 4Arg Gln Arg
Arg Asn Glu Leu Lys Arg Ser Pro 1 5 10 538PRTHomo sapiens 5Asn Gln
Ser Ser Asn Phe Gly Pro Met Lys Gly Gly Asn Phe Gly Gly 1 5 10 15
Arg Ser Ser Gly Pro Tyr Gly Gly Gly Gly Gln Tyr Phe Ala Lys Pro 20
25 30 Arg Asn Gln Gly Gly Tyr 35 642PRTUnknownDescription of
Unknown IBB domain from importin-alpha sequence 6Arg Met Arg Ile
Glx Phe Lys Asn Lys Gly Lys Asp Thr Ala Glu Leu 1 5 10 15 Arg Arg
Arg Arg Val Glu Val Ser Val Glu Leu Arg Lys Ala Lys Lys 20 25 30
Asp Glu Gln Ile Leu Lys Arg Arg Asn Val 35 40
78PRTUnknownDescription of Unknown Myoma T protein sequence 7Val
Ser Arg Lys Arg Pro Arg Pro 1 5 88PRTUnknownDescription of Unknown
Myoma T protein sequence 8Pro Pro Lys Lys Ala Arg Glu Asp 1 5
98PRTHomo sapiens 9Pro Gln Pro Lys Lys Lys Pro Leu 1 5 1012PRTMus
musculus 10Ser Ala Leu Ile Lys Lys Lys Lys Lys Met Ala Pro 1 5 10
115PRTInfluenza virus 11Asp Arg Leu Arg Arg 1 5 127PRTInfluenza
virus 12Pro Lys Gln Lys Lys Arg Lys 1 5 1310PRTHepatitus delta
virus 13Arg Lys Leu Lys Lys Lys Ile Lys Lys Leu 1 5 10 1410PRTMus
musculus 14Arg Glu Lys Lys Lys Phe Leu Lys Arg Arg 1 5 10
1520PRTHomo sapiens 15Lys Arg Lys Gly Asp Glu Val Asp Gly Val Asp
Glu Val Ala Lys Lys 1 5 10 15 Lys Ser Lys Lys 20 1617PRTHomo
sapiens 16Arg Lys Cys Leu Gln Ala Gly Met Asn Leu Glu Ala Arg Lys
Thr Lys 1 5 10 15 Lys 1727DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 17nnnnnnnnnn
nnnnnnnnnn nnagaaw 271819DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 18nnnnnnnnnn
nnnnagaaw 191927DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 19nnnnnnnnnn nnnnnnnnnn nnagaaw
272018DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 20nnnnnnnnnn nnnagaaw
1821137DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 21nnnnnnnnnn nnnnnnnnnn gtttttgtac
tctcaagatt tagaaataaa tcttgcagaa 60gctacaaaga taaggcttca tgccgaaatc
aacaccctgt cattttatgg cagggtgttt 120tcgttattta atttttt
13722123DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 22nnnnnnnnnn nnnnnnnnnn gtttttgtac
tctcagaaat gcagaagcta caaagataag 60gcttcatgcc gaaatcaaca ccctgtcatt
ttatggcagg gtgttttcgt tatttaattt 120ttt 12323110DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
23nnnnnnnnnn nnnnnnnnnn gtttttgtac tctcagaaat gcagaagcta caaagataag
60gcttcatgcc gaaatcaaca ccctgtcatt ttatggcagg gtgttttttt
11024102DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 24nnnnnnnnnn nnnnnnnnnn gttttagagc
tagaaatagc aagttaaaat aaggctagtc 60cgttatcaac ttgaaaaagt ggcaccgagt
cggtgctttt tt 1022588DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 25nnnnnnnnnn
nnnnnnnnnn gttttagagc tagaaatagc aagttaaaat aaggctagtc 60cgttatcaac
ttgaaaaagt gttttttt 882676DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 26nnnnnnnnnn
nnnnnnnnnn gttttagagc tagaaatagc aagttaaaat aaggctagtc 60cgttatcatt
tttttt 762712DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 27gttttagagc ta
122831DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 28tagcaagtta aaataaggct agtccgtttt t
312927DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 29nnnnnnnnnn nnnnnnnnnn nnagaaw
273012RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 30guuuuagagc ua 123133DNAHomo sapiens
31ggacatcgat gtcacctcca atgactaggg tgg 333233DNAHomo sapiens
32cattggaggt gacatcgatg tcctccccat tgg 333333DNAHomo sapiens
33ggaagggcct gagtccgagc agaagaagaa ggg 333433DNAHomo sapiens
34ggtggcgaga ggggccgaga ttgggtgttc agg 333533DNAHomo sapiens
35atgcaggagg gtggcgagag gggccgagat tgg 333621DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
36aaaaccaccc ttctctctgg c 213721DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 37ggagattgga gacacggaga g
213820DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 38ctggaaagcc aatgcctgac 203920DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
39ggcagcaaac tccttgtcct 2040335DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 40gagggcctat
ttcccatgat tccttcatat ttgcatatac gatacaaggc tgttagagag 60ataattggaa
ttaatttgac tgtaaacaca aagatattag tacaaaatac gtgacgtaga
120aagtaataat ttcttgggta gtttgcagtt ttaaaattat gttttaaaat
ggactatcat 180atgcttaccg taacttgaaa gtatttcgat ttcttggctt
tatatatctt gtggaaagga 240cgaaacaccg gaaccattca aaacagcata
gcaagttaaa ataaggctag tccgttatca 300acttgaaaaa gtggcaccga
gtcggtgctt ttttt 33541423DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 41gagggcctat
ttcccatgat tccttcatat ttgcatatac gatacaaggc tgttagagag 60ataattggaa
ttaatttgac tgtaaacaca aagatattag tacaaaatac gtgacgtaga
120aagtaataat ttcttgggta gtttgcagtt ttaaaattat gttttaaaat
ggactatcat 180atgcttaccg taacttgaaa gtatttcgat ttcttggctt
tatatatctt gtggaaagga 240cgaaacaccg gtagtattaa gtattgtttt
atggctgata aatttctttg aatttctcct 300tgattatttg ttataaaagt
tataaaataa tcttgttgga accattcaaa acagcatagc 360aagttaaaat
aaggctagtc cgttatcaac ttgaaaaagt ggcaccgagt cggtgctttt 420ttt
42342339DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 42gagggcctat ttcccatgat tccttcatat
ttgcatatac gatacaaggc tgttagagag 60ataattggaa ttaatttgac tgtaaacaca
aagatattag tacaaaatac gtgacgtaga 120aagtaataat ttcttgggta
gtttgcagtt ttaaaattat gttttaaaat ggactatcat 180atgcttaccg
taacttgaaa gtatttcgat ttcttggctt tatatatctt gtggaaagga
240cgaaacaccg ggttttagag ctatgctgtt ttgaatggtc ccaaaacggg
tcttcgagaa 300gacgttttag agctatgctg ttttgaatgg tcccaaaac
33943309DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 43gagggcctat ttcccatgat tccttcatat
ttgcatatac gatacaaggc tgttagagag 60ataattggaa ttaatttgac tgtaaacaca
aagatattag tacaaaatac gtgacgtaga 120aagtaataat ttcttgggta
gtttgcagtt ttaaaattat gttttaaaat ggactatcat 180atgcttaccg
taacttgaaa gtatttcgat ttcttggctt tatatatctt gtggaaagga
240cgaaacaccg ggtcttcgag aagacctgtt ttagagctag aaatagcaag
ttaaaataag 300gctagtccg 309441648PRTArtificial SequenceDescription
of Artificial Sequence Synthetic polypeptide 44Met Asp Tyr Lys Asp
His Asp Gly Asp Tyr Lys Asp His Asp Ile Asp 1 5 10 15 Tyr Lys Asp
Asp Asp Asp Lys Met Ala Pro Lys Lys Lys Arg Lys Val 20 25 30 Gly
Ile His Gly Val Pro Ala Ala Asp Lys Lys Tyr Ser Ile Gly Leu 35 40
45 Asp Ile Gly Thr Asn Ser Val Gly Trp Ala Val Ile Thr Asp Glu Tyr
50 55 60 Lys Val Pro Ser Lys Lys Phe Lys Val Leu Gly Asn Thr Asp
Arg His 65 70 75 80 Ser Ile Lys Lys Asn Leu Ile Gly Ala Leu Leu Phe
Asp Ser Gly Glu 85 90 95 Thr Ala Glu Ala Thr Arg Leu Lys Arg Thr
Ala Arg Arg Arg Tyr Thr 100 105 110 Arg Arg Lys Asn Arg Ile Cys Tyr
Leu Gln Glu Ile Phe Ser Asn Glu 115 120 125 Met Ala Lys Val Asp Asp
Ser Phe Phe His Arg Leu Glu Glu Ser Phe 130 135 140 Leu Val Glu Glu
Asp Lys Lys His Glu Arg His Pro Ile Phe Gly Asn 145 150 155 160 Ile
Val Asp Glu Val Ala Tyr His Glu Lys Tyr Pro Thr Ile Tyr His 165 170
175 Leu Arg Lys Lys Leu Val Asp Ser Thr Asp Lys Ala Asp Leu Arg Leu
180 185 190 Ile Tyr Leu Ala Leu Ala His Met Ile Lys Phe Arg Gly His
Phe Leu 195 200 205 Ile Glu Gly Asp Leu Asn Pro Asp Asn Ser Asp Val
Asp Lys Leu Phe 210 215 220 Ile Gln Leu Val Gln Thr Tyr Asn Gln Leu
Phe Glu Glu Asn Pro Ile 225 230 235 240 Asn Ala Ser Gly Val Asp Ala
Lys Ala Ile Leu Ser Ala Arg Leu Ser 245 250 255 Lys Ser Arg Arg Leu
Glu Asn Leu Ile Ala Gln Leu Pro Gly Glu Lys 260 265 270 Lys Asn Gly
Leu Phe Gly Asn Leu Ile Ala Leu Ser Leu Gly Leu Thr 275 280 285 Pro
Asn Phe Lys Ser Asn Phe Asp Leu Ala Glu Asp Ala Lys Leu Gln 290 295
300 Leu Ser Lys Asp Thr Tyr Asp Asp Asp Leu Asp Asn Leu Leu Ala Gln
305 310 315 320 Ile Gly Asp Gln Tyr Ala Asp Leu Phe Leu Ala Ala Lys
Asn Leu Ser 325 330 335 Asp Ala Ile Leu Leu Ser Asp Ile Leu Arg Val
Asn Thr Glu Ile Thr 340 345 350 Lys Ala Pro Leu Ser Ala Ser Met Ile
Lys Arg Tyr Asp Glu His His 355 360 365 Gln Asp Leu Thr Leu Leu Lys
Ala Leu Val Arg Gln Gln Leu Pro Glu 370 375 380 Lys Tyr Lys Glu Ile
Phe Phe Asp Gln Ser Lys Asn Gly Tyr Ala Gly 385 390 395 400 Tyr Ile
Asp Gly Gly Ala Ser Gln Glu Glu Phe Tyr Lys Phe Ile Lys 405 410 415
Pro Ile Leu Glu Lys Met Asp Gly Thr Glu Glu Leu Leu Val Lys Leu 420
425 430 Asn Arg Glu Asp Leu Leu Arg Lys Gln Arg Thr Phe Asp Asn Gly
Ser 435 440 445 Ile Pro His Gln Ile His Leu Gly Glu Leu His Ala Ile
Leu Arg Arg 450 455 460 Gln Glu Asp Phe Tyr Pro Phe Leu Lys Asp Asn
Arg Glu Lys Ile Glu 465 470 475 480 Lys Ile Leu Thr Phe Arg Ile Pro
Tyr Tyr Val Gly Pro Leu Ala Arg 485 490 495 Gly Asn Ser Arg Phe Ala
Trp Met Thr Arg Lys Ser Glu Glu Thr Ile 500 505 510 Thr Pro Trp Asn
Phe Glu Glu Val Val Asp Lys Gly Ala Ser Ala Gln 515 520 525 Ser Phe
Ile Glu Arg Met Thr Asn Phe Asp Lys Asn Leu Pro Asn Glu 530 535 540
Lys Val Leu Pro Lys His Ser Leu Leu Tyr Glu Tyr Phe Thr Val Tyr 545
550 555 560 Asn Glu Leu Thr Lys Val Lys Tyr Val Thr Glu Gly Met Arg
Lys Pro 565 570 575 Ala Phe Leu Ser Gly Glu Gln Lys Lys Ala Ile Val
Asp Leu Leu Phe 580 585 590 Lys Thr Asn Arg Lys Val Thr Val Lys Gln
Leu Lys Glu Asp Tyr Phe 595 600 605 Lys Lys Ile Glu Cys Phe Asp Ser
Val Glu Ile Ser Gly Val Glu Asp 610 615 620 Arg Phe Asn Ala Ser Leu
Gly Thr Tyr His Asp Leu Leu Lys Ile Ile 625 630 635 640 Lys Asp Lys
Asp Phe Leu Asp Asn Glu Glu Asn Glu Asp Ile Leu Glu 645 650 655 Asp
Ile Val Leu Thr Leu Thr Leu Phe Glu Asp Arg Glu Met Ile Glu 660 665
670 Glu Arg Leu Lys Thr Tyr Ala His Leu Phe Asp Asp Lys Val Met Lys
675 680 685 Gln Leu Lys Arg Arg Arg Tyr Thr Gly Trp Gly Arg Leu Ser
Arg Lys 690 695 700 Leu Ile Asn Gly Ile Arg Asp Lys Gln Ser Gly Lys
Thr Ile Leu Asp 705 710 715 720 Phe Leu Lys Ser Asp Gly Phe Ala Asn
Arg Asn Phe Met Gln Leu Ile 725 730 735 His Asp Asp Ser Leu Thr Phe
Lys Glu Asp Ile Gln Lys Ala Gln Val 740 745 750 Ser Gly Gln Gly Asp
Ser Leu His Glu His Ile Ala Asn Leu Ala Gly 755 760 765 Ser Pro Ala
Ile Lys Lys Gly Ile Leu Gln Thr Val Lys Val Val Asp 770 775 780 Glu
Leu Val Lys Val Met Gly Arg His Lys Pro Glu Asn Ile Val Ile 785 790
795 800 Glu Met Ala Arg Glu Asn Gln Thr Thr Gln Lys Gly Gln Lys Asn
Ser 805 810 815 Arg Glu Arg Met Lys Arg Ile Glu Glu Gly Ile Lys Glu
Leu Gly Ser 820 825 830 Gln Ile Leu Lys Glu His Pro Val Glu Asn Thr
Gln Leu Gln Asn Glu 835 840 845 Lys Leu Tyr Leu Tyr Tyr Leu Gln Asn
Gly Arg Asp Met Tyr Val Asp 850 855 860 Gln Glu Leu Asp Ile Asn Arg
Leu Ser Asp Tyr Asp Val Asp His Ile 865 870 875 880 Val Pro Gln Ser
Phe Leu Lys Asp Asp Ser Ile Asp Asn Lys Val Leu 885 890 895 Thr Arg
Ser Asp Lys Asn Arg Gly Lys Ser Asp Asn Val Pro Ser Glu 900 905 910
Glu Val Val Lys Lys Met Lys Asn Tyr Trp Arg Gln Leu Leu Asn Ala 915
920 925 Lys Leu Ile Thr Gln Arg Lys Phe Asp Asn Leu Thr Lys Ala Glu
Arg 930 935 940 Gly Gly Leu Ser Glu Leu Asp Lys Ala Gly Phe Ile Lys
Arg Gln Leu 945 950 955 960 Val Glu Thr Arg Gln Ile Thr Lys His Val
Ala Gln Ile Leu Asp Ser 965 970 975 Arg Met Asn Thr Lys Tyr Asp Glu
Asn Asp Lys Leu Ile Arg Glu Val 980 985 990 Lys Val Ile Thr Leu Lys
Ser Lys Leu Val Ser Asp Phe Arg Lys Asp 995 1000 1005 Phe Gln Phe
Tyr Lys Val Arg Glu Ile Asn Asn Tyr His His Ala 1010 1015 1020 His
Asp Ala Tyr Leu Asn Ala Val Val Gly Thr Ala Leu Ile Lys 1025 1030
1035 Lys Tyr Pro Lys Leu Glu Ser Glu Phe Val Tyr Gly Asp Tyr Lys
1040 1045 1050 Val Tyr Asp Val Arg Lys Met Ile Ala Lys Ser Glu Gln
Glu Ile 1055 1060 1065 Gly Lys Ala Thr Ala Lys Tyr Phe Phe Tyr Ser
Asn Ile Met Asn 1070 1075 1080 Phe Phe Lys Thr Glu Ile Thr Leu Ala
Asn Gly Glu Ile Arg Lys 1085 1090 1095 Arg Pro Leu Ile Glu Thr Asn
Gly Glu Thr Gly Glu Ile Val Trp 1100 1105 1110 Asp Lys Gly Arg Asp
Phe Ala Thr Val Arg Lys Val Leu Ser Met 1115 1120 1125 Pro Gln Val
Asn Ile Val Lys Lys Thr Glu Val Gln Thr Gly Gly 1130 1135 1140 Phe
Ser Lys Glu Ser Ile Leu Pro Lys Arg Asn Ser Asp Lys Leu 1145 1150
1155 Ile Ala
Arg Lys Lys Asp Trp Asp Pro Lys Lys Tyr Gly Gly Phe 1160 1165 1170
Asp Ser Pro Thr Val Ala Tyr Ser Val Leu Val Val Ala Lys Val 1175
1180 1185 Glu Lys Gly Lys Ser Lys Lys Leu Lys Ser Val Lys Glu Leu
Leu 1190 1195 1200 Gly Ile Thr Ile Met Glu Arg Ser Ser Phe Glu Lys
Asn Pro Ile 1205 1210 1215 Asp Phe Leu Glu Ala Lys Gly Tyr Lys Glu
Val Lys Lys Asp Leu 1220 1225 1230 Ile Ile Lys Leu Pro Lys Tyr Ser
Leu Phe Glu Leu Glu Asn Gly 1235 1240 1245 Arg Lys Arg Met Leu Ala
Ser Ala Gly Glu Leu Gln Lys Gly Asn 1250 1255 1260 Glu Leu Ala Leu
Pro Ser Lys Tyr Val Asn Phe Leu Tyr Leu Ala 1265 1270 1275 Ser His
Tyr Glu Lys Leu Lys Gly Ser Pro Glu Asp Asn Glu Gln 1280 1285 1290
Lys Gln Leu Phe Val Glu Gln His Lys His Tyr Leu Asp Glu Ile 1295
1300 1305 Ile Glu Gln Ile Ser Glu Phe Ser Lys Arg Val Ile Leu Ala
Asp 1310 1315 1320 Ala Asn Leu Asp Lys Val Leu Ser Ala Tyr Asn Lys
His Arg Asp 1325 1330 1335 Lys Pro Ile Arg Glu Gln Ala Glu Asn Ile
Ile His Leu Phe Thr 1340 1345 1350 Leu Thr Asn Leu Gly Ala Pro Ala
Ala Phe Lys Tyr Phe Asp Thr 1355 1360 1365 Thr Ile Asp Arg Lys Arg
Tyr Thr Ser Thr Lys Glu Val Leu Asp 1370 1375 1380 Ala Thr Leu Ile
His Gln Ser Ile Thr Gly Leu Tyr Glu Thr Arg 1385 1390 1395 Ile Asp
Leu Ser Gln Leu Gly Gly Asp Ala Ala Ala Val Ser Lys 1400 1405 1410
Gly Glu Glu Leu Phe Thr Gly Val Val Pro Ile Leu Val Glu Leu 1415
1420 1425 Asp Gly Asp Val Asn Gly His Lys Phe Ser Val Ser Gly Glu
Gly 1430 1435 1440 Glu Gly Asp Ala Thr Tyr Gly Lys Leu Thr Leu Lys
Phe Ile Cys 1445 1450 1455 Thr Thr Gly Lys Leu Pro Val Pro Trp Pro
Thr Leu Val Thr Thr 1460 1465 1470 Leu Thr Tyr Gly Val Gln Cys Phe
Ser Arg Tyr Pro Asp His Met 1475 1480 1485 Lys Gln His Asp Phe Phe
Lys Ser Ala Met Pro Glu Gly Tyr Val 1490 1495 1500 Gln Glu Arg Thr
Ile Phe Phe Lys Asp Asp Gly Asn Tyr Lys Thr 1505 1510 1515 Arg Ala
Glu Val Lys Phe Glu Gly Asp Thr Leu Val Asn Arg Ile 1520 1525 1530
Glu Leu Lys Gly Ile Asp Phe Lys Glu Asp Gly Asn Ile Leu Gly 1535
1540 1545 His Lys Leu Glu Tyr Asn Tyr Asn Ser His Asn Val Tyr Ile
Met 1550 1555 1560 Ala Asp Lys Gln Lys Asn Gly Ile Lys Val Asn Phe
Lys Ile Arg 1565 1570 1575 His Asn Ile Glu Asp Gly Ser Val Gln Leu
Ala Asp His Tyr Gln 1580 1585 1590 Gln Asn Thr Pro Ile Gly Asp Gly
Pro Val Leu Leu Pro Asp Asn 1595 1600 1605 His Tyr Leu Ser Thr Gln
Ser Ala Leu Ser Lys Asp Pro Asn Glu 1610 1615 1620 Lys Arg Asp His
Met Val Leu Leu Glu Phe Val Thr Ala Ala Gly 1625 1630 1635 Ile Thr
Leu Gly Met Asp Glu Leu Tyr Lys 1640 1645 451625PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
45Met Asp Lys Lys Tyr Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val 1
5 10 15 Gly Trp Ala Val Ile Thr Asp Glu Tyr Lys Val Pro Ser Lys Lys
Phe 20 25 30 Lys Val Leu Gly Asn Thr Asp Arg His Ser Ile Lys Lys
Asn Leu Ile 35 40 45 Gly Ala Leu Leu Phe Asp Ser Gly Glu Thr Ala
Glu Ala Thr Arg Leu 50 55 60 Lys Arg Thr Ala Arg Arg Arg Tyr Thr
Arg Arg Lys Asn Arg Ile Cys 65 70 75 80 Tyr Leu Gln Glu Ile Phe Ser
Asn Glu Met Ala Lys Val Asp Asp Ser 85 90 95 Phe Phe His Arg Leu
Glu Glu Ser Phe Leu Val Glu Glu Asp Lys Lys 100 105 110 His Glu Arg
His Pro Ile Phe Gly Asn Ile Val Asp Glu Val Ala Tyr 115 120 125 His
Glu Lys Tyr Pro Thr Ile Tyr His Leu Arg Lys Lys Leu Val Asp 130 135
140 Ser Thr Asp Lys Ala Asp Leu Arg Leu Ile Tyr Leu Ala Leu Ala His
145 150 155 160 Met Ile Lys Phe Arg Gly His Phe Leu Ile Glu Gly Asp
Leu Asn Pro 165 170 175 Asp Asn Ser Asp Val Asp Lys Leu Phe Ile Gln
Leu Val Gln Thr Tyr 180 185 190 Asn Gln Leu Phe Glu Glu Asn Pro Ile
Asn Ala Ser Gly Val Asp Ala 195 200 205 Lys Ala Ile Leu Ser Ala Arg
Leu Ser Lys Ser Arg Arg Leu Glu Asn 210 215 220 Leu Ile Ala Gln Leu
Pro Gly Glu Lys Lys Asn Gly Leu Phe Gly Asn 225 230 235 240 Leu Ile
Ala Leu Ser Leu Gly Leu Thr Pro Asn Phe Lys Ser Asn Phe 245 250 255
Asp Leu Ala Glu Asp Ala Lys Leu Gln Leu Ser Lys Asp Thr Tyr Asp 260
265 270 Asp Asp Leu Asp Asn Leu Leu Ala Gln Ile Gly Asp Gln Tyr Ala
Asp 275 280 285 Leu Phe Leu Ala Ala Lys Asn Leu Ser Asp Ala Ile Leu
Leu Ser Asp 290 295 300 Ile Leu Arg Val Asn Thr Glu Ile Thr Lys Ala
Pro Leu Ser Ala Ser 305 310 315 320 Met Ile Lys Arg Tyr Asp Glu His
His Gln Asp Leu Thr Leu Leu Lys 325 330 335 Ala Leu Val Arg Gln Gln
Leu Pro Glu Lys Tyr Lys Glu Ile Phe Phe 340 345 350 Asp Gln Ser Lys
Asn Gly Tyr Ala Gly Tyr Ile Asp Gly Gly Ala Ser 355 360 365 Gln Glu
Glu Phe Tyr Lys Phe Ile Lys Pro Ile Leu Glu Lys Met Asp 370 375 380
Gly Thr Glu Glu Leu Leu Val Lys Leu Asn Arg Glu Asp Leu Leu Arg 385
390 395 400 Lys Gln Arg Thr Phe Asp Asn Gly Ser Ile Pro His Gln Ile
His Leu 405 410 415 Gly Glu Leu His Ala Ile Leu Arg Arg Gln Glu Asp
Phe Tyr Pro Phe 420 425 430 Leu Lys Asp Asn Arg Glu Lys Ile Glu Lys
Ile Leu Thr Phe Arg Ile 435 440 445 Pro Tyr Tyr Val Gly Pro Leu Ala
Arg Gly Asn Ser Arg Phe Ala Trp 450 455 460 Met Thr Arg Lys Ser Glu
Glu Thr Ile Thr Pro Trp Asn Phe Glu Glu 465 470 475 480 Val Val Asp
Lys Gly Ala Ser Ala Gln Ser Phe Ile Glu Arg Met Thr 485 490 495 Asn
Phe Asp Lys Asn Leu Pro Asn Glu Lys Val Leu Pro Lys His Ser 500 505
510 Leu Leu Tyr Glu Tyr Phe Thr Val Tyr Asn Glu Leu Thr Lys Val Lys
515 520 525 Tyr Val Thr Glu Gly Met Arg Lys Pro Ala Phe Leu Ser Gly
Glu Gln 530 535 540 Lys Lys Ala Ile Val Asp Leu Leu Phe Lys Thr Asn
Arg Lys Val Thr 545 550 555 560 Val Lys Gln Leu Lys Glu Asp Tyr Phe
Lys Lys Ile Glu Cys Phe Asp 565 570 575 Ser Val Glu Ile Ser Gly Val
Glu Asp Arg Phe Asn Ala Ser Leu Gly 580 585 590 Thr Tyr His Asp Leu
Leu Lys Ile Ile Lys Asp Lys Asp Phe Leu Asp 595 600 605 Asn Glu Glu
Asn Glu Asp Ile Leu Glu Asp Ile Val Leu Thr Leu Thr 610 615 620 Leu
Phe Glu Asp Arg Glu Met Ile Glu Glu Arg Leu Lys Thr Tyr Ala 625 630
635 640 His Leu Phe Asp Asp Lys Val Met Lys Gln Leu Lys Arg Arg Arg
Tyr 645 650 655 Thr Gly Trp Gly Arg Leu Ser Arg Lys Leu Ile Asn Gly
Ile Arg Asp 660 665 670 Lys Gln Ser Gly Lys Thr Ile Leu Asp Phe Leu
Lys Ser Asp Gly Phe 675 680 685 Ala Asn Arg Asn Phe Met Gln Leu Ile
His Asp Asp Ser Leu Thr Phe 690 695 700 Lys Glu Asp Ile Gln Lys Ala
Gln Val Ser Gly Gln Gly Asp Ser Leu 705 710 715 720 His Glu His Ile
Ala Asn Leu Ala Gly Ser Pro Ala Ile Lys Lys Gly 725 730 735 Ile Leu
Gln Thr Val Lys Val Val Asp Glu Leu Val Lys Val Met Gly 740 745 750
Arg His Lys Pro Glu Asn Ile Val Ile Glu Met Ala Arg Glu Asn Gln 755
760 765 Thr Thr Gln Lys Gly Gln Lys Asn Ser Arg Glu Arg Met Lys Arg
Ile 770 775 780 Glu Glu Gly Ile Lys Glu Leu Gly Ser Gln Ile Leu Lys
Glu His Pro 785 790 795 800 Val Glu Asn Thr Gln Leu Gln Asn Glu Lys
Leu Tyr Leu Tyr Tyr Leu 805 810 815 Gln Asn Gly Arg Asp Met Tyr Val
Asp Gln Glu Leu Asp Ile Asn Arg 820 825 830 Leu Ser Asp Tyr Asp Val
Asp His Ile Val Pro Gln Ser Phe Leu Lys 835 840 845 Asp Asp Ser Ile
Asp Asn Lys Val Leu Thr Arg Ser Asp Lys Asn Arg 850 855 860 Gly Lys
Ser Asp Asn Val Pro Ser Glu Glu Val Val Lys Lys Met Lys 865 870 875
880 Asn Tyr Trp Arg Gln Leu Leu Asn Ala Lys Leu Ile Thr Gln Arg Lys
885 890 895 Phe Asp Asn Leu Thr Lys Ala Glu Arg Gly Gly Leu Ser Glu
Leu Asp 900 905 910 Lys Ala Gly Phe Ile Lys Arg Gln Leu Val Glu Thr
Arg Gln Ile Thr 915 920 925 Lys His Val Ala Gln Ile Leu Asp Ser Arg
Met Asn Thr Lys Tyr Asp 930 935 940 Glu Asn Asp Lys Leu Ile Arg Glu
Val Lys Val Ile Thr Leu Lys Ser 945 950 955 960 Lys Leu Val Ser Asp
Phe Arg Lys Asp Phe Gln Phe Tyr Lys Val Arg 965 970 975 Glu Ile Asn
Asn Tyr His His Ala His Asp Ala Tyr Leu Asn Ala Val 980 985 990 Val
Gly Thr Ala Leu Ile Lys Lys Tyr Pro Lys Leu Glu Ser Glu Phe 995
1000 1005 Val Tyr Gly Asp Tyr Lys Val Tyr Asp Val Arg Lys Met Ile
Ala 1010 1015 1020 Lys Ser Glu Gln Glu Ile Gly Lys Ala Thr Ala Lys
Tyr Phe Phe 1025 1030 1035 Tyr Ser Asn Ile Met Asn Phe Phe Lys Thr
Glu Ile Thr Leu Ala 1040 1045 1050 Asn Gly Glu Ile Arg Lys Arg Pro
Leu Ile Glu Thr Asn Gly Glu 1055 1060 1065 Thr Gly Glu Ile Val Trp
Asp Lys Gly Arg Asp Phe Ala Thr Val 1070 1075 1080 Arg Lys Val Leu
Ser Met Pro Gln Val Asn Ile Val Lys Lys Thr 1085 1090 1095 Glu Val
Gln Thr Gly Gly Phe Ser Lys Glu Ser Ile Leu Pro Lys 1100 1105 1110
Arg Asn Ser Asp Lys Leu Ile Ala Arg Lys Lys Asp Trp Asp Pro 1115
1120 1125 Lys Lys Tyr Gly Gly Phe Asp Ser Pro Thr Val Ala Tyr Ser
Val 1130 1135 1140 Leu Val Val Ala Lys Val Glu Lys Gly Lys Ser Lys
Lys Leu Lys 1145 1150 1155 Ser Val Lys Glu Leu Leu Gly Ile Thr Ile
Met Glu Arg Ser Ser 1160 1165 1170 Phe Glu Lys Asn Pro Ile Asp Phe
Leu Glu Ala Lys Gly Tyr Lys 1175 1180 1185 Glu Val Lys Lys Asp Leu
Ile Ile Lys Leu Pro Lys Tyr Ser Leu 1190 1195 1200 Phe Glu Leu Glu
Asn Gly Arg Lys Arg Met Leu Ala Ser Ala Gly 1205 1210 1215 Glu Leu
Gln Lys Gly Asn Glu Leu Ala Leu Pro Ser Lys Tyr Val 1220 1225 1230
Asn Phe Leu Tyr Leu Ala Ser His Tyr Glu Lys Leu Lys Gly Ser 1235
1240 1245 Pro Glu Asp Asn Glu Gln Lys Gln Leu Phe Val Glu Gln His
Lys 1250 1255 1260 His Tyr Leu Asp Glu Ile Ile Glu Gln Ile Ser Glu
Phe Ser Lys 1265 1270 1275 Arg Val Ile Leu Ala Asp Ala Asn Leu Asp
Lys Val Leu Ser Ala 1280 1285 1290 Tyr Asn Lys His Arg Asp Lys Pro
Ile Arg Glu Gln Ala Glu Asn 1295 1300 1305 Ile Ile His Leu Phe Thr
Leu Thr Asn Leu Gly Ala Pro Ala Ala 1310 1315 1320 Phe Lys Tyr Phe
Asp Thr Thr Ile Asp Arg Lys Arg Tyr Thr Ser 1325 1330 1335 Thr Lys
Glu Val Leu Asp Ala Thr Leu Ile His Gln Ser Ile Thr 1340 1345 1350
Gly Leu Tyr Glu Thr Arg Ile Asp Leu Ser Gln Leu Gly Gly Asp 1355
1360 1365 Ala Ala Ala Val Ser Lys Gly Glu Glu Leu Phe Thr Gly Val
Val 1370 1375 1380 Pro Ile Leu Val Glu Leu Asp Gly Asp Val Asn Gly
His Lys Phe 1385 1390 1395 Ser Val Ser Gly Glu Gly Glu Gly Asp Ala
Thr Tyr Gly Lys Leu 1400 1405 1410 Thr Leu Lys Phe Ile Cys Thr Thr
Gly Lys Leu Pro Val Pro Trp 1415 1420 1425 Pro Thr Leu Val Thr Thr
Leu Thr Tyr Gly Val Gln Cys Phe Ser 1430 1435 1440 Arg Tyr Pro Asp
His Met Lys Gln His Asp Phe Phe Lys Ser Ala 1445 1450 1455 Met Pro
Glu Gly Tyr Val Gln Glu Arg Thr Ile Phe Phe Lys Asp 1460 1465 1470
Asp Gly Asn Tyr Lys Thr Arg Ala Glu Val Lys Phe Glu Gly Asp 1475
1480 1485 Thr Leu Val Asn Arg Ile Glu Leu Lys Gly Ile Asp Phe Lys
Glu 1490 1495 1500 Asp Gly Asn Ile Leu Gly His Lys Leu Glu Tyr Asn
Tyr Asn Ser 1505 1510 1515 His Asn Val Tyr Ile Met Ala Asp Lys Gln
Lys Asn Gly Ile Lys 1520 1525 1530 Val Asn Phe Lys Ile Arg His Asn
Ile Glu Asp Gly Ser Val Gln 1535 1540 1545 Leu Ala Asp His Tyr Gln
Gln Asn Thr Pro Ile Gly Asp Gly Pro 1550 1555 1560 Val Leu Leu Pro
Asp Asn His Tyr Leu Ser Thr Gln Ser Ala Leu 1565 1570 1575 Ser Lys
Asp Pro Asn Glu Lys Arg Asp His Met Val Leu Leu Glu 1580 1585 1590
Phe Val Thr Ala Ala Gly Ile Thr Leu Gly Met Asp Glu Leu Tyr 1595
1600 1605 Lys Lys Arg Pro Ala Ala Thr Lys Lys Ala Gly Gln Ala Lys
Lys 1610 1615 1620 Lys Lys 1625 461664PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
46Met Asp Tyr Lys Asp His Asp Gly Asp Tyr Lys Asp His Asp Ile Asp 1
5 10 15 Tyr Lys Asp Asp Asp Asp Lys Met Ala Pro Lys Lys Lys Arg Lys
Val 20 25 30 Gly Ile His Gly Val Pro Ala Ala Asp Lys Lys Tyr Ser
Ile Gly Leu 35 40 45 Asp Ile Gly Thr Asn Ser Val Gly Trp Ala Val
Ile Thr Asp Glu Tyr 50 55 60 Lys Val Pro Ser Lys Lys Phe Lys Val
Leu Gly Asn Thr Asp Arg His 65 70 75 80 Ser Ile Lys Lys Asn Leu Ile
Gly Ala Leu Leu Phe Asp Ser Gly Glu 85 90 95 Thr Ala Glu Ala Thr
Arg Leu Lys Arg Thr Ala Arg Arg Arg Tyr Thr 100 105
110 Arg Arg Lys Asn Arg Ile Cys Tyr Leu Gln Glu Ile Phe Ser Asn Glu
115 120 125 Met Ala Lys Val Asp Asp Ser Phe Phe His Arg Leu Glu Glu
Ser Phe 130 135 140 Leu Val Glu Glu Asp Lys Lys His Glu Arg His Pro
Ile Phe Gly Asn 145 150 155 160 Ile Val Asp Glu Val Ala Tyr His Glu
Lys Tyr Pro Thr Ile Tyr His 165 170 175 Leu Arg Lys Lys Leu Val Asp
Ser Thr Asp Lys Ala Asp Leu Arg Leu 180 185 190 Ile Tyr Leu Ala Leu
Ala His Met Ile Lys Phe Arg Gly His Phe Leu 195 200 205 Ile Glu Gly
Asp Leu Asn Pro Asp Asn Ser Asp Val Asp Lys Leu Phe 210 215 220 Ile
Gln Leu Val Gln Thr Tyr Asn Gln Leu Phe Glu Glu Asn Pro Ile 225 230
235 240 Asn Ala Ser Gly Val Asp Ala Lys Ala Ile Leu Ser Ala Arg Leu
Ser 245 250 255 Lys Ser Arg Arg Leu Glu Asn Leu Ile Ala Gln Leu Pro
Gly Glu Lys 260 265 270 Lys Asn Gly Leu Phe Gly Asn Leu Ile Ala Leu
Ser Leu Gly Leu Thr 275 280 285 Pro Asn Phe Lys Ser Asn Phe Asp Leu
Ala Glu Asp Ala Lys Leu Gln 290 295 300 Leu Ser Lys Asp Thr Tyr Asp
Asp Asp Leu Asp Asn Leu Leu Ala Gln 305 310 315 320 Ile Gly Asp Gln
Tyr Ala Asp Leu Phe Leu Ala Ala Lys Asn Leu Ser 325 330 335 Asp Ala
Ile Leu Leu Ser Asp Ile Leu Arg Val Asn Thr Glu Ile Thr 340 345 350
Lys Ala Pro Leu Ser Ala Ser Met Ile Lys Arg Tyr Asp Glu His His 355
360 365 Gln Asp Leu Thr Leu Leu Lys Ala Leu Val Arg Gln Gln Leu Pro
Glu 370 375 380 Lys Tyr Lys Glu Ile Phe Phe Asp Gln Ser Lys Asn Gly
Tyr Ala Gly 385 390 395 400 Tyr Ile Asp Gly Gly Ala Ser Gln Glu Glu
Phe Tyr Lys Phe Ile Lys 405 410 415 Pro Ile Leu Glu Lys Met Asp Gly
Thr Glu Glu Leu Leu Val Lys Leu 420 425 430 Asn Arg Glu Asp Leu Leu
Arg Lys Gln Arg Thr Phe Asp Asn Gly Ser 435 440 445 Ile Pro His Gln
Ile His Leu Gly Glu Leu His Ala Ile Leu Arg Arg 450 455 460 Gln Glu
Asp Phe Tyr Pro Phe Leu Lys Asp Asn Arg Glu Lys Ile Glu 465 470 475
480 Lys Ile Leu Thr Phe Arg Ile Pro Tyr Tyr Val Gly Pro Leu Ala Arg
485 490 495 Gly Asn Ser Arg Phe Ala Trp Met Thr Arg Lys Ser Glu Glu
Thr Ile 500 505 510 Thr Pro Trp Asn Phe Glu Glu Val Val Asp Lys Gly
Ala Ser Ala Gln 515 520 525 Ser Phe Ile Glu Arg Met Thr Asn Phe Asp
Lys Asn Leu Pro Asn Glu 530 535 540 Lys Val Leu Pro Lys His Ser Leu
Leu Tyr Glu Tyr Phe Thr Val Tyr 545 550 555 560 Asn Glu Leu Thr Lys
Val Lys Tyr Val Thr Glu Gly Met Arg Lys Pro 565 570 575 Ala Phe Leu
Ser Gly Glu Gln Lys Lys Ala Ile Val Asp Leu Leu Phe 580 585 590 Lys
Thr Asn Arg Lys Val Thr Val Lys Gln Leu Lys Glu Asp Tyr Phe 595 600
605 Lys Lys Ile Glu Cys Phe Asp Ser Val Glu Ile Ser Gly Val Glu Asp
610 615 620 Arg Phe Asn Ala Ser Leu Gly Thr Tyr His Asp Leu Leu Lys
Ile Ile 625 630 635 640 Lys Asp Lys Asp Phe Leu Asp Asn Glu Glu Asn
Glu Asp Ile Leu Glu 645 650 655 Asp Ile Val Leu Thr Leu Thr Leu Phe
Glu Asp Arg Glu Met Ile Glu 660 665 670 Glu Arg Leu Lys Thr Tyr Ala
His Leu Phe Asp Asp Lys Val Met Lys 675 680 685 Gln Leu Lys Arg Arg
Arg Tyr Thr Gly Trp Gly Arg Leu Ser Arg Lys 690 695 700 Leu Ile Asn
Gly Ile Arg Asp Lys Gln Ser Gly Lys Thr Ile Leu Asp 705 710 715 720
Phe Leu Lys Ser Asp Gly Phe Ala Asn Arg Asn Phe Met Gln Leu Ile 725
730 735 His Asp Asp Ser Leu Thr Phe Lys Glu Asp Ile Gln Lys Ala Gln
Val 740 745 750 Ser Gly Gln Gly Asp Ser Leu His Glu His Ile Ala Asn
Leu Ala Gly 755 760 765 Ser Pro Ala Ile Lys Lys Gly Ile Leu Gln Thr
Val Lys Val Val Asp 770 775 780 Glu Leu Val Lys Val Met Gly Arg His
Lys Pro Glu Asn Ile Val Ile 785 790 795 800 Glu Met Ala Arg Glu Asn
Gln Thr Thr Gln Lys Gly Gln Lys Asn Ser 805 810 815 Arg Glu Arg Met
Lys Arg Ile Glu Glu Gly Ile Lys Glu Leu Gly Ser 820 825 830 Gln Ile
Leu Lys Glu His Pro Val Glu Asn Thr Gln Leu Gln Asn Glu 835 840 845
Lys Leu Tyr Leu Tyr Tyr Leu Gln Asn Gly Arg Asp Met Tyr Val Asp 850
855 860 Gln Glu Leu Asp Ile Asn Arg Leu Ser Asp Tyr Asp Val Asp His
Ile 865 870 875 880 Val Pro Gln Ser Phe Leu Lys Asp Asp Ser Ile Asp
Asn Lys Val Leu 885 890 895 Thr Arg Ser Asp Lys Asn Arg Gly Lys Ser
Asp Asn Val Pro Ser Glu 900 905 910 Glu Val Val Lys Lys Met Lys Asn
Tyr Trp Arg Gln Leu Leu Asn Ala 915 920 925 Lys Leu Ile Thr Gln Arg
Lys Phe Asp Asn Leu Thr Lys Ala Glu Arg 930 935 940 Gly Gly Leu Ser
Glu Leu Asp Lys Ala Gly Phe Ile Lys Arg Gln Leu 945 950 955 960 Val
Glu Thr Arg Gln Ile Thr Lys His Val Ala Gln Ile Leu Asp Ser 965 970
975 Arg Met Asn Thr Lys Tyr Asp Glu Asn Asp Lys Leu Ile Arg Glu Val
980 985 990 Lys Val Ile Thr Leu Lys Ser Lys Leu Val Ser Asp Phe Arg
Lys Asp 995 1000 1005 Phe Gln Phe Tyr Lys Val Arg Glu Ile Asn Asn
Tyr His His Ala 1010 1015 1020 His Asp Ala Tyr Leu Asn Ala Val Val
Gly Thr Ala Leu Ile Lys 1025 1030 1035 Lys Tyr Pro Lys Leu Glu Ser
Glu Phe Val Tyr Gly Asp Tyr Lys 1040 1045 1050 Val Tyr Asp Val Arg
Lys Met Ile Ala Lys Ser Glu Gln Glu Ile 1055 1060 1065 Gly Lys Ala
Thr Ala Lys Tyr Phe Phe Tyr Ser Asn Ile Met Asn 1070 1075 1080 Phe
Phe Lys Thr Glu Ile Thr Leu Ala Asn Gly Glu Ile Arg Lys 1085 1090
1095 Arg Pro Leu Ile Glu Thr Asn Gly Glu Thr Gly Glu Ile Val Trp
1100 1105 1110 Asp Lys Gly Arg Asp Phe Ala Thr Val Arg Lys Val Leu
Ser Met 1115 1120 1125 Pro Gln Val Asn Ile Val Lys Lys Thr Glu Val
Gln Thr Gly Gly 1130 1135 1140 Phe Ser Lys Glu Ser Ile Leu Pro Lys
Arg Asn Ser Asp Lys Leu 1145 1150 1155 Ile Ala Arg Lys Lys Asp Trp
Asp Pro Lys Lys Tyr Gly Gly Phe 1160 1165 1170 Asp Ser Pro Thr Val
Ala Tyr Ser Val Leu Val Val Ala Lys Val 1175 1180 1185 Glu Lys Gly
Lys Ser Lys Lys Leu Lys Ser Val Lys Glu Leu Leu 1190 1195 1200 Gly
Ile Thr Ile Met Glu Arg Ser Ser Phe Glu Lys Asn Pro Ile 1205 1210
1215 Asp Phe Leu Glu Ala Lys Gly Tyr Lys Glu Val Lys Lys Asp Leu
1220 1225 1230 Ile Ile Lys Leu Pro Lys Tyr Ser Leu Phe Glu Leu Glu
Asn Gly 1235 1240 1245 Arg Lys Arg Met Leu Ala Ser Ala Gly Glu Leu
Gln Lys Gly Asn 1250 1255 1260 Glu Leu Ala Leu Pro Ser Lys Tyr Val
Asn Phe Leu Tyr Leu Ala 1265 1270 1275 Ser His Tyr Glu Lys Leu Lys
Gly Ser Pro Glu Asp Asn Glu Gln 1280 1285 1290 Lys Gln Leu Phe Val
Glu Gln His Lys His Tyr Leu Asp Glu Ile 1295 1300 1305 Ile Glu Gln
Ile Ser Glu Phe Ser Lys Arg Val Ile Leu Ala Asp 1310 1315 1320 Ala
Asn Leu Asp Lys Val Leu Ser Ala Tyr Asn Lys His Arg Asp 1325 1330
1335 Lys Pro Ile Arg Glu Gln Ala Glu Asn Ile Ile His Leu Phe Thr
1340 1345 1350 Leu Thr Asn Leu Gly Ala Pro Ala Ala Phe Lys Tyr Phe
Asp Thr 1355 1360 1365 Thr Ile Asp Arg Lys Arg Tyr Thr Ser Thr Lys
Glu Val Leu Asp 1370 1375 1380 Ala Thr Leu Ile His Gln Ser Ile Thr
Gly Leu Tyr Glu Thr Arg 1385 1390 1395 Ile Asp Leu Ser Gln Leu Gly
Gly Asp Ala Ala Ala Val Ser Lys 1400 1405 1410 Gly Glu Glu Leu Phe
Thr Gly Val Val Pro Ile Leu Val Glu Leu 1415 1420 1425 Asp Gly Asp
Val Asn Gly His Lys Phe Ser Val Ser Gly Glu Gly 1430 1435 1440 Glu
Gly Asp Ala Thr Tyr Gly Lys Leu Thr Leu Lys Phe Ile Cys 1445 1450
1455 Thr Thr Gly Lys Leu Pro Val Pro Trp Pro Thr Leu Val Thr Thr
1460 1465 1470 Leu Thr Tyr Gly Val Gln Cys Phe Ser Arg Tyr Pro Asp
His Met 1475 1480 1485 Lys Gln His Asp Phe Phe Lys Ser Ala Met Pro
Glu Gly Tyr Val 1490 1495 1500 Gln Glu Arg Thr Ile Phe Phe Lys Asp
Asp Gly Asn Tyr Lys Thr 1505 1510 1515 Arg Ala Glu Val Lys Phe Glu
Gly Asp Thr Leu Val Asn Arg Ile 1520 1525 1530 Glu Leu Lys Gly Ile
Asp Phe Lys Glu Asp Gly Asn Ile Leu Gly 1535 1540 1545 His Lys Leu
Glu Tyr Asn Tyr Asn Ser His Asn Val Tyr Ile Met 1550 1555 1560 Ala
Asp Lys Gln Lys Asn Gly Ile Lys Val Asn Phe Lys Ile Arg 1565 1570
1575 His Asn Ile Glu Asp Gly Ser Val Gln Leu Ala Asp His Tyr Gln
1580 1585 1590 Gln Asn Thr Pro Ile Gly Asp Gly Pro Val Leu Leu Pro
Asp Asn 1595 1600 1605 His Tyr Leu Ser Thr Gln Ser Ala Leu Ser Lys
Asp Pro Asn Glu 1610 1615 1620 Lys Arg Asp His Met Val Leu Leu Glu
Phe Val Thr Ala Ala Gly 1625 1630 1635 Ile Thr Leu Gly Met Asp Glu
Leu Tyr Lys Lys Arg Pro Ala Ala 1640 1645 1650 Thr Lys Lys Ala Gly
Gln Ala Lys Lys Lys Lys 1655 1660 471423PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
47Met Asp Tyr Lys Asp His Asp Gly Asp Tyr Lys Asp His Asp Ile Asp 1
5 10 15 Tyr Lys Asp Asp Asp Asp Lys Met Ala Pro Lys Lys Lys Arg Lys
Val 20 25 30 Gly Ile His Gly Val Pro Ala Ala Asp Lys Lys Tyr Ser
Ile Gly Leu 35 40 45 Asp Ile Gly Thr Asn Ser Val Gly Trp Ala Val
Ile Thr Asp Glu Tyr 50 55 60 Lys Val Pro Ser Lys Lys Phe Lys Val
Leu Gly Asn Thr Asp Arg His 65 70 75 80 Ser Ile Lys Lys Asn Leu Ile
Gly Ala Leu Leu Phe Asp Ser Gly Glu 85 90 95 Thr Ala Glu Ala Thr
Arg Leu Lys Arg Thr Ala Arg Arg Arg Tyr Thr 100 105 110 Arg Arg Lys
Asn Arg Ile Cys Tyr Leu Gln Glu Ile Phe Ser Asn Glu 115 120 125 Met
Ala Lys Val Asp Asp Ser Phe Phe His Arg Leu Glu Glu Ser Phe 130 135
140 Leu Val Glu Glu Asp Lys Lys His Glu Arg His Pro Ile Phe Gly Asn
145 150 155 160 Ile Val Asp Glu Val Ala Tyr His Glu Lys Tyr Pro Thr
Ile Tyr His 165 170 175 Leu Arg Lys Lys Leu Val Asp Ser Thr Asp Lys
Ala Asp Leu Arg Leu 180 185 190 Ile Tyr Leu Ala Leu Ala His Met Ile
Lys Phe Arg Gly His Phe Leu 195 200 205 Ile Glu Gly Asp Leu Asn Pro
Asp Asn Ser Asp Val Asp Lys Leu Phe 210 215 220 Ile Gln Leu Val Gln
Thr Tyr Asn Gln Leu Phe Glu Glu Asn Pro Ile 225 230 235 240 Asn Ala
Ser Gly Val Asp Ala Lys Ala Ile Leu Ser Ala Arg Leu Ser 245 250 255
Lys Ser Arg Arg Leu Glu Asn Leu Ile Ala Gln Leu Pro Gly Glu Lys 260
265 270 Lys Asn Gly Leu Phe Gly Asn Leu Ile Ala Leu Ser Leu Gly Leu
Thr 275 280 285 Pro Asn Phe Lys Ser Asn Phe Asp Leu Ala Glu Asp Ala
Lys Leu Gln 290 295 300 Leu Ser Lys Asp Thr Tyr Asp Asp Asp Leu Asp
Asn Leu Leu Ala Gln 305 310 315 320 Ile Gly Asp Gln Tyr Ala Asp Leu
Phe Leu Ala Ala Lys Asn Leu Ser 325 330 335 Asp Ala Ile Leu Leu Ser
Asp Ile Leu Arg Val Asn Thr Glu Ile Thr 340 345 350 Lys Ala Pro Leu
Ser Ala Ser Met Ile Lys Arg Tyr Asp Glu His His 355 360 365 Gln Asp
Leu Thr Leu Leu Lys Ala Leu Val Arg Gln Gln Leu Pro Glu 370 375 380
Lys Tyr Lys Glu Ile Phe Phe Asp Gln Ser Lys Asn Gly Tyr Ala Gly 385
390 395 400 Tyr Ile Asp Gly Gly Ala Ser Gln Glu Glu Phe Tyr Lys Phe
Ile Lys 405 410 415 Pro Ile Leu Glu Lys Met Asp Gly Thr Glu Glu Leu
Leu Val Lys Leu 420 425 430 Asn Arg Glu Asp Leu Leu Arg Lys Gln Arg
Thr Phe Asp Asn Gly Ser 435 440 445 Ile Pro His Gln Ile His Leu Gly
Glu Leu His Ala Ile Leu Arg Arg 450 455 460 Gln Glu Asp Phe Tyr Pro
Phe Leu Lys Asp Asn Arg Glu Lys Ile Glu 465 470 475 480 Lys Ile Leu
Thr Phe Arg Ile Pro Tyr Tyr Val Gly Pro Leu Ala Arg 485 490 495 Gly
Asn Ser Arg Phe Ala Trp Met Thr Arg Lys Ser Glu Glu Thr Ile 500 505
510 Thr Pro Trp Asn Phe Glu Glu Val Val Asp Lys Gly Ala Ser Ala Gln
515 520 525 Ser Phe Ile Glu Arg Met Thr Asn Phe Asp Lys Asn Leu Pro
Asn Glu 530 535 540 Lys Val Leu Pro Lys His Ser Leu Leu Tyr Glu Tyr
Phe Thr Val Tyr 545 550 555 560 Asn Glu Leu Thr Lys Val Lys Tyr Val
Thr Glu Gly Met Arg Lys Pro 565 570 575 Ala Phe Leu Ser Gly Glu Gln
Lys Lys Ala Ile Val Asp Leu Leu Phe 580 585 590 Lys Thr Asn Arg Lys
Val Thr Val Lys Gln Leu Lys Glu Asp Tyr Phe 595 600 605 Lys Lys Ile
Glu Cys Phe Asp Ser Val Glu Ile Ser Gly Val Glu Asp 610 615 620 Arg
Phe Asn Ala Ser Leu Gly Thr Tyr His Asp Leu Leu Lys Ile Ile 625 630
635 640 Lys Asp Lys Asp Phe Leu Asp Asn Glu Glu Asn Glu Asp Ile Leu
Glu 645 650 655 Asp Ile Val Leu Thr Leu Thr Leu Phe Glu Asp Arg Glu
Met Ile Glu 660 665 670 Glu Arg Leu Lys Thr Tyr Ala His Leu Phe Asp
Asp Lys Val Met Lys 675 680 685 Gln Leu Lys Arg Arg Arg Tyr Thr Gly
Trp Gly Arg Leu Ser Arg Lys 690 695 700 Leu Ile Asn Gly
Ile Arg Asp Lys Gln Ser Gly Lys Thr Ile Leu Asp 705 710 715 720 Phe
Leu Lys Ser Asp Gly Phe Ala Asn Arg Asn Phe Met Gln Leu Ile 725 730
735 His Asp Asp Ser Leu Thr Phe Lys Glu Asp Ile Gln Lys Ala Gln Val
740 745 750 Ser Gly Gln Gly Asp Ser Leu His Glu His Ile Ala Asn Leu
Ala Gly 755 760 765 Ser Pro Ala Ile Lys Lys Gly Ile Leu Gln Thr Val
Lys Val Val Asp 770 775 780 Glu Leu Val Lys Val Met Gly Arg His Lys
Pro Glu Asn Ile Val Ile 785 790 795 800 Glu Met Ala Arg Glu Asn Gln
Thr Thr Gln Lys Gly Gln Lys Asn Ser 805 810 815 Arg Glu Arg Met Lys
Arg Ile Glu Glu Gly Ile Lys Glu Leu Gly Ser 820 825 830 Gln Ile Leu
Lys Glu His Pro Val Glu Asn Thr Gln Leu Gln Asn Glu 835 840 845 Lys
Leu Tyr Leu Tyr Tyr Leu Gln Asn Gly Arg Asp Met Tyr Val Asp 850 855
860 Gln Glu Leu Asp Ile Asn Arg Leu Ser Asp Tyr Asp Val Asp His Ile
865 870 875 880 Val Pro Gln Ser Phe Leu Lys Asp Asp Ser Ile Asp Asn
Lys Val Leu 885 890 895 Thr Arg Ser Asp Lys Asn Arg Gly Lys Ser Asp
Asn Val Pro Ser Glu 900 905 910 Glu Val Val Lys Lys Met Lys Asn Tyr
Trp Arg Gln Leu Leu Asn Ala 915 920 925 Lys Leu Ile Thr Gln Arg Lys
Phe Asp Asn Leu Thr Lys Ala Glu Arg 930 935 940 Gly Gly Leu Ser Glu
Leu Asp Lys Ala Gly Phe Ile Lys Arg Gln Leu 945 950 955 960 Val Glu
Thr Arg Gln Ile Thr Lys His Val Ala Gln Ile Leu Asp Ser 965 970 975
Arg Met Asn Thr Lys Tyr Asp Glu Asn Asp Lys Leu Ile Arg Glu Val 980
985 990 Lys Val Ile Thr Leu Lys Ser Lys Leu Val Ser Asp Phe Arg Lys
Asp 995 1000 1005 Phe Gln Phe Tyr Lys Val Arg Glu Ile Asn Asn Tyr
His His Ala 1010 1015 1020 His Asp Ala Tyr Leu Asn Ala Val Val Gly
Thr Ala Leu Ile Lys 1025 1030 1035 Lys Tyr Pro Lys Leu Glu Ser Glu
Phe Val Tyr Gly Asp Tyr Lys 1040 1045 1050 Val Tyr Asp Val Arg Lys
Met Ile Ala Lys Ser Glu Gln Glu Ile 1055 1060 1065 Gly Lys Ala Thr
Ala Lys Tyr Phe Phe Tyr Ser Asn Ile Met Asn 1070 1075 1080 Phe Phe
Lys Thr Glu Ile Thr Leu Ala Asn Gly Glu Ile Arg Lys 1085 1090 1095
Arg Pro Leu Ile Glu Thr Asn Gly Glu Thr Gly Glu Ile Val Trp 1100
1105 1110 Asp Lys Gly Arg Asp Phe Ala Thr Val Arg Lys Val Leu Ser
Met 1115 1120 1125 Pro Gln Val Asn Ile Val Lys Lys Thr Glu Val Gln
Thr Gly Gly 1130 1135 1140 Phe Ser Lys Glu Ser Ile Leu Pro Lys Arg
Asn Ser Asp Lys Leu 1145 1150 1155 Ile Ala Arg Lys Lys Asp Trp Asp
Pro Lys Lys Tyr Gly Gly Phe 1160 1165 1170 Asp Ser Pro Thr Val Ala
Tyr Ser Val Leu Val Val Ala Lys Val 1175 1180 1185 Glu Lys Gly Lys
Ser Lys Lys Leu Lys Ser Val Lys Glu Leu Leu 1190 1195 1200 Gly Ile
Thr Ile Met Glu Arg Ser Ser Phe Glu Lys Asn Pro Ile 1205 1210 1215
Asp Phe Leu Glu Ala Lys Gly Tyr Lys Glu Val Lys Lys Asp Leu 1220
1225 1230 Ile Ile Lys Leu Pro Lys Tyr Ser Leu Phe Glu Leu Glu Asn
Gly 1235 1240 1245 Arg Lys Arg Met Leu Ala Ser Ala Gly Glu Leu Gln
Lys Gly Asn 1250 1255 1260 Glu Leu Ala Leu Pro Ser Lys Tyr Val Asn
Phe Leu Tyr Leu Ala 1265 1270 1275 Ser His Tyr Glu Lys Leu Lys Gly
Ser Pro Glu Asp Asn Glu Gln 1280 1285 1290 Lys Gln Leu Phe Val Glu
Gln His Lys His Tyr Leu Asp Glu Ile 1295 1300 1305 Ile Glu Gln Ile
Ser Glu Phe Ser Lys Arg Val Ile Leu Ala Asp 1310 1315 1320 Ala Asn
Leu Asp Lys Val Leu Ser Ala Tyr Asn Lys His Arg Asp 1325 1330 1335
Lys Pro Ile Arg Glu Gln Ala Glu Asn Ile Ile His Leu Phe Thr 1340
1345 1350 Leu Thr Asn Leu Gly Ala Pro Ala Ala Phe Lys Tyr Phe Asp
Thr 1355 1360 1365 Thr Ile Asp Arg Lys Arg Tyr Thr Ser Thr Lys Glu
Val Leu Asp 1370 1375 1380 Ala Thr Leu Ile His Gln Ser Ile Thr Gly
Leu Tyr Glu Thr Arg 1385 1390 1395 Ile Asp Leu Ser Gln Leu Gly Gly
Asp Lys Arg Pro Ala Ala Thr 1400 1405 1410 Lys Lys Ala Gly Gln Ala
Lys Lys Lys Lys 1415 1420 48483PRTArtificial SequenceDescription of
Artificial Sequence Synthetic polypeptide 48Met Phe Leu Phe Leu Ser
Leu Thr Ser Phe Leu Ser Ser Ser Arg Thr 1 5 10 15 Leu Val Ser Lys
Gly Glu Glu Asp Asn Met Ala Ile Ile Lys Glu Phe 20 25 30 Met Arg
Phe Lys Val His Met Glu Gly Ser Val Asn Gly His Glu Phe 35 40 45
Glu Ile Glu Gly Glu Gly Glu Gly Arg Pro Tyr Glu Gly Thr Gln Thr 50
55 60 Ala Lys Leu Lys Val Thr Lys Gly Gly Pro Leu Pro Phe Ala Trp
Asp 65 70 75 80 Ile Leu Ser Pro Gln Phe Met Tyr Gly Ser Lys Ala Tyr
Val Lys His 85 90 95 Pro Ala Asp Ile Pro Asp Tyr Leu Lys Leu Ser
Phe Pro Glu Gly Phe 100 105 110 Lys Trp Glu Arg Val Met Asn Phe Glu
Asp Gly Gly Val Val Thr Val 115 120 125 Thr Gln Asp Ser Ser Leu Gln
Asp Gly Glu Phe Ile Tyr Lys Val Lys 130 135 140 Leu Arg Gly Thr Asn
Phe Pro Ser Asp Gly Pro Val Met Gln Lys Lys 145 150 155 160 Thr Met
Gly Trp Glu Ala Ser Ser Glu Arg Met Tyr Pro Glu Asp Gly 165 170 175
Ala Leu Lys Gly Glu Ile Lys Gln Arg Leu Lys Leu Lys Asp Gly Gly 180
185 190 His Tyr Asp Ala Glu Val Lys Thr Thr Tyr Lys Ala Lys Lys Pro
Val 195 200 205 Gln Leu Pro Gly Ala Tyr Asn Val Asn Ile Lys Leu Asp
Ile Thr Ser 210 215 220 His Asn Glu Asp Tyr Thr Ile Val Glu Gln Tyr
Glu Arg Ala Glu Gly 225 230 235 240 Arg His Ser Thr Gly Gly Met Asp
Glu Leu Tyr Lys Gly Ser Lys Gln 245 250 255 Leu Glu Glu Leu Leu Ser
Thr Ser Phe Asp Ile Gln Phe Asn Asp Leu 260 265 270 Thr Leu Leu Glu
Thr Ala Phe Thr His Thr Ser Tyr Ala Asn Glu His 275 280 285 Arg Leu
Leu Asn Val Ser His Asn Glu Arg Leu Glu Phe Leu Gly Asp 290 295 300
Ala Val Leu Gln Leu Ile Ile Ser Glu Tyr Leu Phe Ala Lys Tyr Pro 305
310 315 320 Lys Lys Thr Glu Gly Asp Met Ser Lys Leu Arg Ser Met Ile
Val Arg 325 330 335 Glu Glu Ser Leu Ala Gly Phe Ser Arg Phe Cys Ser
Phe Asp Ala Tyr 340 345 350 Ile Lys Leu Gly Lys Gly Glu Glu Lys Ser
Gly Gly Arg Arg Arg Asp 355 360 365 Thr Ile Leu Gly Asp Leu Phe Glu
Ala Phe Leu Gly Ala Leu Leu Leu 370 375 380 Asp Lys Gly Ile Asp Ala
Val Arg Arg Phe Leu Lys Gln Val Met Ile 385 390 395 400 Pro Gln Val
Glu Lys Gly Asn Phe Glu Arg Val Lys Asp Tyr Lys Thr 405 410 415 Cys
Leu Gln Glu Phe Leu Gln Thr Lys Gly Asp Val Ala Ile Asp Tyr 420 425
430 Gln Val Ile Ser Glu Lys Gly Pro Ala His Ala Lys Gln Phe Glu Val
435 440 445 Ser Ile Val Val Asn Gly Ala Val Leu Ser Lys Gly Leu Gly
Lys Ser 450 455 460 Lys Lys Leu Ala Glu Gln Asp Ala Ala Lys Asn Ala
Leu Ala Gln Leu 465 470 475 480 Ser Glu Val 49483PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
49Met Lys Gln Leu Glu Glu Leu Leu Ser Thr Ser Phe Asp Ile Gln Phe 1
5 10 15 Asn Asp Leu Thr Leu Leu Glu Thr Ala Phe Thr His Thr Ser Tyr
Ala 20 25 30 Asn Glu His Arg Leu Leu Asn Val Ser His Asn Glu Arg
Leu Glu Phe 35 40 45 Leu Gly Asp Ala Val Leu Gln Leu Ile Ile Ser
Glu Tyr Leu Phe Ala 50 55 60 Lys Tyr Pro Lys Lys Thr Glu Gly Asp
Met Ser Lys Leu Arg Ser Met 65 70 75 80 Ile Val Arg Glu Glu Ser Leu
Ala Gly Phe Ser Arg Phe Cys Ser Phe 85 90 95 Asp Ala Tyr Ile Lys
Leu Gly Lys Gly Glu Glu Lys Ser Gly Gly Arg 100 105 110 Arg Arg Asp
Thr Ile Leu Gly Asp Leu Phe Glu Ala Phe Leu Gly Ala 115 120 125 Leu
Leu Leu Asp Lys Gly Ile Asp Ala Val Arg Arg Phe Leu Lys Gln 130 135
140 Val Met Ile Pro Gln Val Glu Lys Gly Asn Phe Glu Arg Val Lys Asp
145 150 155 160 Tyr Lys Thr Cys Leu Gln Glu Phe Leu Gln Thr Lys Gly
Asp Val Ala 165 170 175 Ile Asp Tyr Gln Val Ile Ser Glu Lys Gly Pro
Ala His Ala Lys Gln 180 185 190 Phe Glu Val Ser Ile Val Val Asn Gly
Ala Val Leu Ser Lys Gly Leu 195 200 205 Gly Lys Ser Lys Lys Leu Ala
Glu Gln Asp Ala Ala Lys Asn Ala Leu 210 215 220 Ala Gln Leu Ser Glu
Val Gly Ser Val Ser Lys Gly Glu Glu Asp Asn 225 230 235 240 Met Ala
Ile Ile Lys Glu Phe Met Arg Phe Lys Val His Met Glu Gly 245 250 255
Ser Val Asn Gly His Glu Phe Glu Ile Glu Gly Glu Gly Glu Gly Arg 260
265 270 Pro Tyr Glu Gly Thr Gln Thr Ala Lys Leu Lys Val Thr Lys Gly
Gly 275 280 285 Pro Leu Pro Phe Ala Trp Asp Ile Leu Ser Pro Gln Phe
Met Tyr Gly 290 295 300 Ser Lys Ala Tyr Val Lys His Pro Ala Asp Ile
Pro Asp Tyr Leu Lys 305 310 315 320 Leu Ser Phe Pro Glu Gly Phe Lys
Trp Glu Arg Val Met Asn Phe Glu 325 330 335 Asp Gly Gly Val Val Thr
Val Thr Gln Asp Ser Ser Leu Gln Asp Gly 340 345 350 Glu Phe Ile Tyr
Lys Val Lys Leu Arg Gly Thr Asn Phe Pro Ser Asp 355 360 365 Gly Pro
Val Met Gln Lys Lys Thr Met Gly Trp Glu Ala Ser Ser Glu 370 375 380
Arg Met Tyr Pro Glu Asp Gly Ala Leu Lys Gly Glu Ile Lys Gln Arg 385
390 395 400 Leu Lys Leu Lys Asp Gly Gly His Tyr Asp Ala Glu Val Lys
Thr Thr 405 410 415 Tyr Lys Ala Lys Lys Pro Val Gln Leu Pro Gly Ala
Tyr Asn Val Asn 420 425 430 Ile Lys Leu Asp Ile Thr Ser His Asn Glu
Asp Tyr Thr Ile Val Glu 435 440 445 Gln Tyr Glu Arg Ala Glu Gly Arg
His Ser Thr Gly Gly Met Asp Glu 450 455 460 Leu Tyr Lys Lys Arg Pro
Ala Ala Thr Lys Lys Ala Gly Gln Ala Lys 465 470 475 480 Lys Lys Lys
501423PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 50Met Asp Tyr Lys Asp His Asp Gly Asp Tyr Lys
Asp His Asp Ile Asp 1 5 10 15 Tyr Lys Asp Asp Asp Asp Lys Met Ala
Pro Lys Lys Lys Arg Lys Val 20 25 30 Gly Ile His Gly Val Pro Ala
Ala Asp Lys Lys Tyr Ser Ile Gly Leu 35 40 45 Ala Ile Gly Thr Asn
Ser Val Gly Trp Ala Val Ile Thr Asp Glu Tyr 50 55 60 Lys Val Pro
Ser Lys Lys Phe Lys Val Leu Gly Asn Thr Asp Arg His 65 70 75 80 Ser
Ile Lys Lys Asn Leu Ile Gly Ala Leu Leu Phe Asp Ser Gly Glu 85 90
95 Thr Ala Glu Ala Thr Arg Leu Lys Arg Thr Ala Arg Arg Arg Tyr Thr
100 105 110 Arg Arg Lys Asn Arg Ile Cys Tyr Leu Gln Glu Ile Phe Ser
Asn Glu 115 120 125 Met Ala Lys Val Asp Asp Ser Phe Phe His Arg Leu
Glu Glu Ser Phe 130 135 140 Leu Val Glu Glu Asp Lys Lys His Glu Arg
His Pro Ile Phe Gly Asn 145 150 155 160 Ile Val Asp Glu Val Ala Tyr
His Glu Lys Tyr Pro Thr Ile Tyr His 165 170 175 Leu Arg Lys Lys Leu
Val Asp Ser Thr Asp Lys Ala Asp Leu Arg Leu 180 185 190 Ile Tyr Leu
Ala Leu Ala His Met Ile Lys Phe Arg Gly His Phe Leu 195 200 205 Ile
Glu Gly Asp Leu Asn Pro Asp Asn Ser Asp Val Asp Lys Leu Phe 210 215
220 Ile Gln Leu Val Gln Thr Tyr Asn Gln Leu Phe Glu Glu Asn Pro Ile
225 230 235 240 Asn Ala Ser Gly Val Asp Ala Lys Ala Ile Leu Ser Ala
Arg Leu Ser 245 250 255 Lys Ser Arg Arg Leu Glu Asn Leu Ile Ala Gln
Leu Pro Gly Glu Lys 260 265 270 Lys Asn Gly Leu Phe Gly Asn Leu Ile
Ala Leu Ser Leu Gly Leu Thr 275 280 285 Pro Asn Phe Lys Ser Asn Phe
Asp Leu Ala Glu Asp Ala Lys Leu Gln 290 295 300 Leu Ser Lys Asp Thr
Tyr Asp Asp Asp Leu Asp Asn Leu Leu Ala Gln 305 310 315 320 Ile Gly
Asp Gln Tyr Ala Asp Leu Phe Leu Ala Ala Lys Asn Leu Ser 325 330 335
Asp Ala Ile Leu Leu Ser Asp Ile Leu Arg Val Asn Thr Glu Ile Thr 340
345 350 Lys Ala Pro Leu Ser Ala Ser Met Ile Lys Arg Tyr Asp Glu His
His 355 360 365 Gln Asp Leu Thr Leu Leu Lys Ala Leu Val Arg Gln Gln
Leu Pro Glu 370 375 380 Lys Tyr Lys Glu Ile Phe Phe Asp Gln Ser Lys
Asn Gly Tyr Ala Gly 385 390 395 400 Tyr Ile Asp Gly Gly Ala Ser Gln
Glu Glu Phe Tyr Lys Phe Ile Lys 405 410 415 Pro Ile Leu Glu Lys Met
Asp Gly Thr Glu Glu Leu Leu Val Lys Leu 420 425 430 Asn Arg Glu Asp
Leu Leu Arg Lys Gln Arg Thr Phe Asp Asn Gly Ser 435 440 445 Ile Pro
His Gln Ile His Leu Gly Glu Leu His Ala Ile Leu Arg Arg 450 455 460
Gln Glu Asp Phe Tyr Pro Phe Leu Lys Asp Asn Arg Glu Lys Ile Glu 465
470 475 480 Lys Ile Leu Thr Phe Arg Ile Pro Tyr Tyr Val Gly Pro Leu
Ala Arg 485 490 495 Gly Asn Ser Arg Phe Ala Trp Met Thr Arg Lys Ser
Glu Glu Thr Ile 500 505 510 Thr Pro Trp Asn Phe Glu Glu Val Val Asp
Lys Gly Ala Ser Ala Gln 515 520 525 Ser Phe Ile Glu Arg Met Thr Asn
Phe Asp Lys Asn Leu Pro Asn Glu 530 535 540 Lys Val Leu Pro Lys His
Ser Leu Leu Tyr Glu Tyr Phe Thr Val Tyr 545 550 555 560 Asn Glu Leu
Thr Lys Val Lys Tyr Val Thr Glu Gly Met Arg Lys Pro 565
570 575 Ala Phe Leu Ser Gly Glu Gln Lys Lys Ala Ile Val Asp Leu Leu
Phe 580 585 590 Lys Thr Asn Arg Lys Val Thr Val Lys Gln Leu Lys Glu
Asp Tyr Phe 595 600 605 Lys Lys Ile Glu Cys Phe Asp Ser Val Glu Ile
Ser Gly Val Glu Asp 610 615 620 Arg Phe Asn Ala Ser Leu Gly Thr Tyr
His Asp Leu Leu Lys Ile Ile 625 630 635 640 Lys Asp Lys Asp Phe Leu
Asp Asn Glu Glu Asn Glu Asp Ile Leu Glu 645 650 655 Asp Ile Val Leu
Thr Leu Thr Leu Phe Glu Asp Arg Glu Met Ile Glu 660 665 670 Glu Arg
Leu Lys Thr Tyr Ala His Leu Phe Asp Asp Lys Val Met Lys 675 680 685
Gln Leu Lys Arg Arg Arg Tyr Thr Gly Trp Gly Arg Leu Ser Arg Lys 690
695 700 Leu Ile Asn Gly Ile Arg Asp Lys Gln Ser Gly Lys Thr Ile Leu
Asp 705 710 715 720 Phe Leu Lys Ser Asp Gly Phe Ala Asn Arg Asn Phe
Met Gln Leu Ile 725 730 735 His Asp Asp Ser Leu Thr Phe Lys Glu Asp
Ile Gln Lys Ala Gln Val 740 745 750 Ser Gly Gln Gly Asp Ser Leu His
Glu His Ile Ala Asn Leu Ala Gly 755 760 765 Ser Pro Ala Ile Lys Lys
Gly Ile Leu Gln Thr Val Lys Val Val Asp 770 775 780 Glu Leu Val Lys
Val Met Gly Arg His Lys Pro Glu Asn Ile Val Ile 785 790 795 800 Glu
Met Ala Arg Glu Asn Gln Thr Thr Gln Lys Gly Gln Lys Asn Ser 805 810
815 Arg Glu Arg Met Lys Arg Ile Glu Glu Gly Ile Lys Glu Leu Gly Ser
820 825 830 Gln Ile Leu Lys Glu His Pro Val Glu Asn Thr Gln Leu Gln
Asn Glu 835 840 845 Lys Leu Tyr Leu Tyr Tyr Leu Gln Asn Gly Arg Asp
Met Tyr Val Asp 850 855 860 Gln Glu Leu Asp Ile Asn Arg Leu Ser Asp
Tyr Asp Val Asp His Ile 865 870 875 880 Val Pro Gln Ser Phe Leu Lys
Asp Asp Ser Ile Asp Asn Lys Val Leu 885 890 895 Thr Arg Ser Asp Lys
Asn Arg Gly Lys Ser Asp Asn Val Pro Ser Glu 900 905 910 Glu Val Val
Lys Lys Met Lys Asn Tyr Trp Arg Gln Leu Leu Asn Ala 915 920 925 Lys
Leu Ile Thr Gln Arg Lys Phe Asp Asn Leu Thr Lys Ala Glu Arg 930 935
940 Gly Gly Leu Ser Glu Leu Asp Lys Ala Gly Phe Ile Lys Arg Gln Leu
945 950 955 960 Val Glu Thr Arg Gln Ile Thr Lys His Val Ala Gln Ile
Leu Asp Ser 965 970 975 Arg Met Asn Thr Lys Tyr Asp Glu Asn Asp Lys
Leu Ile Arg Glu Val 980 985 990 Lys Val Ile Thr Leu Lys Ser Lys Leu
Val Ser Asp Phe Arg Lys Asp 995 1000 1005 Phe Gln Phe Tyr Lys Val
Arg Glu Ile Asn Asn Tyr His His Ala 1010 1015 1020 His Asp Ala Tyr
Leu Asn Ala Val Val Gly Thr Ala Leu Ile Lys 1025 1030 1035 Lys Tyr
Pro Lys Leu Glu Ser Glu Phe Val Tyr Gly Asp Tyr Lys 1040 1045 1050
Val Tyr Asp Val Arg Lys Met Ile Ala Lys Ser Glu Gln Glu Ile 1055
1060 1065 Gly Lys Ala Thr Ala Lys Tyr Phe Phe Tyr Ser Asn Ile Met
Asn 1070 1075 1080 Phe Phe Lys Thr Glu Ile Thr Leu Ala Asn Gly Glu
Ile Arg Lys 1085 1090 1095 Arg Pro Leu Ile Glu Thr Asn Gly Glu Thr
Gly Glu Ile Val Trp 1100 1105 1110 Asp Lys Gly Arg Asp Phe Ala Thr
Val Arg Lys Val Leu Ser Met 1115 1120 1125 Pro Gln Val Asn Ile Val
Lys Lys Thr Glu Val Gln Thr Gly Gly 1130 1135 1140 Phe Ser Lys Glu
Ser Ile Leu Pro Lys Arg Asn Ser Asp Lys Leu 1145 1150 1155 Ile Ala
Arg Lys Lys Asp Trp Asp Pro Lys Lys Tyr Gly Gly Phe 1160 1165 1170
Asp Ser Pro Thr Val Ala Tyr Ser Val Leu Val Val Ala Lys Val 1175
1180 1185 Glu Lys Gly Lys Ser Lys Lys Leu Lys Ser Val Lys Glu Leu
Leu 1190 1195 1200 Gly Ile Thr Ile Met Glu Arg Ser Ser Phe Glu Lys
Asn Pro Ile 1205 1210 1215 Asp Phe Leu Glu Ala Lys Gly Tyr Lys Glu
Val Lys Lys Asp Leu 1220 1225 1230 Ile Ile Lys Leu Pro Lys Tyr Ser
Leu Phe Glu Leu Glu Asn Gly 1235 1240 1245 Arg Lys Arg Met Leu Ala
Ser Ala Gly Glu Leu Gln Lys Gly Asn 1250 1255 1260 Glu Leu Ala Leu
Pro Ser Lys Tyr Val Asn Phe Leu Tyr Leu Ala 1265 1270 1275 Ser His
Tyr Glu Lys Leu Lys Gly Ser Pro Glu Asp Asn Glu Gln 1280 1285 1290
Lys Gln Leu Phe Val Glu Gln His Lys His Tyr Leu Asp Glu Ile 1295
1300 1305 Ile Glu Gln Ile Ser Glu Phe Ser Lys Arg Val Ile Leu Ala
Asp 1310 1315 1320 Ala Asn Leu Asp Lys Val Leu Ser Ala Tyr Asn Lys
His Arg Asp 1325 1330 1335 Lys Pro Ile Arg Glu Gln Ala Glu Asn Ile
Ile His Leu Phe Thr 1340 1345 1350 Leu Thr Asn Leu Gly Ala Pro Ala
Ala Phe Lys Tyr Phe Asp Thr 1355 1360 1365 Thr Ile Asp Arg Lys Arg
Tyr Thr Ser Thr Lys Glu Val Leu Asp 1370 1375 1380 Ala Thr Leu Ile
His Gln Ser Ile Thr Gly Leu Tyr Glu Thr Arg 1385 1390 1395 Ile Asp
Leu Ser Gln Leu Gly Gly Asp Lys Arg Pro Ala Ala Thr 1400 1405 1410
Lys Lys Ala Gly Gln Ala Lys Lys Lys Lys 1415 1420
512012DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 51gaatgctgcc ctcagacccg cttcctccct
gtccttgtct gtccaaggag aatgaggtct 60cactggtgga tttcggacta ccctgaggag
ctggcacctg agggacaagg ccccccacct 120gcccagctcc agcctctgat
gaggggtggg agagagctac atgaggttgc taagaaagcc 180tcccctgaag
gagaccacac agtgtgtgag gttggagtct ctagcagcgg gttctgtgcc
240cccagggata gtctggctgt ccaggcactg ctcttgatat aaacaccacc
tcctagttat 300gaaaccatgc ccattctgcc tctctgtatg gaaaagagca
tggggctggc ccgtggggtg 360gtgtccactt taggccctgt gggagatcat
gggaacccac gcagtgggtc ataggctctc 420tcatttacta ctcacatcca
ctctgtgaag aagcgattat gatctctcct ctagaaactc 480gtagagtccc
atgtctgccg gcttccagag cctgcactcc tccaccttgg cttggctttg
540ctggggctag aggagctagg atgcacagca gctctgtgac cctttgtttg
agaggaacag 600gaaaaccacc cttctctctg gcccactgtg tcctcttcct
gccctgccat ccccttctgt 660gaatgttaga cccatgggag cagctggtca
gaggggaccc cggcctgggg cccctaaccc 720tatgtagcct cagtcttccc
atcaggctct cagctcagcc tgagtgttga ggccccagtg 780gctgctctgg
gggcctcctg agtttctcat ctgtgcccct ccctccctgg cccaggtgaa
840ggtgtggttc cagaaccgga ggacaaagta caaacggcag aagctggagg
aggaagggcc 900tgagtccgag cagaagaaga agggctccca tcacatcaac
cggtggcgca ttgccacgaa 960gcaggccaat ggggaggaca tcgatgtcac
ctccaatgac aagcttgcta gcggtgggca 1020accacaaacc cacgagggca
gagtgctgct tgctgctggc caggcccctg cgtgggccca 1080agctggactc
tggccactcc ctggccaggc tttggggagg cctggagtca tggccccaca
1140gggcttgaag cccggggccg ccattgacag agggacaagc aatgggctgg
ctgaggcctg 1200ggaccacttg gccttctcct cggagagcct gcctgcctgg
gcgggcccgc ccgccaccgc 1260agcctcccag ctgctctccg tgtctccaat
ctcccttttg ttttgatgca tttctgtttt 1320aatttatttt ccaggcacca
ctgtagttta gtgatcccca gtgtccccct tccctatggg 1380aataataaaa
gtctctctct taatgacacg ggcatccagc tccagcccca gagcctgggg
1440tggtagattc cggctctgag ggccagtggg ggctggtaga gcaaacgcgt
tcagggcctg 1500ggagcctggg gtggggtact ggtggagggg gtcaagggta
attcattaac tcctctcttt 1560tgttggggga ccctggtctc tacctccagc
tccacagcag gagaaacagg ctagacatag 1620ggaagggcca tcctgtatct
tgagggagga caggcccagg tctttcttaa cgtattgaga 1680ggtgggaatc
aggcccaggt agttcaatgg gagagggaga gtgcttccct ctgcctagag
1740actctggtgg cttctccagt tgaggagaaa ccagaggaaa ggggaggatt
ggggtctggg 1800ggagggaaca ccattcacaa aggctgacgg ttccagtccg
aagtcgtggg cccaccagga 1860tgctcacctg tccttggaga accgctgggc
aggttgagac tgcagagaca gggcttaagg 1920ctgagcctgc aaccagtccc
cagtgactca gggcctcctc agcccaagaa agagcaacgt 1980gccagggccc
gctgagctct tgtgttcacc tg 2012521153PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
52Met Lys Arg Pro Ala Ala Thr Lys Lys Ala Gly Gln Ala Lys Lys Lys 1
5 10 15 Lys Ser Asp Leu Val Leu Gly Leu Asp Ile Gly Ile Gly Ser Val
Gly 20 25 30 Val Gly Ile Leu Asn Lys Val Thr Gly Glu Ile Ile His
Lys Asn Ser 35 40 45 Arg Ile Phe Pro Ala Ala Gln Ala Glu Asn Asn
Leu Val Arg Arg Thr 50 55 60 Asn Arg Gln Gly Arg Arg Leu Ala Arg
Arg Lys Lys His Arg Arg Val 65 70 75 80 Arg Leu Asn Arg Leu Phe Glu
Glu Ser Gly Leu Ile Thr Asp Phe Thr 85 90 95 Lys Ile Ser Ile Asn
Leu Asn Pro Tyr Gln Leu Arg Val Lys Gly Leu 100 105 110 Thr Asp Glu
Leu Ser Asn Glu Glu Leu Phe Ile Ala Leu Lys Asn Met 115 120 125 Val
Lys His Arg Gly Ile Ser Tyr Leu Asp Asp Ala Ser Asp Asp Gly 130 135
140 Asn Ser Ser Val Gly Asp Tyr Ala Gln Ile Val Lys Glu Asn Ser Lys
145 150 155 160 Gln Leu Glu Thr Lys Thr Pro Gly Gln Ile Gln Leu Glu
Arg Tyr Gln 165 170 175 Thr Tyr Gly Gln Leu Arg Gly Asp Phe Thr Val
Glu Lys Asp Gly Lys 180 185 190 Lys His Arg Leu Ile Asn Val Phe Pro
Thr Ser Ala Tyr Arg Ser Glu 195 200 205 Ala Leu Arg Ile Leu Gln Thr
Gln Gln Glu Phe Asn Pro Gln Ile Thr 210 215 220 Asp Glu Phe Ile Asn
Arg Tyr Leu Glu Ile Leu Thr Gly Lys Arg Lys 225 230 235 240 Tyr Tyr
His Gly Pro Gly Asn Glu Lys Ser Arg Thr Asp Tyr Gly Arg 245 250 255
Tyr Arg Thr Ser Gly Glu Thr Leu Asp Asn Ile Phe Gly Ile Leu Ile 260
265 270 Gly Lys Cys Thr Phe Tyr Pro Asp Glu Phe Arg Ala Ala Lys Ala
Ser 275 280 285 Tyr Thr Ala Gln Glu Phe Asn Leu Leu Asn Asp Leu Asn
Asn Leu Thr 290 295 300 Val Pro Thr Glu Thr Lys Lys Leu Ser Lys Glu
Gln Lys Asn Gln Ile 305 310 315 320 Ile Asn Tyr Val Lys Asn Glu Lys
Ala Met Gly Pro Ala Lys Leu Phe 325 330 335 Lys Tyr Ile Ala Lys Leu
Leu Ser Cys Asp Val Ala Asp Ile Lys Gly 340 345 350 Tyr Arg Ile Asp
Lys Ser Gly Lys Ala Glu Ile His Thr Phe Glu Ala 355 360 365 Tyr Arg
Lys Met Lys Thr Leu Glu Thr Leu Asp Ile Glu Gln Met Asp 370 375 380
Arg Glu Thr Leu Asp Lys Leu Ala Tyr Val Leu Thr Leu Asn Thr Glu 385
390 395 400 Arg Glu Gly Ile Gln Glu Ala Leu Glu His Glu Phe Ala Asp
Gly Ser 405 410 415 Phe Ser Gln Lys Gln Val Asp Glu Leu Val Gln Phe
Arg Lys Ala Asn 420 425 430 Ser Ser Ile Phe Gly Lys Gly Trp His Asn
Phe Ser Val Lys Leu Met 435 440 445 Met Glu Leu Ile Pro Glu Leu Tyr
Glu Thr Ser Glu Glu Gln Met Thr 450 455 460 Ile Leu Thr Arg Leu Gly
Lys Gln Lys Thr Thr Ser Ser Ser Asn Lys 465 470 475 480 Thr Lys Tyr
Ile Asp Glu Lys Leu Leu Thr Glu Glu Ile Tyr Asn Pro 485 490 495 Val
Val Ala Lys Ser Val Arg Gln Ala Ile Lys Ile Val Asn Ala Ala 500 505
510 Ile Lys Glu Tyr Gly Asp Phe Asp Asn Ile Val Ile Glu Met Ala Arg
515 520 525 Glu Thr Asn Glu Asp Asp Glu Lys Lys Ala Ile Gln Lys Ile
Gln Lys 530 535 540 Ala Asn Lys Asp Glu Lys Asp Ala Ala Met Leu Lys
Ala Ala Asn Gln 545 550 555 560 Tyr Asn Gly Lys Ala Glu Leu Pro His
Ser Val Phe His Gly His Lys 565 570 575 Gln Leu Ala Thr Lys Ile Arg
Leu Trp His Gln Gln Gly Glu Arg Cys 580 585 590 Leu Tyr Thr Gly Lys
Thr Ile Ser Ile His Asp Leu Ile Asn Asn Ser 595 600 605 Asn Gln Phe
Glu Val Asp His Ile Leu Pro Leu Ser Ile Thr Phe Asp 610 615 620 Asp
Ser Leu Ala Asn Lys Val Leu Val Tyr Ala Thr Ala Asn Gln Glu 625 630
635 640 Lys Gly Gln Arg Thr Pro Tyr Gln Ala Leu Asp Ser Met Asp Asp
Ala 645 650 655 Trp Ser Phe Arg Glu Leu Lys Ala Phe Val Arg Glu Ser
Lys Thr Leu 660 665 670 Ser Asn Lys Lys Lys Glu Tyr Leu Leu Thr Glu
Glu Asp Ile Ser Lys 675 680 685 Phe Asp Val Arg Lys Lys Phe Ile Glu
Arg Asn Leu Val Asp Thr Arg 690 695 700 Tyr Ala Ser Arg Val Val Leu
Asn Ala Leu Gln Glu His Phe Arg Ala 705 710 715 720 His Lys Ile Asp
Thr Lys Val Ser Val Val Arg Gly Gln Phe Thr Ser 725 730 735 Gln Leu
Arg Arg His Trp Gly Ile Glu Lys Thr Arg Asp Thr Tyr His 740 745 750
His His Ala Val Asp Ala Leu Ile Ile Ala Ala Ser Ser Gln Leu Asn 755
760 765 Leu Trp Lys Lys Gln Lys Asn Thr Leu Val Ser Tyr Ser Glu Asp
Gln 770 775 780 Leu Leu Asp Ile Glu Thr Gly Glu Leu Ile Ser Asp Asp
Glu Tyr Lys 785 790 795 800 Glu Ser Val Phe Lys Ala Pro Tyr Gln His
Phe Val Asp Thr Leu Lys 805 810 815 Ser Lys Glu Phe Glu Asp Ser Ile
Leu Phe Ser Tyr Gln Val Asp Ser 820 825 830 Lys Phe Asn Arg Lys Ile
Ser Asp Ala Thr Ile Tyr Ala Thr Arg Gln 835 840 845 Ala Lys Val Gly
Lys Asp Lys Ala Asp Glu Thr Tyr Val Leu Gly Lys 850 855 860 Ile Lys
Asp Ile Tyr Thr Gln Asp Gly Tyr Asp Ala Phe Met Lys Ile 865 870 875
880 Tyr Lys Lys Asp Lys Ser Lys Phe Leu Met Tyr Arg His Asp Pro Gln
885 890 895 Thr Phe Glu Lys Val Ile Glu Pro Ile Leu Glu Asn Tyr Pro
Asn Lys 900 905 910 Gln Ile Asn Glu Lys Gly Lys Glu Val Pro Cys Asn
Pro Phe Leu Lys 915 920 925 Tyr Lys Glu Glu His Gly Tyr Ile Arg Lys
Tyr Ser Lys Lys Gly Asn 930 935 940 Gly Pro Glu Ile Lys Ser Leu Lys
Tyr Tyr Asp Ser Lys Leu Gly Asn 945 950 955 960 His Ile Asp Ile Thr
Pro Lys Asp Ser Asn Asn Lys Val Val Leu Gln 965 970 975 Ser Val Ser
Pro Trp Arg Ala Asp Val Tyr Phe Asn Lys Thr Thr Gly 980 985 990 Lys
Tyr Glu Ile Leu Gly Leu Lys Tyr Ala Asp Leu Gln Phe Glu Lys 995
1000 1005 Gly Thr Gly Thr Tyr Lys Ile Ser Gln Glu Lys Tyr Asn Asp
Ile 1010 1015 1020 Lys Lys Lys Glu Gly Val Asp Ser Asp Ser Glu Phe
Lys Phe Thr 1025 1030 1035 Leu Tyr Lys Asn Asp Leu Leu Leu Val Lys
Asp Thr Glu Thr Lys 1040 1045 1050 Glu Gln Gln Leu Phe Arg Phe Leu
Ser Arg Thr Met Pro Lys Gln 1055 1060 1065 Lys His Tyr Val Glu Leu
Lys Pro Tyr Asp Lys Gln Lys Phe Glu 1070 1075 1080 Gly Gly Glu Ala
Leu Ile Lys Val Leu Gly Asn Val
Ala Asn Ser 1085 1090 1095 Gly Gln Cys Lys Lys Gly Leu Gly Lys Ser
Asn Ile Ser Ile Tyr 1100 1105 1110 Lys Val Arg Thr Asp Val Leu Gly
Asn Gln His Ile Ile Lys Asn 1115 1120 1125 Glu Gly Asp Lys Pro Lys
Leu Asp Phe Lys Arg Pro Ala Ala Thr 1130 1135 1140 Lys Lys Ala Gly
Gln Ala Lys Lys Lys Lys 1145 1150 53340DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
53gagggcctat ttcccatgat tccttcatat ttgcatatac gatacaaggc tgttagagag
60ataattggaa ttaatttgac tgtaaacaca aagatattag tacaaaatac gtgacgtaga
120aagtaataat ttcttgggta gtttgcagtt ttaaaattat gttttaaaat
ggactatcat 180atgcttaccg taacttgaaa gtatttcgat ttcttggctt
tatatatctt gtggaaagga 240cgaaacaccg ttacttaaat cttgcagaag
ctacaaagat aaggcttcat gccgaaatca 300acaccctgtc attttatggc
agggtgtttt cgttatttaa 34054360DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 54gagggcctat
ttcccatgat tccttcatat ttgcatatac gatacaaggc tgttagagag 60ataattggaa
ttaatttgac tgtaaacaca aagatattag tacaaaatac gtgacgtaga
120aagtaataat ttcttgggta gtttgcagtt ttaaaattat gttttaaaat
ggactatcat 180atgcttaccg taacttgaaa gtatttcgat ttcttggctt
tatatatctt gtggaaagga 240cgaaacaccg ggttttagag ctatgctgtt
ttgaatggtc ccaaaacnnn nnnnnnnnnn 300nnnnnnnnnn nnnnnnngtt
ttagagctat gctgttttga atggtcccaa aacttttttt 36055318DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
55gagggcctat ttcccatgat tccttcatat ttgcatatac gatacaaggc tgttagagag
60ataattggaa ttaatttgac tgtaaacaca aagatattag tacaaaatac gtgacgtaga
120aagtaataat ttcttgggta gtttgcagtt ttaaaattat gttttaaaat
ggactatcat 180atgcttaccg taacttgaaa gtatttcgat ttcttggctt
tatatatctt gtggaaagga 240cgaaacaccn nnnnnnnnnn nnnnnnnnng
ttttagagct agaaatagca agttaaaata 300aggctagtcc gttttttt
31856325DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 56gagggcctat ttcccatgat tccttcatat
ttgcatatac gatacaaggc tgttagagag 60ataattggaa ttaatttgac tgtaaacaca
aagatattag tacaaaatac gtgacgtaga 120aagtaataat ttcttgggta
gtttgcagtt ttaaaattat gttttaaaat ggactatcat 180atgcttaccg
taacttgaaa gtatttcgat ttcttggctt tatatatctt gtggaaagga
240cgaaacaccn nnnnnnnnnn nnnnnnnnng ttttagagct agaaatagca
agttaaaata 300aggctagtcc gttatcattt ttttt 32557337DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
57gagggcctat ttcccatgat tccttcatat ttgcatatac gatacaaggc tgttagagag
60ataattggaa ttaatttgac tgtaaacaca aagatattag tacaaaatac gtgacgtaga
120aagtaataat ttcttgggta gtttgcagtt ttaaaattat gttttaaaat
ggactatcat 180atgcttaccg taacttgaaa gtatttcgat ttcttggctt
tatatatctt gtggaaagga 240cgaaacaccn nnnnnnnnnn nnnnnnnnng
ttttagagct agaaatagca agttaaaata 300aggctagtcc gttatcaact
tgaaaaagtg ttttttt 33758352DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 58gagggcctat
ttcccatgat tccttcatat ttgcatatac gatacaaggc tgttagagag 60ataattggaa
ttaatttgac tgtaaacaca aagatattag tacaaaatac gtgacgtaga
120aagtaataat ttcttgggta gtttgcagtt ttaaaattat gttttaaaat
ggactatcat 180atgcttaccg taacttgaaa gtatttcgat ttcttggctt
tatatatctt gtggaaagga 240cgaaacaccn nnnnnnnnnn nnnnnnnnng
ttttagagct agaaatagca agttaaaata 300aggctagtcc gttatcaact
tgaaaaagtg gcaccgagtc ggtgcttttt tt 352595101DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
59cgttacataa cttacggtaa atggcccgcc tggctgaccg cccaacgacc cccgcccatt
60gacgtcaata atgacgtatg ttcccatagt aacgccaata gggactttcc attgacgtca
120atgggtggag tatttacggt aaactgccca cttggcagta catcaagtgt
atcatatgcc 180aagtacgccc cctattgacg tcaatgacgg taaatggccc
gcctggcatt atgcccagta 240catgacctta tgggactttc ctacttggca
gtacatctac gtattagtca tcgctattac 300catggtcgag gtgagcccca
cgttctgctt cactctcccc atctcccccc cctccccacc 360cccaattttg
tatttattta ttttttaatt attttgtgca gcgatggggg cggggggggg
420gggggggcgc gcgccaggcg gggcggggcg gggcgagggg cggggcgggg
cgaggcggag 480aggtgcggcg gcagccaatc agagcggcgc gctccgaaag
tttcctttta tggcgaggcg 540gcggcggcgg cggccctata aaaagcgaag
cgcgcggcgg gcgggagtcg ctgcgacgct 600gccttcgccc cgtgccccgc
tccgccgccg cctcgcgccg cccgccccgg ctctgactga 660ccgcgttact
cccacaggtg agcgggcggg acggcccttc tcctccgggc tgtaattagc
720tgagcaagag gtaagggttt aagggatggt tggttggtgg ggtattaatg
tttaattacc 780tggagcacct gcctgaaatc actttttttc aggttggacc
ggtgccacca tggactataa 840ggaccacgac ggagactaca aggatcatga
tattgattac aaagacgatg acgataagat 900ggccccaaag aagaagcgga
aggtcggtat ccacggagtc ccagcagccg acaagaagta 960cagcatcggc
ctggacatcg gcaccaactc tgtgggctgg gccgtgatca ccgacgagta
1020caaggtgccc agcaagaaat tcaaggtgct gggcaacacc gaccggcaca
gcatcaagaa 1080gaacctgatc ggagccctgc tgttcgacag cggcgaaaca
gccgaggcca cccggctgaa 1140gagaaccgcc agaagaagat acaccagacg
gaagaaccgg atctgctatc tgcaagagat 1200cttcagcaac gagatggcca
aggtggacga cagcttcttc cacagactgg aagagtcctt 1260cctggtggaa
gaggataaga agcacgagcg gcaccccatc ttcggcaaca tcgtggacga
1320ggtggcctac cacgagaagt accccaccat ctaccacctg agaaagaaac
tggtggacag 1380caccgacaag gccgacctgc ggctgatcta tctggccctg
gcccacatga tcaagttccg 1440gggccacttc ctgatcgagg gcgacctgaa
ccccgacaac agcgacgtgg acaagctgtt 1500catccagctg gtgcagacct
acaaccagct gttcgaggaa aaccccatca acgccagcgg 1560cgtggacgcc
aaggccatcc tgtctgccag actgagcaag agcagacggc tggaaaatct
1620gatcgcccag ctgcccggcg agaagaagaa tggcctgttc ggcaacctga
ttgccctgag 1680cctgggcctg acccccaact tcaagagcaa cttcgacctg
gccgaggatg ccaaactgca 1740gctgagcaag gacacctacg acgacgacct
ggacaacctg ctggcccaga tcggcgacca 1800gtacgccgac ctgtttctgg
ccgccaagaa cctgtccgac gccatcctgc tgagcgacat 1860cctgagagtg
aacaccgaga tcaccaaggc ccccctgagc gcctctatga tcaagagata
1920cgacgagcac caccaggacc tgaccctgct gaaagctctc gtgcggcagc
agctgcctga 1980gaagtacaaa gagattttct tcgaccagag caagaacggc
tacgccggct acattgacgg 2040cggagccagc caggaagagt tctacaagtt
catcaagccc atcctggaaa agatggacgg 2100caccgaggaa ctgctcgtga
agctgaacag agaggacctg ctgcggaagc agcggacctt 2160cgacaacggc
agcatccccc accagatcca cctgggagag ctgcacgcca ttctgcggcg
2220gcaggaagat ttttacccat tcctgaagga caaccgggaa aagatcgaga
agatcctgac 2280cttccgcatc ccctactacg tgggccctct ggccagggga
aacagcagat tcgcctggat 2340gaccagaaag agcgaggaaa ccatcacccc
ctggaacttc gaggaagtgg tggacaaggg 2400cgcttccgcc cagagcttca
tcgagcggat gaccaacttc gataagaacc tgcccaacga 2460gaaggtgctg
cccaagcaca gcctgctgta cgagtacttc accgtgtata acgagctgac
2520caaagtgaaa tacgtgaccg agggaatgag aaagcccgcc ttcctgagcg
gcgagcagaa 2580aaaggccatc gtggacctgc tgttcaagac caaccggaaa
gtgaccgtga agcagctgaa 2640agaggactac ttcaagaaaa tcgagtgctt
cgactccgtg gaaatctccg gcgtggaaga 2700tcggttcaac gcctccctgg
gcacatacca cgatctgctg aaaattatca aggacaagga 2760cttcctggac
aatgaggaaa acgaggacat tctggaagat atcgtgctga ccctgacact
2820gtttgaggac agagagatga tcgaggaacg gctgaaaacc tatgcccacc
tgttcgacga 2880caaagtgatg aagcagctga agcggcggag atacaccggc
tggggcaggc tgagccggaa 2940gctgatcaac ggcatccggg acaagcagtc
cggcaagaca atcctggatt tcctgaagtc 3000cgacggcttc gccaacagaa
acttcatgca gctgatccac gacgacagcc tgacctttaa 3060agaggacatc
cagaaagccc aggtgtccgg ccagggcgat agcctgcacg agcacattgc
3120caatctggcc ggcagccccg ccattaagaa gggcatcctg cagacagtga
aggtggtgga 3180cgagctcgtg aaagtgatgg gccggcacaa gcccgagaac
atcgtgatcg aaatggccag 3240agagaaccag accacccaga agggacagaa
gaacagccgc gagagaatga agcggatcga 3300agagggcatc aaagagctgg
gcagccagat cctgaaagaa caccccgtgg aaaacaccca 3360gctgcagaac
gagaagctgt acctgtacta cctgcagaat gggcgggata tgtacgtgga
3420ccaggaactg gacatcaacc ggctgtccga ctacgatgtg gaccatatcg
tgcctcagag 3480ctttctgaag gacgactcca tcgacaacaa ggtgctgacc
agaagcgaca agaaccgggg 3540caagagcgac aacgtgccct ccgaagaggt
cgtgaagaag atgaagaact actggcggca 3600gctgctgaac gccaagctga
ttacccagag aaagttcgac aatctgacca aggccgagag 3660aggcggcctg
agcgaactgg ataaggccgg cttcatcaag agacagctgg tggaaacccg
3720gcagatcaca aagcacgtgg cacagatcct ggactcccgg atgaacacta
agtacgacga 3780gaatgacaag ctgatccggg aagtgaaagt gatcaccctg
aagtccaagc tggtgtccga 3840tttccggaag gatttccagt tttacaaagt
gcgcgagatc aacaactacc accacgccca 3900cgacgcctac ctgaacgccg
tcgtgggaac cgccctgatc aaaaagtacc ctaagctgga 3960aagcgagttc
gtgtacggcg actacaaggt gtacgacgtg cggaagatga tcgccaagag
4020cgagcaggaa atcggcaagg ctaccgccaa gtacttcttc tacagcaaca
tcatgaactt 4080tttcaagacc gagattaccc tggccaacgg cgagatccgg
aagcggcctc tgatcgagac 4140aaacggcgaa accggggaga tcgtgtggga
taagggccgg gattttgcca ccgtgcggaa 4200agtgctgagc atgccccaag
tgaatatcgt gaaaaagacc gaggtgcaga caggcggctt 4260cagcaaagag
tctatcctgc ccaagaggaa cagcgataag ctgatcgcca gaaagaagga
4320ctgggaccct aagaagtacg gcggcttcga cagccccacc gtggcctatt
ctgtgctggt 4380ggtggccaaa gtggaaaagg gcaagtccaa gaaactgaag
agtgtgaaag agctgctggg 4440gatcaccatc atggaaagaa gcagcttcga
gaagaatccc atcgactttc tggaagccaa 4500gggctacaaa gaagtgaaaa
aggacctgat catcaagctg cctaagtact ccctgttcga 4560gctggaaaac
ggccggaaga gaatgctggc ctctgccggc gaactgcaga agggaaacga
4620actggccctg ccctccaaat atgtgaactt cctgtacctg gccagccact
atgagaagct 4680gaagggctcc cccgaggata atgagcagaa acagctgttt
gtggaacagc acaagcacta 4740cctggacgag atcatcgagc agatcagcga
gttctccaag agagtgatcc tggccgacgc 4800taatctggac aaagtgctgt
ccgcctacaa caagcaccgg gataagccca tcagagagca 4860ggccgagaat
atcatccacc tgtttaccct gaccaatctg ggagcccctg ccgccttcaa
4920gtactttgac accaccatcg accggaagag gtacaccagc accaaagagg
tgctggacgc 4980caccctgatc caccagagca tcaccggcct gtacgagaca
cggatcgacc tgtctcagct 5040gggaggcgac tttctttttc ttagcttgac
cagctttctt agtagcagca ggacgcttta 5100a 510160137DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
60nnnnnnnnnn nnnnnnnnnn gttattgtac tctcaagatt tagaaataaa tcttgcagaa
60gctacaaaga taaggcttca tgccgaaatc aacaccctgt cattttatgg cagggtgttt
120tcgttattta atttttt 13761123DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 61nnnnnnnnnn
nnnnnnnnnn gttattgtac tctcagaaat gcagaagcta caaagataag 60gcttcatgcc
gaaatcaaca ccctgtcatt ttatggcagg gtgttttcgt tatttaattt 120ttt
12362110DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 62nnnnnnnnnn nnnnnnnnnn gttattgtac
tctcagaaat gcagaagcta caaagataag 60gcttcatgcc gaaatcaaca ccctgtcatt
ttatggcagg gtgttttttt 11063137DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 63nnnnnnnnnn
nnnnnnnnnn gttattgtac tctcaagatt tagaaataaa tcttgcagaa 60gctacaatga
taaggcttca tgccgaaatc aacaccctgt cattttatgg cagggtgttt
120tcgttattta atttttt 13764123DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 64nnnnnnnnnn
nnnnnnnnnn gttattgtac tctcagaaat gcagaagcta caatgataag 60gcttcatgcc
gaaatcaaca ccctgtcatt ttatggcagg gtgttttcgt tatttaattt 120ttt
12365110DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 65nnnnnnnnnn nnnnnnnnnn gttattgtac
tctcagaaat gcagaagcta caatgataag 60gcttcatgcc gaaatcaaca ccctgtcatt
ttatggcagg gtgttttttt 11066107DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 66nnnnnnnnnn
nnnnnnnnnn gttttagagc tgtggaaaca cagcgagtta aaataaggct 60tagtccgtac
tcaacttgaa aaggtggcac cgattcggtg ttttttt 107674263DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
67atgaaaaggc cggcggccac gaaaaaggcc ggccaggcaa aaaagaaaaa gaccaagccc
60tacagcatcg gcctggacat cggcaccaat agcgtgggct gggccgtgac caccgacaac
120tacaaggtgc ccagcaagaa aatgaaggtg ctgggcaaca cctccaagaa
gtacatcaag 180aaaaacctgc tgggcgtgct gctgttcgac agcggcatta
cagccgaggg cagacggctg 240aagagaaccg ccagacggcg gtacacccgg
cggagaaaca gaatcctgta tctgcaagag 300atcttcagca ccgagatggc
taccctggac gacgccttct tccagcggct ggacgacagc 360ttcctggtgc
ccgacgacaa gcgggacagc aagtacccca tcttcggcaa cctggtggaa
420gagaaggcct accacgacga gttccccacc atctaccacc tgagaaagta
cctggccgac 480agcaccaaga aggccgacct gagactggtg tatctggccc
tggcccacat gatcaagtac 540cggggccact tcctgatcga gggcgagttc
aacagcaaga acaacgacat ccagaagaac 600ttccaggact tcctggacac
ctacaacgcc atcttcgaga gcgacctgtc cctggaaaac 660agcaagcagc
tggaagagat cgtgaaggac aagatcagca agctggaaaa gaaggaccgc
720atcctgaagc tgttccccgg cgagaagaac agcggaatct tcagcgagtt
tctgaagctg 780atcgtgggca accaggccga cttcagaaag tgcttcaacc
tggacgagaa agccagcctg 840cacttcagca aagagagcta cgacgaggac
ctggaaaccc tgctgggata tatcggcgac 900gactacagcg acgtgttcct
gaaggccaag aagctgtacg acgctatcct gctgagcggc 960ttcctgaccg
tgaccgacaa cgagacagag gccccactga gcagcgccat gattaagcgg
1020tacaacgagc acaaagagga tctggctctg ctgaaagagt acatccggaa
catcagcctg 1080aaaacctaca atgaggtgtt caaggacgac accaagaacg
gctacgccgg ctacatcgac 1140ggcaagacca accaggaaga tttctatgtg
tacctgaaga agctgctggc cgagttcgag 1200ggggccgact actttctgga
aaaaatcgac cgcgaggatt tcctgcggaa gcagcggacc 1260ttcgacaacg
gcagcatccc ctaccagatc catctgcagg aaatgcgggc catcctggac
1320aagcaggcca agttctaccc attcctggcc aagaacaaag agcggatcga
gaagatcctg 1380accttccgca tcccttacta cgtgggcccc ctggccagag
gcaacagcga ttttgcctgg 1440tccatccgga agcgcaatga gaagatcacc
ccctggaact tcgaggacgt gatcgacaaa 1500gagtccagcg ccgaggcctt
catcaaccgg atgaccagct tcgacctgta cctgcccgag 1560gaaaaggtgc
tgcccaagca cagcctgctg tacgagacat tcaatgtgta taacgagctg
1620accaaagtgc ggtttatcgc cgagtctatg cgggactacc agttcctgga
ctccaagcag 1680aaaaaggaca tcgtgcggct gtacttcaag gacaagcgga
aagtgaccga taaggacatc 1740atcgagtacc tgcacgccat ctacggctac
gatggcatcg agctgaaggg catcgagaag 1800cagttcaact ccagcctgag
cacataccac gacctgctga acattatcaa cgacaaagaa 1860tttctggacg
actccagcaa cgaggccatc atcgaagaga tcatccacac cctgaccatc
1920tttgaggacc gcgagatgat caagcagcgg ctgagcaagt tcgagaacat
cttcgacaag 1980agcgtgctga aaaagctgag cagacggcac tacaccggct
ggggcaagct gagcgccaag 2040ctgatcaacg gcatccggga cgagaagtcc
ggcaacacaa tcctggacta cctgatcgac 2100gacggcatca gcaaccggaa
cttcatgcag ctgatccacg acgacgccct gagcttcaag 2160aagaagatcc
agaaggccca gatcatcggg gacgaggaca agggcaacat caaagaagtc
2220gtgaagtccc tgcccggcag ccccgccatc aagaagggaa tcctgcagag
catcaagatc 2280gtggacgagc tcgtgaaagt gatgggcggc agaaagcccg
agagcatcgt ggtggaaatg 2340gctagagaga accagtacac caatcagggc
aagagcaaca gccagcagag actgaagaga 2400ctggaaaagt ccctgaaaga
gctgggcagc aagattctga aagagaatat ccctgccaag 2460ctgtccaaga
tcgacaacaa cgccctgcag aacgaccggc tgtacctgta ctacctgcag
2520aatggcaagg acatgtatac aggcgacgac ctggatatcg accgcctgag
caactacgac 2580atcgaccata ttatccccca ggccttcctg aaagacaaca
gcattgacaa caaagtgctg 2640gtgtcctccg ccagcaaccg cggcaagtcc
gatgatgtgc ccagcctgga agtcgtgaaa 2700aagagaaaga ccttctggta
tcagctgctg aaaagcaagc tgattagcca gaggaagttc 2760gacaacctga
ccaaggccga gagaggcggc ctgagccctg aagataaggc cggcttcatc
2820cagagacagc tggtggaaac ccggcagatc accaagcacg tggccagact
gctggatgag 2880aagtttaaca acaagaagga cgagaacaac cgggccgtgc
ggaccgtgaa gatcatcacc 2940ctgaagtcca ccctggtgtc ccagttccgg
aaggacttcg agctgtataa agtgcgcgag 3000atcaatgact ttcaccacgc
ccacgacgcc tacctgaatg ccgtggtggc ttccgccctg 3060ctgaagaagt
accctaagct ggaacccgag ttcgtgtacg gcgactaccc caagtacaac
3120tccttcagag agcggaagtc cgccaccgag aaggtgtact tctactccaa
catcatgaat 3180atctttaaga agtccatctc cctggccgat ggcagagtga
tcgagcggcc cctgatcgaa 3240gtgaacgaag agacaggcga gagcgtgtgg
aacaaagaaa gcgacctggc caccgtgcgg 3300cgggtgctga gttatcctca
agtgaatgtc gtgaagaagg tggaagaaca gaaccacggc 3360ctggatcggg
gcaagcccaa gggcctgttc aacgccaacc tgtccagcaa gcctaagccc
3420aactccaacg agaatctcgt gggggccaaa gagtacctgg accctaagaa
gtacggcgga 3480tacgccggca tctccaatag cttcaccgtg ctcgtgaagg
gcacaatcga gaagggcgct 3540aagaaaaaga tcacaaacgt gctggaattt
caggggatct ctatcctgga ccggatcaac 3600taccggaagg ataagctgaa
ctttctgctg gaaaaaggct acaaggacat tgagctgatt 3660atcgagctgc
ctaagtactc cctgttcgaa ctgagcgacg gctccagacg gatgctggcc
3720tccatcctgt ccaccaacaa caagcggggc gagatccaca agggaaacca
gatcttcctg 3780agccagaaat ttgtgaaact gctgtaccac gccaagcgga
tctccaacac catcaatgag 3840aaccaccgga aatacgtgga aaaccacaag
aaagagtttg aggaactgtt ctactacatc 3900ctggagttca acgagaacta
tgtgggagcc aagaagaacg gcaaactgct gaactccgcc 3960ttccagagct
ggcagaacca cagcatcgac gagctgtgca gctccttcat cggccctacc
4020ggcagcgagc ggaagggact gtttgagctg acctccagag gctctgccgc
cgactttgag 4080ttcctgggag tgaagatccc ccggtacaga gactacaccc
cctctagtct gctgaaggac 4140gccaccctga tccaccagag cgtgaccggc
ctgtacgaaa cccggatcga cctggctaag 4200ctgggcgagg gaaagcgtcc
tgctgctact aagaaagctg gtcaagctaa gaaaaagaaa 4260taa
42636853DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 68tcctagcagg atttctgata ttactgtcac gttttagagc
tatgctgttt tga 536953DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 69gtgacagtaa tatcagaaat
cctgctagga gttttgggac cattcaaaac agc 537025DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
70gggtttcaag tctttgtagc aagag 257124DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
71gccaatgaac gggaaccctt ggtc 247225DNAArtificial
SequenceDescription of
Artificial Sequence Synthetic primer 72nnnngacgag gcaatggctg aaatc
257325DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 73nnnnttattt ggctcatatt tgctg 257425DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
74ctttacacca atcgctgcaa cagac 257545DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
75caaaatttct agtcttcttt gcctttcccc ataaaaccct cctta
457645DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 76agggttttat ggggaaaggc aaagaagact agaaattttg
atacc 457725DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 77cttacggtgc ataaagtcaa tttcc
257821DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 78tggctcgatt tcagccattg c 217943DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
79ctttgacgag gcaatggctg aaatcgagcc aanaaagcgc aag
438043DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 80ctttgacgag gcaatggctg aaatcgagcc aaanaagcgc aag
438143DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 81ctttgacgag gcaatggctg aaatcgagcc aaaanagcgc aag
438243DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 82ctttgacgag gcaatggctg aaatcgagcc aaaaangcgc aag
438343DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 83ctttgacgag gcaatggctg aaatcgagcc aaaaaancgc aag
438443DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 84ctttgacgag gcaatggctg aaatcgagcc aaaaaagngc aag
438546DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 85ctttgacgag gcaatggctg aaatcgagcc aaaaaagcnc
aagaag 468646DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 86ctttgacgag gcaatggctg aaatcgagcc
aaaaaagcgn aagaag 468746DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 87ctttgacgag gcaatggctg
aaatcgagcc aaaaaagcgc nagaag 468823DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
88gcgctttttt ggctcgattt cag 238940DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 89caatggctga aatcgagcca
aaaaagcgca ngaagaaatc 409040DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 90caatggctga aatcgagcca
aaaaagcgca anaagaaatc 409140DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 91caatggctga aatcgagcca
aaaaagcgca agnagaaatc 409240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 92caatggctga aatcgagcca
aaaaagcgca agangaaatc 409340DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 93caatggctga aatcgagcca
aaaaagcgca agaanaaatc 409444DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 94caatggctga aatcgagcca
aaaaagcgca agaagnaatc aacc 449544DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 95caatggctga aatcgagcca
aaaaagcgca agaaganatc aacc 449644DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 96caatggctga aatcgagcca
aaaaagcgca agaagaantc aacc 449744DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 97caatggctga aatcgagcca
aaaaagcgca agaagaaanc aacc 449847DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 98caatggctga aatcgagcca
aaaaagcgca agaagaaatn aaccagc 479947DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
99caatggctga aatcgagcca aaaaagcgca agaagaaatc naccagc
4710031DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 100gatcctccat ccgtacaacc cacaaccctg g
3110131DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 101aattccaggg ttgtgggttg tacggatgga g
3110234DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 102catggatcct atttcttaat aactaaaaat atgg
3410333DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 103catgaattca actcaacaag tctcagtgtg ctg
3310435DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 104aaacattttt tctccattta ggaaaaagga tgctg
3510535DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 105aaaacagcat cctttttcct aaatggagaa aaaat
3510635DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 106aaaccttaaa tcagtcacaa atagcagcaa aattg
3510735DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 107aaaacaattt tgctgctatt tgtgactgat ttaag
3510835DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 108aaacttttca tcatacgacc aatctgcttt atttg
3510935DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 109aaaacaaata aagcagattg gtcgtatgat gaaaa
3511035DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 110aaactcgtcc agaagttatc gtaaaagaaa tcgag
3511135DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 111aaaactcgat ttcttttacg ataacttctg gacga
3511235DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 112aaacaatctc tccaaggttt ccttaaaaat ctctg
3511335DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 113aaaacagaga tttttaagga aaccttggag agatt
3511435DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 114aaacgccatc gtcaggaaga agctatgctt gagtg
3511535DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 115aaaacactca agcatagctt cttcctgacg atggc
3511635DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 116aaacatctct atacttattg aaatttcttt gtatg
3511735DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 117aaaacataca aagaaatttc aataagtata gagat
3511835DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 118aaactagctg tgatagtccg caaaaccagc cttcg
3511935DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 119aaaacgaagg ctggttttgc ggactatcac agcta
3512035DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 120aaacatcgga aggtcgagca agtaattatc ttttg
3512135DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 121aaaacaaaag ataattactt gctcgacctt ccgat
3512235DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 122aaacaagatg gtatcgcaaa gtaagtgaca ataag
3512335DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 123aaaacttatt gtcacttact ttgcgatacc atctt
3512452DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 124gagacctttg agcttccgag actggtctca gttttgggac
cattcaaaac ag 5212552DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 125tgagaccagt ctcggaagct
caaaggtctc gttttagagc tatgctgttt tg 5212635DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
126aaactacttt acgcagcgcg gagttcggtt ttttg 3512735DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
127aaaacaaaaa accgaactcc gcgctgcgta aagta 3512845DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
128atgccggtac tgccgggcct cttgcgggat tacgaaatca tcctg
4512945DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 129gtgactggcg atgctgtcgg aatggacgat cacactactc
ttctt 4513050DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 130ttaagaaata atcttcatct aaaatatact
tcagtcacct cctagctgac 5013148DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 131attgatttga gtcagctagg
aggtgactga agtatatttt agatgaag 4813285DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
132gagacctttg agcttccgag actggtctca gttttgggac cattcaaaac
agcatagctc 60taaaacctcg tagactattt ttgtc 8513384DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
133gagaccagtc tcggaagctc aaaggtctcg ttttagagct atgctgtttt
gaatggtccc 60aaaacttcag cacactgaga cttg 8413421DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
134agtcatccca gcaacaaatg g 2113531DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 135cgtggtaaat cggataacgt
tccaagtgaa g 3113622DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 136tgctcttctt cacaaacaag gg
2213721DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 137aagccaaagt ttggcaccac c 2113822DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
138gtagcttatt cagtcctagt gg 2213945DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
139cgtttgttga actaatgggt gcaaattacg aatcttctcc tgacg
4514045DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 140cgtcaggaga agattcgtaa tttgcaccca ttagttcaac
aaacg 4514148DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 141gatattatgg agcctatttt tgtgggtttt
taggcataaa actatatg 4814248DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 142catatagttt tatgcctaaa
aacccacaaa aataggctcc ataatatc 4814327DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
143attatttctt aataactaaa aatatgg 2714424DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
144cgtgtacaat tgctagcgta cggc 2414524DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
145gcaccggtga tcactagtcc tagg 2414647DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
146cctaggacta gtgatcaccg gtgcaaatat gagccaaata aatatat
4714744DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 147gccgtacgct agcaattgta cacgtttgtt gaactaatgg
gtgc 4414825DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 148ttcaaatttt cccatttgat tctcc
2514947DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 149ccatattttt agttattaag aaataatacc agccatcagt
cacctcc 4715023DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 150agacgattca atagacaata agg
2315145DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 151gttttgggac cattcaaaac agcatagctc taaaacctcg
tagac 4515250DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 152gctatgctgt tttgaatggt cccaaaacca
ttattttaac acacgaggtg 5015350DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 153gctatgctgt tttgaatggt
cccaaaacgc acccattagt tcaacaaacg 5015423DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
154aattcttttc ttcatcatcg gtc 2315524DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
155aagaaagaat gaagattgtt catg 2415625DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
156ggtactaatc aaaatagtga ggagg 2515723DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
157gtttttcaaa atctgcggtt gcg 2315826DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
158aaaaattgaa aaaatggtgg aaacac 2615953DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
159atttcgtaaa cggtatcggt ttcttttaaa gttttgggac cattcaaaac agc
5316053DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 160tttaaaagaa accgataccg tttacgaaat gttttagagc
tatgctgttt tga 5316153DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 161aaacggtatc ggtttctttt
aaattcaatt gttttgggac cattcaaaac agc 5316253DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
162aattgaattt aaaagaaacc gataccgttt gttttagagc tatgctgttt tga
5316339DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 163gttccttaaa ccaaaacggt atcggtttct tttaaattc
3916447DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 164gaaaccgata ccgttttggt ttaaggaaca ggtaaagggc
atttaac 4716522DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 165cgatttcagc cattgcctcg tc
2216656DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 166gcctttgacg aggcaatggc tgaaatcgnn nnnaaaaagc
gcaagaagaa atcaac 5616753DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 167tccgtacaac ccacaaccct
gctagtgagc gttttgggac cattcaaaac agc 5316853DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
168gctcactagc agggttgtgg gttgtacgga gttttagagc tatgctgttt tga
5316923DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 169ttgttgccac tcttccttct ttc 2317041DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
170cagggttgtg ggttgttgcg atggagttaa ctcccatctc c
4117141DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 171gggagttaac tccatcgcaa caacccacaa ccctgctagt g
4117222DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 172gtggtatcta tcgtgatgtg ac 2217323DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
173ttaccgaaac ggaatttatc tgc 2317422DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
174aaagctagag ttccgcaatt gg 2217537DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
175gtgggttgta cggattgagt taactcccat ctccttc 3717638DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
176gatgggagtt aactcaatcc gtacaaccca caaccctg 3817740DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
177gcttcaccta ttgcagcacc aattgaccac atgaagatag 4017841DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
178gtggtcaatt ggtgctgcaa taggtgaagc taatggtgat g
4117939DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 179ctgatttgta ttaattttga gacattatgc ttcaccttc
3918040DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 180gcataatgtc tcaaaattaa tacaaatcag tgaaatcatg
4018152DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 181gttttgggac cattcaaaac agcatagctc taaaacgtga
cagtaatatc ag
5218253DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 182gttttagagc tatgctgttt tgaatggtcc caaaacgctc
actagcaggg ttg 5318359DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 183atactttacg cagcgcggag
ttcggttttg taggagtggt agtatataca cgagtacat 5918433DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 184gctcactagc agggttgtgg gttgtacgga tgg
3318533DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 185tcctagcagg atttctgata ttactgtcac tgg
3318633DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 186tttaaaagaa accgataccg tttacgaaat tgg
3318784DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 187ggaaccattc ataacagcat agcaagttat
aataaggcta gtccgttatc aacttgaaaa 60agtggcaccg agtcggtgct tttt
8418836DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 188gttatagagc tatgctgtta tgaatggtcc
caaaac 3618984DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 189ggaaccattc aatacagcat
agcaagttaa tataaggcta gtccgttatc aacttgaaaa 60agtggcaccg agtcggtgct
tttt 8419036DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 190gtattagagc tatgctgtat
tgaatggtcc caaaac 36191103DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 191nnnnnnnnnn
nnnnnnnnnn gttttagagc tagaaatagc aagttaaaat aaggctagtc 60cgttatcaac
ttgaaaaagt ggcaccgagt cggtgctttt ttt 103192103DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
192nnnnnnnnnn nnnnnnnnnn gtattagagc tagaaatagc aagttaatat
aaggctagtc 60cgttatcaac ttgaaaaagt ggcaccgagt cggtgctttt ttt
103193123DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 193nnnnnnnnnn nnnnnnnnnn gttttagagc
tatgctgttt tggaaacaaa acagcatagc 60aagttaaaat aaggctagtc cgttatcaac
ttgaaaaagt ggcaccgagt cggtgctttt 120ttt 123194123DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
194nnnnnnnnnn nnnnnnnnnn gtattagagc tatgctgtat tggaaacaat
acagcatagc 60aagttaatat aaggctagtc cgttatcaac ttgaaaaagt ggcaccgagt
cggtgctttt 120ttt 12319520DNAHomo sapiens 195gtcacctcca atgactaggg
2019623DNAHomo sapiens 196gacatcgatg tcctccccat tgg 2319723DNAHomo
sapiens 197gagtccgagc agaagaagaa ggg 2319823DNAHomo sapiens
198gcgccaccgg ttgatgtgat ggg 2319923DNAHomo sapiens 199ggggcacaga
tgagaaactc agg 2320023DNAHomo sapiens 200gtacaaacgg cagaagctgg agg
2320123DNAHomo sapiens 201ggcagaagct ggaggaggaa ggg 2320223DNAHomo
sapiens 202ggagcccttc ttcttctgct cgg 2320323DNAHomo sapiens
203gggcaaccac aaacccacga ggg 2320423DNAHomo sapiens 204gctcccatca
catcaaccgg tgg 2320523DNAHomo sapiens 205gtggcgcatt gccacgaagc agg
2320623DNAHomo sapiens 206ggcagagtgc tgcttgctgc tgg 2320723DNAHomo
sapiens 207gcccctgcgt gggcccaagc tgg 2320823DNAHomo sapiens
208gagtggccag agtccagctt ggg 2320923DNAHomo sapiens 209ggcctcccca
aagcctggcc agg 2321023DNAHomo sapiens 210ggggccgaga ttgggtgttc agg
2321123DNAHomo sapiens 211gtggcgagag gggccgagat tgg 2321223DNAHomo
sapiens 212gagtgccgcc gaggcggggc ggg 2321323DNAHomo sapiens
213ggagtgccgc cgaggcgggg cgg 2321423DNAHomo sapiens 214ggagaggagt
gccgccgagg cgg 2321520DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 215ccatcccctt ctgtgaatgt
2021620DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 216ggagattgga gacacggaga 2021720DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
217aagcaccgac tcggtgccac 2021820DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 218tcacctccaa tgactagggg
2021922DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 219caagttgata acggactagc ct 2222023DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
220agtccgagca gaagaagaag ttt 2322125DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
221tttcaagttg ataacggact agcct 2522220DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
222aaacagcaga ttcgcctgga 2022320DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 223tcatccgctc gatgaagctc
2022420DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 224tccaaaatca agtggggcga 2022520DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
225tgatgaccct tttggctccc 2022645DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 226gaggaattct ttttttgtty
gaatatgttg gaggtttttt ggaag 4522742DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
227gagaagctta aataaaaaac racaatactc aacccaacaa cc
4222817DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 228caggaaacag ctatgac 1722939DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
229gcctctagag gtacctgagg gcctatttcc catgattcc 39230133DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
230acctctagaa aaaaagcacc gactcggtgc cactttttca agttgataac
ggactagcct 60tattttaact tgctatttct agctctaaaa cnnnnnnnnn nnnnnnnnnn
nggtgtttcg 120tcctttccac aag 133231133DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
231acctctagaa aaaaagcacc gactcggtgc cactttttca agttgataac
ggactagcct 60tatattaact tgctatttct agctctaata cnnnnnnnnn nnnnnnnnnn
nggtgtttcg 120tcctttccac aag 133232153DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
232acctctagaa aaaaagcacc gactcggtgc cactttttca agttgataac
ggactagcct 60tattttaact tgctatgctg ttttgtttcc aaaacagcat agctctaaaa
cnnnnnnnnn 120nnnnnnnnnn nggtgtttcg tcctttccac aag
153233153DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 233acctctagaa aaaaagcacc gactcggtgc cactttttca
agttgataac ggactagcct 60tatattaact tgctatgctg tattgtttcc aatacagcat
agctctaata cnnnnnnnnn 120nnnnnnnnnn nggtgtttcg tcctttccac aag
15323422DNAHomo sapiensmodified_base(20)..(20)a, c, t, g, unknown
or other 234aggccccagt ggctgctctn aa 2223522DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
235acatcaaccg gtggcgcatn at 2223622DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
236aaggtgtggt tccagaaccn ac 2223722DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
237ccatcacatc aaccggtggn ag 2223822DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
238aaacggcaga agctggaggn ta 2223922DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
239ggcagaagct ggaggaggan tt 2224022DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
240ggtgtggttc cagaaccggn tc 2224122DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
241aaccggagga caaagtacan tg 2224222DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
242ttccagaacc ggaggacaan ca 2224322DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
243gtgtggttcc agaaccggan ct 2224422DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
244tccagaaccg gaggacaaan cc 2224522DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
245cagaagctgg aggaggaagn cg 2224622DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
246catcaaccgg tggcgcattn ga 2224722DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
247gcagaagctg gaggaggaan gt 2224822DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
248cctccctccc tggcccaggn gc 2224922DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
249tcatctgtgc ccctccctcn aa 2225022DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
250gggaggacat cgatgtcacn at 2225122DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
251caaacggcag aagctggagn ac 2225222DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
252gggtgggcaa ccacaaaccn ag 2225322DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
253ggtgggcaac cacaaacccn ta 2225422DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
254ggctcccatc acatcaaccn tt 2225522DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
255gaagggcctg agtccgagcn tc 2225622DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
256caaccggtgg cgcattgccn tg 2225722DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
257aggaggaagg gcctgagtcn ca 2225822DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
258agctggagga ggaagggccn ct 2225922DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
259gcattgccac gaagcaggcn cc 2226022DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
260attgccacga agcaggccan cg 2226122DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
261agaaccggag gacaaagtan ga 2226222DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
262tcaaccggtg gcgcattgcn gt 2226322DNAHomo
sapiensmodified_base(20)..(20)a, c, t, g, unknown or other
263gaagctggag gaggaagggn gc 22264123DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
264ccaatgggga ggacatcgat gtcacctcca atgactaggg tgggcaacca
caaacccacg 60agggcagagt gctgcttgct gctggccagg cccctgcgtg ggcccaagct
ggactctggc 120cac 123265121DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 265cgagcagaag
aagaagggct cccatcacat caaccggtgg cgcattgcca cgaagcaggc 60caatggggag
gacatcgatg tcacctccaa tgactagggt gggcaaccac aaacccacga 120g
121266128DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 266ggaggacaaa gtacaaacgg cagaagctgg
aggaggaagg gcctgagtcc gagcagaaga 60agaagggctc ccatcacatc aaccggtggc
gcattgccac gaagcaggcc aatggggagg 120acatcgat 128267130DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
267agaagctgga ggaggaaggg cctgagtccg agcagaagaa gaagggctcc
catcacatca 60accggtggcg cattgccacg aagcaggcca atggggagga catcgatgtc
acctccaatg 120actagggtgg 130268125DNAArtificial SequenceDescription
of Artificial Sequence Synthetic polynucleotide 268cctcagtctt
cccatcaggc tctcagctca gcctgagtgt tgaggcccca gtggctgctc 60tgggggcctc
ctgagtttct catctgtgcc cctccctccc tggcccaggt gaaggtgtgg 120ttcca
125269129DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 269tcatctgtgc ccctccctcc ctggcccagg
tgaaggtgtg gttccagaac cggaggacaa 60agtacaaacg gcagaagctg gaggaggaag
ggcctgagtc cgagcagaag aagaagggct 120cccatcaca
129270129DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 270ctccaatgac tagggtgggc aaccacaaac
ccacgagggc agagtgctgc ttgctgctgg 60ccaggcccct gcgtgggccc aagctggact
ctggccactc cctggccagg ctttggggag 120gcctggagt
129271127DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 271ctgcttgctg ctggccaggc ccctgcgtgg
gcccaagctg gactctggcc actccctggc 60caggctttgg ggaggcctgg agtcatggcc
ccacagggct tgaagcccgg ggccgccatt 120gacagag 12727225DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 272gaaattaata cgactcacta taggg
25273126DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 273aaaaaagcac cgactcggtg ccactttttc
aagttgataa cggactagcc ttattttaac 60ttgctatttc tagctctaaa acaacgacga
gcgtgacacc accctatagt gagtcgtatt 120aatttc 126274126DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
274aaaaaagcac cgactcggtg ccactttttc aagttgataa cggactagcc
ttattttaac 60ttgctatttc tagctctaaa acgcaacaat taatagactg gacctatagt
gagtcgtatt 120aatttc 1262754677DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 275tctttcttgc
gctatgacac ttccagcaaa aggtagggcg ggctgcgaga cggcttcccg 60gcgctgcatg
caacaccgat gatgcttcga ccccccgaag ctccttcggg gctgcatggg
120cgctccgatg ccgctccagg gcgagcgctg tttaaatagc caggcccccg
attgcaaaga 180cattatagcg agctaccaaa gccatattca aacacctaga
tcactaccac ttctacacag 240gccactcgag cttgtgatcg cactccgcta
agggggcgcc tcttcctctt cgtttcagtc 300acaacccgca aacatgtacc
catacgatgt tccagattac gcttcgccga agaaaaagcg 360caaggtcgaa
gcgtccgaca agaagtacag catcggcctg gacatcggca ccaactctgt
420gggctgggcc gtgatcaccg acgagtacaa ggtgcccagc aagaaattca
aggtgctggg 480caacaccgac cggcacagca tcaagaagaa cctgatcgga
gccctgctgt tcgacagcgg 540cgaaacagcc gaggccaccc ggctgaagag
aaccgccaga agaagataca ccagacggaa 600gaaccggatc tgctatctgc
aagagatctt cagcaacgag atggccaagg tggacgacag 660cttcttccac
agactggaag agtccttcct ggtggaagag gataagaagc acgagcggca
720ccccatcttc ggcaacatcg tggacgaggt ggcctaccac gagaagtacc
ccaccatcta 780ccacctgaga aagaaactgg tggacagcac cgacaaggcc
gacctgcggc tgatctatct 840ggccctggcc cacatgatca agttccgggg
ccacttcctg atcgagggcg acctgaaccc 900cgacaacagc gacgtggaca
agctgttcat ccagctggtg cagacctaca accagctgtt 960cgaggaaaac
cccatcaacg ccagcggcgt ggacgccaag gccatcctgt ctgccagact
1020gagcaagagc agacggctgg aaaatctgat cgcccagctg cccggcgaga
agaagaatgg 1080cctgttcggc aacctgattg ccctgagcct gggcctgacc
cccaacttca agagcaactt 1140cgacctggcc gaggatgcca aactgcagct
gagcaaggac acctacgacg acgacctgga 1200caacctgctg gcccagatcg
gcgaccagta cgccgacctg tttctggccg ccaagaacct 1260gtccgacgcc
atcctgctga gcgacatcct gagagtgaac accgagatca ccaaggcccc
1320cctgagcgcc tctatgatca agagatacga cgagcaccac caggacctga
ccctgctgaa 1380agctctcgtg cggcagcagc tgcctgagaa gtacaaagag
attttcttcg accagagcaa
1440gaacggctac gccggctaca ttgacggcgg agccagccag gaagagttct
acaagttcat 1500caagcccatc ctggaaaaga tggacggcac cgaggaactg
ctcgtgaagc tgaacagaga 1560ggacctgctg cggaagcagc ggaccttcga
caacggcagc atcccccacc agatccacct 1620gggagagctg cacgccattc
tgcggcggca ggaagatttt tacccattcc tgaaggacaa 1680ccgggaaaag
atcgagaaga tcctgacctt ccgcatcccc tactacgtgg gccctctggc
1740caggggaaac agcagattcg cctggatgac cagaaagagc gaggaaacca
tcaccccctg 1800gaacttcgag gaagtggtgg acaagggcgc ttccgcccag
agcttcatcg agcggatgac 1860caacttcgat aagaacctgc ccaacgagaa
ggtgctgccc aagcacagcc tgctgtacga 1920gtacttcacc gtgtataacg
agctgaccaa agtgaaatac gtgaccgagg gaatgagaaa 1980gcccgccttc
ctgagcggcg agcagaaaaa ggccatcgtg gacctgctgt tcaagaccaa
2040ccggaaagtg accgtgaagc agctgaaaga ggactacttc aagaaaatcg
agtgcttcga 2100ctccgtggaa atctccggcg tggaagatcg gttcaacgcc
tccctgggca cataccacga 2160tctgctgaaa attatcaagg acaaggactt
cctggacaat gaggaaaacg aggacattct 2220ggaagatatc gtgctgaccc
tgacactgtt tgaggacaga gagatgatcg aggaacggct 2280gaaaacctat
gcccacctgt tcgacgacaa agtgatgaag cagctgaagc ggcggagata
2340caccggctgg ggcaggctga gccggaagct gatcaacggc atccgggaca
agcagtccgg 2400caagacaatc ctggatttcc tgaagtccga cggcttcgcc
aacagaaact tcatgcagct 2460gatccacgac gacagcctga cctttaaaga
ggacatccag aaagcccagg tgtccggcca 2520gggcgatagc ctgcacgagc
acattgccaa tctggccggc agccccgcca ttaagaaggg 2580catcctgcag
acagtgaagg tggtggacga gctcgtgaaa gtgatgggcc ggcacaagcc
2640cgagaacatc gtgatcgaaa tggccagaga gaaccagacc acccagaagg
gacagaagaa 2700cagccgcgag agaatgaagc ggatcgaaga gggcatcaaa
gagctgggca gccagatcct 2760gaaagaacac cccgtggaaa acacccagct
gcagaacgag aagctgtacc tgtactacct 2820gcagaatggg cgggatatgt
acgtggacca ggaactggac atcaaccggc tgtccgacta 2880cgatgtggac
catatcgtgc ctcagagctt tctgaaggac gactccatcg acaacaaggt
2940gctgaccaga agcgacaaga accggggcaa gagcgacaac gtgccctccg
aagaggtcgt 3000gaagaagatg aagaactact ggcggcagct gctgaacgcc
aagctgatta cccagagaaa 3060gttcgacaat ctgaccaagg ccgagagagg
cggcctgagc gaactggata aggccggctt 3120catcaagaga cagctggtgg
aaacccggca gatcacaaag cacgtggcac agatcctgga 3180ctcccggatg
aacactaagt acgacgagaa tgacaagctg atccgggaag tgaaagtgat
3240caccctgaag tccaagctgg tgtccgattt ccggaaggat ttccagtttt
acaaagtgcg 3300cgagatcaac aactaccacc acgcccacga cgcctacctg
aacgccgtcg tgggaaccgc 3360cctgatcaaa aagtacccta agctggaaag
cgagttcgtg tacggcgact acaaggtgta 3420cgacgtgcgg aagatgatcg
ccaagagcga gcaggaaatc ggcaaggcta ccgccaagta 3480cttcttctac
agcaacatca tgaacttttt caagaccgag attaccctgg ccaacggcga
3540gatccggaag cggcctctga tcgagacaaa cggcgaaacc ggggagatcg
tgtgggataa 3600gggccgggat tttgccaccg tgcggaaagt gctgagcatg
ccccaagtga atatcgtgaa 3660aaagaccgag gtgcagacag gcggcttcag
caaagagtct atcctgccca agaggaacag 3720cgataagctg atcgccagaa
agaaggactg ggaccctaag aagtacggcg gcttcgacag 3780ccccaccgtg
gcctattctg tgctggtggt ggccaaagtg gaaaagggca agtccaagaa
3840actgaagagt gtgaaagagc tgctggggat caccatcatg gaaagaagca
gcttcgagaa 3900gaatcccatc gactttctgg aagccaaggg ctacaaagaa
gtgaaaaagg acctgatcat 3960caagctgcct aagtactccc tgttcgagct
ggaaaacggc cggaagagaa tgctggcctc 4020tgccggcgaa ctgcagaagg
gaaacgaact ggccctgccc tccaaatatg tgaacttcct 4080gtacctggcc
agccactatg agaagctgaa gggctccccc gaggataatg agcagaaaca
4140gctgtttgtg gaacagcaca agcactacct ggacgagatc atcgagcaga
tcagcgagtt 4200ctccaagaga gtgatcctgg ccgacgctaa tctggacaaa
gtgctgtccg cctacaacaa 4260gcaccgggat aagcccatca gagagcaggc
cgagaatatc atccacctgt ttaccctgac 4320caatctggga gcccctgccg
ccttcaagta ctttgacacc accatcgacc ggaagaggta 4380caccagcacc
aaagaggtgc tggacgccac cctgatccac cagagcatca ccggcctgta
4440cgagacacgg atcgacctgt ctcagctggg aggcgacagc cccaagaaga
agagaaaggt 4500ggaggccagc taaggatccg gcaagactgg ccccgcttgg
caacgcaaca gtgagcccct 4560ccctagtgtg tttggggatg tgactatgta
ttcgtgtgtt ggccaacggg tcaacccgaa 4620cagattgata cccgccttgg
catttcctgt cagaatgtaa cgtcagttga tggtact 46772763150DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
276tctttcttgc gctatgacac ttccagcaaa aggtagggcg ggctgcgaga
cggcttcccg 60gcgctgcatg caacaccgat gatgcttcga ccccccgaag ctccttcggg
gctgcatggg 120cgctccgatg ccgctccagg gcgagcgctg tttaaatagc
caggcccccg attgcaaaga 180cattatagcg agctaccaaa gccatattca
aacacctaga tcactaccac ttctacacag 240gccactcgag cttgtgatcg
cactccgcta agggggcgcc tcttcctctt cgtttcagtc 300acaacccgca
aacatgccta agaagaagag gaaggttaac acgattaaca tcgctaagaa
360cgacttctct gacatcgaac tggctgctat cccgttcaac actctggctg
accattacgg 420tgagcgttta gctcgcgaac agttggccct tgagcatgag
tcttacgaga tgggtgaagc 480acgcttccgc aagatgtttg agcgtcaact
taaagctggt gaggttgcgg ataacgctgc 540cgccaagcct ctcatcacta
ccctactccc taagatgatt gcacgcatca acgactggtt 600tgaggaagtg
aaagctaagc gcggcaagcg cccgacagcc ttccagttcc tgcaagaaat
660caagccggaa gccgtagcgt acatcaccat taagaccact ctggcttgcc
taaccagtgc 720tgacaataca accgttcagg ctgtagcaag cgcaatcggt
cgggccattg aggacgaggc 780tcgcttcggt cgtatccgtg accttgaagc
taagcacttc aagaaaaacg ttgaggaaca 840actcaacaag cgcgtagggc
acgtctacaa gaaagcattt atgcaagttg tcgaggctga 900catgctctct
aagggtctac tcggtggcga ggcgtggtct tcgtggcata aggaagactc
960tattcatgta ggagtacgct gcatcgagat gctcattgag tcaaccggaa
tggttagctt 1020acaccgccaa aatgctggcg tagtaggtca agactctgag
actatcgaac tcgcacctga 1080atacgctgag gctatcgcaa cccgtgcagg
tgcgctggct ggcatctctc cgatgttcca 1140accttgcgta gttcctccta
agccgtggac tggcattact ggtggtggct attgggctaa 1200cggtcgtcgt
cctctggcgc tggtgcgtac tcacagtaag aaagcactga tgcgctacga
1260agacgtttac atgcctgagg tgtacaaagc gattaacatt gcgcaaaaca
ccgcatggaa 1320aatcaacaag aaagtcctag cggtcgccaa cgtaatcacc
aagtggaagc attgtccggt 1380cgaggacatc cctgcgattg agcgtgaaga
actcccgatg aaaccggaag acatcgacat 1440gaatcctgag gctctcaccg
cgtggaaacg tgctgccgct gctgtgtacc gcaaggacaa 1500ggctcgcaag
tctcgccgta tcagccttga gttcatgctt gagcaagcca ataagtttgc
1560taaccataag gccatctggt tcccttacaa catggactgg cgcggtcgtg
tttacgctgt 1620gtcaatgttc aacccgcaag gtaacgatat gaccaaagga
ctgcttacgc tggcgaaagg 1680taaaccaatc ggtaaggaag gttactactg
gctgaaaatc cacggtgcaa actgtgcggg 1740tgtcgacaag gttccgttcc
ctgagcgcat caagttcatt gaggaaaacc acgagaacat 1800catggcttgc
gctaagtctc cactggagaa cacttggtgg gctgagcaag attctccgtt
1860ctgcttcctt gcgttctgct ttgagtacgc tggggtacag caccacggcc
tgagctataa 1920ctgctccctt ccgctggcgt ttgacgggtc ttgctctggc
atccagcact tctccgcgat 1980gctccgagat gaggtaggtg gtcgcgcggt
taacttgctt cctagtgaaa ccgttcagga 2040catctacggg attgttgcta
agaaagtcaa cgagattcta caagcagacg caatcaatgg 2100gaccgataac
gaagtagtta ccgtgaccga tgagaacact ggtgaaatct ctgagaaagt
2160caagctgggc actaaggcac tggctggtca atggctggct tacggtgtta
ctcgcagtgt 2220gactaagcgt tcagtcatga cgctggctta cgggtccaaa
gagttcggct tccgtcaaca 2280agtgctggaa gataccattc agccagctat
tgattccggc aagggtctga tgttcactca 2340gccgaatcag gctgctggat
acatggctaa gctgatttgg gaatctgtga gcgtgacggt 2400ggtagctgcg
gttgaagcaa tgaactggct taagtctgct gctaagctgc tggctgctga
2460ggtcaaagat aagaagactg gagagattct tcgcaagcgt tgcgctgtgc
attgggtaac 2520tcctgatggt ttccctgtgt ggcaggaata caagaagcct
attcagacgc gcttgaacct 2580gatgttcctc ggtcagttcc gcttacagcc
taccattaac accaacaaag atagcgagat 2640tgatgcacac aaacaggagt
ctggtatcgc tcctaacttt gtacacagcc aagacggtag 2700ccaccttcgt
aagactgtag tgtgggcaca cgagaagtac ggaatcgaat cttttgcact
2760gattcacgac tccttcggta cgattccggc tgacgctgcg aacctgttca
aagcagtgcg 2820cgaaactatg gttgacacat atgagtcttg tgatgtactg
gctgatttct acgaccagtt 2880cgctgaccag ttgcacgagt ctcaattgga
caaaatgcca gcacttccgg ctaaaggtaa 2940cttgaacctc cgtgacatct
tagagtcgga cttcgcgttc gcgtaaggat ccggcaagac 3000tggccccgct
tggcaacgca acagtgagcc cctccctagt gtgtttgggg atgtgactat
3060gtattcgtgt gttggccaac gggtcaaccc gaacagattg atacccgcct
tggcatttcc 3120tgtcagaatg taacgtcagt tgatggtact
3150277125DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 277gaaattaata cgactcacta tannnnnnnn
nnnnnnnnnn nngttttaga gctagaaata 60gcaagttaaa ataaggctag tccgttatca
acttgaaaaa gtggcaccga gtcggtgctt 120ttttt 1252788452DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
278tgcggtattt cacaccgcat caggtggcac ttttcgggga aatgtgcgcg
gaacccctat 60ttgtttattt ttctaaatac attcaaatat gtatccgctc atgagattat
caaaaaggat 120cttcacctag atccttttaa attaaaaatg aagttttaaa
tcaatctaaa gtatatatga 180gtaaacttgg tctgacagtt accaatgctt
aatcagtgag gcacctatct cagcgatctg 240tctatttcgt tcatccatag
ttgcctgact ccccgtcgtg tagataacta cgatacggga 300gggcttacca
tctggcccca gtgctgcaat gataccgcga gacccacgct caccggctcc
360agatttatca gcaataaacc agccagccgg aagggccgag cgcagaagtg
gtcctgcaac 420tttatccgcc tccatccagt ctattaattg ttgccgggaa
gctagagtaa gtagttcgcc 480agttaatagt ttgcgcaacg ttgttgccat
tgctacaggc atcgtggtgt cacgctcgtc 540gtttggtatg gcttcattca
gctccggttc ccaacgatca aggcgagtta catgatcccc 600catgttgtgc
aaaaaagcgg ttagctcctt cggtcctccg atcgttgtca gaagtaagtt
660ggccgcagtg ttatcactca tggttatggc agcactgcat aattctctta
ctgtcatgcc 720atccgtaaga tgcttttctg tgactggtga gtactcaacc
aagtcattct gagaatagtg 780tatgcggcga ccgagttgct cttgcccggc
gtcaatacgg gataataccg cgccacatag 840cagaacttta aaagtgctca
tcattggaaa acgttcttcg gggcgaaaac tctcaaggat 900cttaccgctg
ttgagatcca gttcgatgta acccactcgt gcacccaact gatcttcagc
960atcttttact ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa
atgccgcaaa 1020aaagggaata agggcgacac ggaaatgttg aatactcata
ctcttccttt ttcaatatta 1080ttgaagcatt tatcagggtt attgtctcat
gaccaaaatc ccttaacgtg agttttcgtt 1140ccactgagcg tcagaccccg
tagaaaagat caaaggatct tcttgagatc ctttttttct 1200gcgcgtaatc
tgctgcttgc aaacaaaaaa accaccgcta ccagcggtgg tttgtttgcc
1260ggatcaagag ctaccaactc tttttccgaa ggtaactggc ttcagcagag
cgcagatacc 1320aaatactgtt cttctagtgt agccgtagtt aggccaccac
ttcaagaact ctgtagcacc 1380gcctacatac ctcgctctgc taatcctgtt
accagtggct gttgccagtg gcgataagtc 1440gtgtcttacc gggttggact
caagacgata gttaccggat aaggcgcagc ggtcgggctg 1500aacggggggt
tcgtgcacac agcccagctt ggagcgaacg acctacaccg aactgagata
1560cctacagcgt gagctatgag aaagcgccac gcttcccgaa gggagaaagg
cggacaggta 1620tccggtaagc ggcagggtcg gaacaggaga gcgcacgagg
gagcttccag ggggaaacgc 1680ctggtatctt tatagtcctg tcgggtttcg
ccacctctga cttgagcgtc gatttttgtg 1740atgctcgtca ggggggcgga
gcctatggaa aaacgccagc aacgcggcct ttttacggtt 1800cctggccttt
tgctggcctt ttgctcacat gttctttcct gcgttatccc ctgattctgt
1860ggataaccgt attaccgcct ttgagtgagc tgataccgct cgccgcagcc
gaacgaccga 1920gcgcagcgag tcagtgagcg aggaagcggt cgctgaggct
tgacatgatt ggtgcgtatg 1980tttgtatgaa gctacaggac tgatttggcg
ggctatgagg gcgggggaag ctctggaagg 2040gccgcgatgg ggcgcgcggc
gtccagaagg cgccatacgg cccgctggcg gcacccatcc 2100ggtataaaag
cccgcgaccc cgaacggtga cctccacttt cagcgacaaa cgagcactta
2160tacatacgcg actattctgc cgctatacat aaccactcag ctagcttaag
atcccatcaa 2220gcttgcatgc cgggcgcgcc agaaggagcg cagccaaacc
aggatgatgt ttgatggggt 2280atttgagcac ttgcaaccct tatccggaag
ccccctggcc cacaaaggct aggcgccaat 2340gcaagcagtt cgcatgcagc
ccctggagcg gtgccctcct gataaaccgg ccagggggcc 2400tatgttcttt
acttttttac aagagaagtc actcaacatc ttaaaatggc caggtgagtc
2460gacgagcaag cccggcggat caggcagcgt gcttgcagat ttgacttgca
acgcccgcat 2520tgtgtcgacg aaggcttttg gctcctctgt cgctgtctca
agcagcatct aaccctgcgt 2580cgccgtttcc atttgcagga gattcgaggt
accatgtacc catacgatgt tccagattac 2640gcttcgccga agaaaaagcg
caaggtcgaa gcgtccgaca agaagtacag catcggcctg 2700gacatcggca
ccaactctgt gggctgggcc gtgatcaccg acgagtacaa ggtgcccagc
2760aagaaattca aggtgctggg caacaccgac cggcacagca tcaagaagaa
cctgatcgga 2820gccctgctgt tcgacagcgg cgaaacagcc gaggccaccc
ggctgaagag aaccgccaga 2880agaagataca ccagacggaa gaaccggatc
tgctatctgc aagagatctt cagcaacgag 2940atggccaagg tggacgacag
cttcttccac agactggaag agtccttcct ggtggaagag 3000gataagaagc
acgagcggca ccccatcttc ggcaacatcg tggacgaggt ggcctaccac
3060gagaagtacc ccaccatcta ccacctgaga aagaaactgg tggacagcac
cgacaaggcc 3120gacctgcggc tgatctatct ggccctggcc cacatgatca
agttccgggg ccacttcctg 3180atcgagggcg acctgaaccc cgacaacagc
gacgtggaca agctgttcat ccagctggtg 3240cagacctaca accagctgtt
cgaggaaaac cccatcaacg ccagcggcgt ggacgccaag 3300gccatcctgt
ctgccagact gagcaagagc agacggctgg aaaatctgat cgcccagctg
3360cccggcgaga agaagaatgg cctgttcggc aacctgattg ccctgagcct
gggcctgacc 3420cccaacttca agagcaactt cgacctggcc gaggatgcca
aactgcagct gagcaaggac 3480acctacgacg acgacctgga caacctgctg
gcccagatcg gcgaccagta cgccgacctg 3540tttctggccg ccaagaacct
gtccgacgcc atcctgctga gcgacatcct gagagtgaac 3600accgagatca
ccaaggcccc cctgagcgcc tctatgatca agagatacga cgagcaccac
3660caggacctga ccctgctgaa agctctcgtg cggcagcagc tgcctgagaa
gtacaaagag 3720attttcttcg accagagcaa gaacggctac gccggctaca
ttgacggcgg agccagccag 3780gaagagttct acaagttcat caagcccatc
ctggaaaaga tggacggcac cgaggaactg 3840ctcgtgaagc tgaacagaga
ggacctgctg cggaagcagc ggaccttcga caacggcagc 3900atcccccacc
agatccacct gggagagctg cacgccattc tgcggcggca ggaagatttt
3960tacccattcc tgaaggacaa ccgggaaaag atcgagaaga tcctgacctt
ccgcatcccc 4020tactacgtgg gccctctggc caggggaaac agcagattcg
cctggatgac cagaaagagc 4080gaggaaacca tcaccccctg gaacttcgag
gaagtggtgg acaagggcgc ttccgcccag 4140agcttcatcg agcggatgac
caacttcgat aagaacctgc ccaacgagaa ggtgctgccc 4200aagcacagcc
tgctgtacga gtacttcacc gtgtataacg agctgaccaa agtgaaatac
4260gtgaccgagg gaatgagaaa gcccgccttc ctgagcggcg agcagaaaaa
ggccatcgtg 4320gacctgctgt tcaagaccaa ccggaaagtg accgtgaagc
agctgaaaga ggactacttc 4380aagaaaatcg agtgcttcga ctccgtggaa
atctccggcg tggaagatcg gttcaacgcc 4440tccctgggca cataccacga
tctgctgaaa attatcaagg acaaggactt cctggacaat 4500gaggaaaacg
aggacattct ggaagatatc gtgctgaccc tgacactgtt tgaggacaga
4560gagatgatcg aggaacggct gaaaacctat gcccacctgt tcgacgacaa
agtgatgaag 4620cagctgaagc ggcggagata caccggctgg ggcaggctga
gccggaagct gatcaacggc 4680atccgggaca agcagtccgg caagacaatc
ctggatttcc tgaagtccga cggcttcgcc 4740aacagaaact tcatgcagct
gatccacgac gacagcctga cctttaaaga ggacatccag 4800aaagcccagg
tgtccggcca gggcgatagc ctgcacgagc acattgccaa tctggccggc
4860agccccgcca ttaagaaggg catcctgcag acagtgaagg tggtggacga
gctcgtgaaa 4920gtgatgggcc ggcacaagcc cgagaacatc gtgatcgaaa
tggccagaga gaaccagacc 4980acccagaagg gacagaagaa cagccgcgag
agaatgaagc ggatcgaaga gggcatcaaa 5040gagctgggca gccagatcct
gaaagaacac cccgtggaaa acacccagct gcagaacgag 5100aagctgtacc
tgtactacct gcagaatggg cgggatatgt acgtggacca ggaactggac
5160atcaaccggc tgtccgacta cgatgtggac catatcgtgc ctcagagctt
tctgaaggac 5220gactccatcg acaacaaggt gctgaccaga agcgacaaga
accggggcaa gagcgacaac 5280gtgccctccg aagaggtcgt gaagaagatg
aagaactact ggcggcagct gctgaacgcc 5340aagctgatta cccagagaaa
gttcgacaat ctgaccaagg ccgagagagg cggcctgagc 5400gaactggata
aggccggctt catcaagaga cagctggtgg aaacccggca gatcacaaag
5460cacgtggcac agatcctgga ctcccggatg aacactaagt acgacgagaa
tgacaagctg 5520atccgggaag tgaaagtgat caccctgaag tccaagctgg
tgtccgattt ccggaaggat 5580ttccagtttt acaaagtgcg cgagatcaac
aactaccacc acgcccacga cgcctacctg 5640aacgccgtcg tgggaaccgc
cctgatcaaa aagtacccta agctggaaag cgagttcgtg 5700tacggcgact
acaaggtgta cgacgtgcgg aagatgatcg ccaagagcga gcaggaaatc
5760ggcaaggcta ccgccaagta cttcttctac agcaacatca tgaacttttt
caagaccgag 5820attaccctgg ccaacggcga gatccggaag cggcctctga
tcgagacaaa cggcgaaacc 5880ggggagatcg tgtgggataa gggccgggat
tttgccaccg tgcggaaagt gctgagcatg 5940ccccaagtga atatcgtgaa
aaagaccgag gtgcagacag gcggcttcag caaagagtct 6000atcctgccca
agaggaacag cgataagctg atcgccagaa agaaggactg ggaccctaag
6060aagtacggcg gcttcgacag ccccaccgtg gcctattctg tgctggtggt
ggccaaagtg 6120gaaaagggca agtccaagaa actgaagagt gtgaaagagc
tgctggggat caccatcatg 6180gaaagaagca gcttcgagaa gaatcccatc
gactttctgg aagccaaggg ctacaaagaa 6240gtgaaaaagg acctgatcat
caagctgcct aagtactccc tgttcgagct ggaaaacggc 6300cggaagagaa
tgctggcctc tgccggcgaa ctgcagaagg gaaacgaact ggccctgccc
6360tccaaatatg tgaacttcct gtacctggcc agccactatg agaagctgaa
gggctccccc 6420gaggataatg agcagaaaca gctgtttgtg gaacagcaca
agcactacct ggacgagatc 6480atcgagcaga tcagcgagtt ctccaagaga
gtgatcctgg ccgacgctaa tctggacaaa 6540gtgctgtccg cctacaacaa
gcaccgggat aagcccatca gagagcaggc cgagaatatc 6600atccacctgt
ttaccctgac caatctggga gcccctgccg ccttcaagta ctttgacacc
6660accatcgacc ggaagaggta caccagcacc aaagaggtgc tggacgccac
cctgatccac 6720cagagcatca ccggcctgta cgagacacgg atcgacctgt
ctcagctggg aggcgacagc 6780cccaagaaga agagaaaggt ggaggccagc
taacatatga ttcgaatgtc tttcttgcgc 6840tatgacactt ccagcaaaag
gtagggcggg ctgcgagacg gcttcccggc gctgcatgca 6900acaccgatga
tgcttcgacc ccccgaagct ccttcggggc tgcatgggcg ctccgatgcc
6960gctccagggc gagcgctgtt taaatagcca ggcccccgat tgcaaagaca
ttatagcgag 7020ctaccaaagc catattcaaa cacctagatc actaccactt
ctacacaggc cactcgagct 7080tgtgatcgca ctccgctaag ggggcgcctc
ttcctcttcg tttcagtcac aacccgcaaa 7140catgacacaa gaatccctgt
tacttctcga ccgtattgat tcggatgatt cctacgcgag 7200cctgcggaac
gaccaggaat tctgggaggt gagtcgacga gcaagcccgg cggatcaggc
7260agcgtgcttg cagatttgac ttgcaacgcc cgcattgtgt cgacgaaggc
ttttggctcc 7320tctgtcgctg tctcaagcag catctaaccc tgcgtcgccg
tttccatttg cagccgctgg 7380cccgccgagc cctggaggag ctcgggctgc
cggtgccgcc ggtgctgcgg gtgcccggcg 7440agagcaccaa ccccgtactg
gtcggcgagc ccggcccggt gatcaagctg ttcggcgagc 7500actggtgcgg
tccggagagc ctcgcgtcgg agtcggaggc gtacgcggtc ctggcggacg
7560ccccggtgcc ggtgccccgc ctcctcggcc gcggcgagct gcggcccggc
accggagcct 7620ggccgtggcc ctacctggtg atgagccgga tgaccggcac
cacctggcgg tccgcgatgg 7680acggcacgac cgaccggaac gcgctgctcg
ccctggcccg cgaactcggc cgggtgctcg 7740gccggctgca cagggtgccg
ctgaccggga acaccgtgct caccccccat tccgaggtct 7800tcccggaact
gctgcgggaa cgccgcgcgg cgaccgtcga ggaccaccgc gggtggggct
7860acctctcgcc ccggctgctg gaccgcctgg aggactggct gccggacgtg
gacacgctgc 7920tggccggccg cgaaccccgg ttcgtccacg gcgacctgca
cgggaccaac atcttcgtgg 7980acctggccgc gaccgaggtc accgggatcg
tcgacttcac cgacgtctat gcgggagact 8040cccgctacag cctggtgcaa
ctgcatctca acgccttccg gggcgaccgc gagatcctgg 8100ccgcgctgct
cgacggggcg cagtggaagc ggaccgagga cttcgcccgc gaactgctcg
8160ccttcacctt cctgcacgac ttcgaggtgt
tcgaggagac cccgctggat ctctccggct 8220tcaccgatcc ggaggaactg
gcgcagttcc tctgggggcc gccggacacc gcccccggcg 8280cctgataagg
atccggcaag actggccccg cttggcaacg caacagtgag cccctcccta
8340gtgtgtttgg ggatgtgact atgtattcgt gtgttggcca acgggtcaac
ccgaacagat 8400tgatacccgc cttggcattt cctgtcagaa tgtaacgtca
gttgatggta ct 8452279102DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 279gttttagagc
tatgctgttt tgaatggtcc caaaacggaa gggcctgagt ccgagcagaa 60gaagaagttt
tagagctatg ctgttttgaa tggtcccaaa ac 102280100DNAHomo sapiens
280cggaggacaa agtacaaacg gcagaagctg gaggaggaag ggcctgagtc
cgagcagaag 60aagaagggct cccatcacat caaccggtgg cgcattgcca
10028150DNAHomo sapiens 281agctggagga ggaagggcct gagtccgagc
agaagaagaa gggctcccac 5028230RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 282gaguccgagc
agaagaagaa guuuuagagc 3028349DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 283agctggagga
ggaagggcct gagtccgagc agaagagaag ggctcccat 4928453DNAHomo sapiens
284ctggaggagg aagggcctga gtccgagcag aagaagaagg gctcccatca cat
5328552DNAHomo sapiens 285ctggaggagg aagggcctga gtccgagcag
aagagaaggg ctcccatcac at 5228654DNAHomo sapiens 286ctggaggagg
aagggcctga gtccgagcag aagaaagaag ggctcccatc acat 5428750DNAHomo
sapiens 287ctggaggagg aagggcctga gtccgagcag aagaagggct cccatcacat
5028847DNAHomo sapiens 288ctggaggagg aagggcctga gcccgagcag
aagggctccc atcacat 4728966DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 289nnnnnnnnnn
nnnnnnnnnn guuuuagagc uagaaauagc aaguuaaaau aaggctagtc 60cguuuu
6629020RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 290gaguccgagc agaagaagaa
2029120RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 291gacaucgaug uccuccccau
2029220RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 292gucaccucca augacuaggg
2029320RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 293auuggguguu cagggcagag
2029420RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 294guggcgagag gggccgagau
2029520RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 295ggggccgaga uuggguguuc
2029620RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 296gugccauuag cuaaaugcau
2029720RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 297guaccaccca caggugccag
2029820RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 298gaaagccucu gggccaggaa
2029948DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 299ctggaggagg aagggcctga gtccgagcag
aagaagaagg gctcccat 4830020RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 300gaguccgagc
agaagaagau 2030120RNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 301gaguccgagc agaagaagua
2030220RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 302gaguccgagc agaagaacaa
2030320RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 303gaguccgagc agaagaugaa
2030420RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 304gaguccgagc agaaguagaa
2030520RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 305gaguccgagc agaugaagaa
2030620RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 306gaguccgagc acaagaagaa
2030720RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 307gaguccgagg agaagaagaa
2030820RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 308gaguccgugc agaagaagaa
2030920RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 309gagucggagc agaagaagaa
2031020RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 310gagaccgagc agaagaagaa
2031124DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 311aatgacaagc ttgctagcgg tggg
2431239DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 312aaaacggaag ggcctgagtc cgagcagaag
aagaagttt 3931339DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 313aaacaggggc cgagattggg
tgttcagggc agaggtttt 3931438DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 314aaaacggaag
ggcctgagtc cgagcagaag aagaagtt 3831540DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 315aacggaggga ggggcacaga tgagaaactc agggttttag
4031638DNAHomo sapiens 316agcccttctt cttctgctcg gactcaggcc cttcctcc
3831740DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 317cagggaggga ggggcacaga tgagaaactc
aggaggcccc 4031880DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 318ggcaatgcgc caccggttga
tgtgatggga gcccttctag gaggccccca gagcagccac 60tggggcctca acactcaggc
8031923DNAHomo sapiens 319gtcacctcca atgactaggg tgg
2332025DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 320caccgnnnnn nnnnnnnnnn nnnnn
2532125DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 321aaacnnnnnn nnnnnnnnnn nnnnc
2532233DNAHomo sapiens 322catcgatgtc ctccccattg gcctgcttcg tgg
3332333DNAHomo sapiens 323ttcgtggcaa tgcgccaccg gttgatgtga tgg
3332433DNAHomo sapiens 324tcgtggcaat gcgccaccgg ttgatgtgat ggg
3332533DNAHomo sapiens 325tccagcttct gccgtttgta ctttgtcctc cgg
3332633DNAHomo sapiens 326ggagggaggg gcacagatga gaaactcagg agg
3332733DNAHomo sapiens 327aggggccgag attgggtgtt cagggcagag agg
3332854DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 328aacaccgggt cttcgagaag acctgtttta
gagctagaaa tagcaagtta aaat 5432954DNAArtificial SequenceDescription
of Artificial Sequence Synthetic oligonucleotide 329caaaacgggt
cttcgagaag acgttttaga gctatgctgt tttgaatggt ccca 5433033DNAMus
musculus 330caagcactga gtgccattag ctaaatgcat agg 3333133DNAMus
musculus 331aatgcatagg gtaccaccca caggtgccag ggg 3333233DNAMus
musculus 332acacacatgg gaaagcctct gggccaggaa agg 3333337DNAHomo
sapiens 333ggaggaggta gtatacagaa acacagagaa gtagaat 3733437DNAHomo
sapiens 334agaatgtaga ggagtcacag aaactcagca ctagaaa
3733598DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 335ggacgaaaca ccggaaccat tcaaaacagc
atagcaagtt aaaataaggc tagtccgtta 60tcaacttgaa aaagtggcac cgagtcggtg
cttttttt 98336186DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 336ggacgaaaca ccggtagtat
taagtattgt tttatggctg ataaatttct ttgaatttct 60ccttgattat ttgttataaa
agttataaaa taatcttgtt ggaaccattc aaaacagcat 120agcaagttaa
aataaggcta gtccgttatc aacttgaaaa agtggcaccg agtcggtgct 180tttttt
18633795DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 337gggttttaga gctatgctgt tttgaatggt
cccaaaacgg gtcttcgaga agacgtttta 60gagctatgct gttttgaatg gtcccaaaac
ttttt 9533836DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 338aaacnnnnnn nnnnnnnnnn
nnnnnnnnnn nnnngt 3633936DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 339taaaacnnnn
nnnnnnnnnn nnnnnnnnnn nnnnnn 3634084DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 340gtggaaagga cgaaacaccg ggtcttcgag aagacctgtt
ttagagctag aaatagcaag 60ttaaaataag gctagtccgt tttt
8434124DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 341caccgnnnnn nnnnnnnnnn nnnn
2434224DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 342aaacnnnnnn nnnnnnnnnn nnnc
2434388DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 343gttttagagc tatgctgttt tgaatggtcc
caaaactgag accaaaggtc tcgttttaga 60gctatgctgt tttgaatggt cccaaaac
8834435DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 344aaacggaagg gcctgagtcc gagcagaaga agaag
3534535DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 345aaaacttctt cttctgctcg gactcaggcc cttcc
3534646RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 346nnnnnnnnnn nnnnnnnnng uuauuguacu
cucaagauuu auuuuu 4634791RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 347guuacuuaaa
ucuugcagaa gcuacaaaga uaaggcuuca ugccgaaauc aacacccugu 60cauuuuaugg
caggguguuu ucguuauuua a 9134870DNAHomo sapiens 348ttttctagtg
ctgagtttct gtgactcctc tacattctac ttctctgtgt ttctgtatac 60tacctcctcc
70349122DNAHomo sapiens 349ggaggaaggg cctgagtccg agcagaagaa
gaagggctcc catcacatca accggtggcg 60cattgccacg aagcaggcca atggggagga
catcgatgtc acctccaatg actagggtgg 120gc 12235048RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 350acnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnguuuuaga
gcuaugcu 4835167DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 351agcauagcaa guuaaaauaa
ggctaguccg uuaucaacuu gaaaaagugg caccgagucg 60gugcuuu
6735262RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 352nnnnnnnnnn nnnnnnnnnn guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cg 6235373DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 353tgaatggtcc caaaacggaa gggcctgagt ccgagcagaa
gaagaagttt tagagctatg 60ctgttttgaa tgg 7335469DNAHomo sapiens
354ctggtcttcc acctctctgc cctgaacacc caatctcggc ccctctcgcc
accctcctgc 60atttctgtt 69355138DNAMus musculus 355acccaagcac
tgagtgccat tagctaaatg catagggtac cacccacagg tgccaggggc 60ctttcccaaa
gttcccagcc ccttctccaa cctttcctgg cccagaggct ttcccatgtg
120tgtggctgga ccctttga 13835620DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 356gtgctttgca gaggcctacc
2035720DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 357cctggagcgc atgcagtagt 2035822DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
358accttctgtg tttccaccat tc 2235920DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
359ttggggagtg cacagacttc 2036020DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 360ggctccctgg gttcaaagta
2036121DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 361agaggggtct ggatgtcgta a 2136230DNAArtificial
SequenceDescription of Artificial Sequence Synthetic probe
362tagctctaaa acttcttctt ctgctcggac 3036330DNAArtificial
SequenceDescription of Artificial Sequence Synthetic probe
363ctagccttat tttaacttgc tatgctgttt 3036499RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 364nnnnnnnnnn nnnnnnnnnn guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu ggcaccgagu cggugcuuu
9936512DNAHomo sapiens 365tagcgggtaa gc 1236612DNAHomo sapiens
366tcggtgacat gt 1236712DNAHomo sapiens 367actccccgta gg
1236812DNAHomo sapiens 368actgcgtgtt aa 1236912DNAHomo sapiens
369acgtcgcctg at 1237012DNAHomo sapiens 370taggtcgacc ag
1237112DNAHomo sapiens 371ggcgttaatg at 1237212DNAHomo sapiens
372tgtcgcatgt ta 1237312DNAHomo sapiens 373atggaaacgc at
1237412DNAHomo sapiens 374gccgaattcc tc 1237512DNAHomo sapiens
375gcatggtacg ga 1237612DNAHomo sapiens 376cggtactctt ac
1237712DNAHomo sapiens 377gcctgtgccg ta 1237812DNAHomo sapiens
378tacggtaagt cg 1237912DNAHomo sapiens 379cacgaaatta cc
1238012DNAHomo sapiens 380aaccaagata cg 1238112DNAHomo sapiens
381gagtcgatac gc 1238212DNAHomo sapiens 382gtctcacgat cg
1238312DNAHomo sapiens 383tcgtcgggtg ca 1238412DNAHomo sapiens
384actccgtagt ga 1238512DNAHomo sapiens 385caggacgtcc gt
1238612DNAHomo sapiens 386tcgtatccct ac 1238712DNAHomo sapiens
387tttcaaggcc gg 1238812DNAHomo sapiens 388cgccggtgga at
1238912DNAHomo sapiens 389gaacccgtcc ta 1239012DNAHomo sapiens
390gattcatcag cg 1239112DNAHomo sapiens 391acaccggtct tc
1239212DNAHomo sapiens 392atcgtgccct aa 1239312DNAHomo sapiens
393gcgtcaatgt tc 1239412DNAHomo sapiens 394ctccgtatct cg
1239512DNAHomo sapiens 395ccgattcctt cg
1239612DNAHomo sapiens 396tgcgcctcca gt 1239712DNAHomo sapiens
397taacgtcgga gc 1239812DNAHomo sapiens 398aaggtcgccc at
1239912DNAHomo sapiens 399gtcggggact at 1240012DNAHomo sapiens
400ttcgagcgat tt 1240112DNAHomo sapiens 401tgagtcgtcg ag
1240212DNAHomo sapiens 402tttacgcaga gg 1240312DNAHomo sapiens
403aggaagtatc gc 1240412DNAHomo sapiens 404actcgatacc at
1240512DNAHomo sapiens 405cgctacatag ca 1240612DNAHomo sapiens
406ttcataaccg gc 1240712DNAHomo sapiens 407ccaaacggtt aa
1240812DNAHomo sapiens 408cgattccttc gt 1240912DNAHomo sapiens
409cgtcatgaat aa 1241012DNAHomo sapiens 410agtggcgatg ac
1241112DNAHomo sapiens 411cccctacggc ac 1241212DNAHomo sapiens
412gccaacccgc ac 1241312DNAHomo sapiens 413tgggacaccg gt
1241412DNAHomo sapiens 414ttgactgcgg cg 1241512DNAHomo sapiens
415actatgcgta gg 1241612DNAHomo sapiens 416tcacccaaag cg
1241712DNAHomo sapiens 417gcaggacgtc cg 1241812DNAHomo sapiens
418acaccgaaaa cg 1241912DNAHomo sapiens 419cggtgtattg ag
1242012DNAHomo sapiens 420cacgaggtat gc 1242112DNAHomo sapiens
421taaagcgacc cg 1242212DNAHomo sapiens 422cttagtcggc ca
1242312DNAHomo sapiens 423cgaaaacgtg gc 1242412DNAHomo sapiens
424cgtgccctga ac 1242512DNAHomo sapiens 425tttaccatcg aa
1242612DNAHomo sapiens 426cgtagccatg tt 1242712DNAHomo sapiens
427cccaaacggt ta 1242812DNAHomo sapiens 428gcgttatcag aa
1242912DNAHomo sapiens 429tcgatggtaa ac 1243012DNAHomo sapiens
430cgactttttg ca 1243112DNAHomo sapiens 431tcgacgactc ac
1243212DNAHomo sapiens 432acgcgtcaga ta 1243312DNAHomo sapiens
433cgtacggcac ag 1243412DNAHomo sapiens 434ctatgccgtg ca
1243512DNAHomo sapiens 435cgcgtcagat at 1243612DNAHomo sapiens
436aagatcggta gc 1243712DNAHomo sapiens 437cttcgcaagg ag
1243812DNAHomo sapiens 438gtcgtggact ac 1243912DNAHomo sapiens
439ggtcgtcatc aa 1244012DNAHomo sapiens 440gttaacagcg tg
1244112DNAHomo sapiens 441tagctaaccg tt 1244212DNAHomo sapiens
442agtaaaggcg ct 1244312DNAHomo sapiens 443ggtaatttcg tg
1244469RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 444gucaccucca augacuaggg guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuuuuuu 6944569RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 445gacaucgaug uccuccccau guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuuuuuu 6944669RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 446gaguccgagc agaagaagaa guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuuuuuu 6944769RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 447ggggccgaga uuggguguuc guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuuuuuu 6944869RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 448guggcgagag gggccgagau guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuuuuuu 6944976RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 449gucaccucca augacuaggg guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucauu uuuuuu 7645076RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 450gacaucgaug uccuccccau guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucauu uuuuuu 7645176RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 451gaguccgagc agaagaagaa guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucauu uuuuuu 7645276RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 452ggggccgaga uuggguguuc guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucauu uuuuuu 7645376RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 453guggcgagag gggccgagau guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucauu uuuuuu 7645488RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 454gucaccucca augacuaggg guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu guuuuuuu
8845588RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 455gacaucgaug uccuccccau guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu guuuuuuu
8845688RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 456gaguccgagc agaagaagaa guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu guuuuuuu
8845788RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 457ggggccgaga uuggguguuc guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu guuuuuuu
8845888RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 458guggcgagag gggccgagau guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu guuuuuuu
88459103RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 459gucaccucca augacuaggg guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu ggcaccgagu
cggugcuuuu uuu 103460103RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 460gacaucgaug
uccuccccau guuuuagagc uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac
uugaaaaagu ggcaccgagu cggugcuuuu uuu 103461103RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 461gaguccgagc agaagaagaa guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu ggcaccgagu cggugcuuuu
uuu 103462103RNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 462ggggccgaga uuggguguuc
guuuuagagc uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu
ggcaccgagu cggugcuuuu uuu 103463103RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 463guggcgagag gggccgagau guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu ggcaccgagu cggugcuuuu
uuu 103464120DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 464gtggaaagga cgaaacaccg
ggtcttcgag aagacctgtt ttagagctag aaatagcaag 60ttaaaataag gctagtccgt
tatcaacttg aaaaagtggc accgagtcgg tgcttttttt 12046540DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 465tcggtgcgct ggttgatttc ttcttgcgct tttttggctt
4046626RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 466gauuucuucu ugcgcuuuuu guuuua
2646726DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 467tgatttcttc ttgcgctttt tnnnnn
2646826DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 468tgatttcttc ttgcgctttt ntggct
2646926DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 469tnatttcttc ttgcgctttt ttggct
2647023DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 470gatttcttct tgcgcttttt tgg
2347134DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 471tcc atc cgt aca acc cac aac cct gct
agt gag c 34Ser Ile Arg Thr Thr His Asn Pro Ala Ser Glu 1 5 10
47211PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 472Ser Ile Arg Thr Thr His Asn Pro Ala Ser Glu1 5
10 47334DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 473tcc atc gca aca acc cac aac cct gct
agt gag c 34Ser Ile Ala Thr Thr His Asn Pro Ala Ser Glu 1 5 10
47411PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 474Ser Ile Ala Thr Thr His Asn Pro Ala Ser Glu 1
5 10 47534DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 475tca atc cgt aca acc cac aac cct gct
agt gag c 34Ser Ile Arg Thr Thr His Asn Pro Ala Ser Glu 1 5 10
47642DNAHomo sapiensCDS(1)..(36) 476caa ttg aat tta aaa gaa acc gat
acc gtt ttg gtt taagga 42Gln Leu Asn Leu Lys Glu Thr Asp Thr Val
Leu Val 1 5 10 47712PRTHomo sapiens 477Gln Leu Asn Leu Lys Glu Thr
Asp Thr Val Leu Val 1 5 10 47842DNAHomo sapiensCDS(1)..(42) 478caa
ttg aat tta aaa gaa acc gat acc gtt tac gaa att gga 42Gln Leu Asn
Leu Lys Glu Thr Asp Thr Val Tyr Glu Ile Gly 1 5 10 47914PRTHomo
sapiens 479Gln Leu Asn Leu Lys Glu Thr Asp Thr Val Tyr Glu Ile Gly
1 5 10 48034DNAHomo sapiensCDS(2)..(34) 480t cct aaa aaa ccg aac
tcc gcg ctg cgt aaa gta 34Pro Lys Lys Pro Asn Ser Ala Leu Arg Lys
Val 1 5 10 48111PRTHomo sapiens 481Pro Lys Lys Pro Asn Ser Ala Leu
Arg Lys Val 1 5 10 48234DNAHomo sapiensCDS(2)..(34) 482t cct aca
aaa ccg aac tcc gcg ctg cgt aaa gta 34Pro Thr Lys Pro Asn Ser Ala
Leu Arg Lys Val 1 5 10 48311PRTHomo sapiens 483Pro Thr Lys Pro Asn
Ser Ala Leu Arg Lys Val 1 5 10 48433DNAHomo sapiens 484tgcgctggtt
gatttcttct tgcgcttttt tgg 3348533DNAHomo sapiens 485tacgctggtt
gatttcttct tgcgcttttt ttg 3348627DNAHomo sapiens 486ggagggtttt
atggggaaag gccattg 2748729DNAHomo sapiens 487gtaaaaaaga agactagaaa
ttttgatac 2948846DNAHomo sapiens 488ggagggtttt atggggaaag
gcaaagaaga ctagaaattt tgatac 4648927DNAHomo sapiens 489aggtgaagca
taatgtctca aaaaata 2749029DNAHomo sapiens 490attttattaa tacaaatcag
tgaaatcat 2949146DNAHomo sapiens 491aggtgaagca taatgtctca
aaattaatac aaatcagtga aatcat 4649236DNAHomo sapiensCDS(1)..(36)
492aat tta aaa gaa acc gat acc gtt tac gaa att gga 36Asn Leu Lys
Glu Thr Asp Thr Val Tyr Glu Ile Gly 1 5 10 49312PRTHomo sapiens
493Asn Leu Lys Glu Thr Asp Thr Val Tyr Glu Ile Gly 1 5 10
49436DNAHomo sapiensCDS(1)..(30) 494aat tta aaa gaa acc gat acc gtt
ttg gtt taagga 36Asn Leu Lys Glu Thr Asp Thr Val Leu Val 1 5 10
49510PRTHomo sapiens 495Asn Leu Lys Glu Thr Asp Thr Val Leu Val 1 5
10 49636DNAHomo sapiensCDS(1)..(36) 496tgg gat cca aaa aaa tat ggt
ggt ttt gat agt cca 36Trp Asp Pro Lys Lys Tyr Gly Gly Phe Asp Ser
Pro 1 5 10 49712PRTHomo sapiens 497Trp Asp Pro Lys Lys Tyr Gly Gly
Phe Asp Ser Pro 1 5 10 49836DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 498tgg gat cca aaa
aaa tat tgt ggt ttt gat agt cca 36Trp Asp Pro Lys Lys Tyr Cys Gly
Phe Asp Ser Pro 1 5 10 49912PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptide 499Trp Asp Pro Lys Lys Tyr
Cys Gly Phe Asp Ser Pro 1 5 10 50035DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 500aaactacttt acgcagcgcg gagttcggtt ttttg
355014104DNAHomo sapiensCDS(1)..(4104) 501atg gac aag aag tac agc
atc ggc ctg gac atc ggc acc aac tct gtg 48Met Asp Lys Lys Tyr Ser
Ile Gly Leu Asp Ile Gly Thr Asn Ser Val 1 5 10 15 ggc tgg gcc gtg
atc acc gac gag tac aag gtg ccc agc aag aaa ttc 96Gly Trp Ala Val
Ile Thr Asp Glu Tyr Lys Val Pro Ser Lys Lys Phe 20 25 30 aag gtg
ctg ggc aac acc gac cgg cac agc atc aag aag aac ctg atc 144Lys Val
Leu Gly Asn Thr Asp Arg His Ser Ile Lys Lys Asn Leu Ile 35 40 45
gga gcc ctg ctg ttc gac agc ggc gaa aca gcc gag gcc acc cgg ctg
192Gly Ala Leu Leu Phe Asp Ser Gly Glu Thr Ala Glu Ala Thr Arg Leu
50 55 60 aag aga acc gcc aga aga aga tac acc aga cgg aag aac cgg
atc tgc 240Lys Arg Thr Ala Arg Arg Arg Tyr Thr Arg Arg Lys Asn Arg
Ile Cys 65 70 75 80 tat ctg caa gag atc ttc agc aac gag atg gcc aag
gtg gac gac agc 288Tyr Leu Gln Glu Ile Phe Ser Asn Glu Met Ala Lys
Val Asp Asp Ser 85 90 95 ttc ttc cac aga ctg gaa gag tcc ttc ctg
gtg gaa gag gat aag aag 336Phe Phe His Arg Leu Glu Glu Ser Phe Leu
Val Glu Glu Asp Lys Lys 100 105 110 cac gag cgg cac ccc atc ttc ggc
aac atc gtg gac gag gtg gcc tac 384His Glu Arg His Pro Ile Phe Gly
Asn Ile Val Asp Glu Val Ala Tyr 115 120 125 cac gag aag tac ccc acc
atc tac cac ctg aga
aag aaa ctg gtg gac 432His Glu Lys Tyr Pro Thr Ile Tyr His Leu Arg
Lys Lys Leu Val Asp 130 135 140 agc acc gac aag gcc gac ctg cgg ctg
atc tat ctg gcc ctg gcc cac 480Ser Thr Asp Lys Ala Asp Leu Arg Leu
Ile Tyr Leu Ala Leu Ala His 145 150 155 160 atg atc aag ttc cgg ggc
cac ttc ctg atc gag ggc gac ctg aac ccc 528Met Ile Lys Phe Arg Gly
His Phe Leu Ile Glu Gly Asp Leu Asn Pro 165 170 175 gac aac agc gac
gtg gac aag ctg ttc atc cag ctg gtg cag acc tac 576Asp Asn Ser Asp
Val Asp Lys Leu Phe Ile Gln Leu Val Gln Thr Tyr 180 185 190 aac cag
ctg ttc gag gaa aac ccc atc aac gcc agc ggc gtg gac gcc 624Asn Gln
Leu Phe Glu Glu Asn Pro Ile Asn Ala Ser Gly Val Asp Ala 195 200 205
aag gcc atc ctg tct gcc aga ctg agc aag agc aga cgg ctg gaa aat
672Lys Ala Ile Leu Ser Ala Arg Leu Ser Lys Ser Arg Arg Leu Glu Asn
210 215 220 ctg atc gcc cag ctg ccc ggc gag aag aag aat ggc ctg ttc
ggc aac 720Leu Ile Ala Gln Leu Pro Gly Glu Lys Lys Asn Gly Leu Phe
Gly Asn 225 230 235 240 ctg att gcc ctg agc ctg ggc ctg acc ccc aac
ttc aag agc aac ttc 768Leu Ile Ala Leu Ser Leu Gly Leu Thr Pro Asn
Phe Lys Ser Asn Phe 245 250 255 gac ctg gcc gag gat gcc aaa ctg cag
ctg agc aag gac acc tac gac 816Asp Leu Ala Glu Asp Ala Lys Leu Gln
Leu Ser Lys Asp Thr Tyr Asp 260 265 270 gac gac ctg gac aac ctg ctg
gcc cag atc ggc gac cag tac gcc gac 864Asp Asp Leu Asp Asn Leu Leu
Ala Gln Ile Gly Asp Gln Tyr Ala Asp 275 280 285 ctg ttt ctg gcc gcc
aag aac ctg tcc gac gcc atc ctg ctg agc gac 912Leu Phe Leu Ala Ala
Lys Asn Leu Ser Asp Ala Ile Leu Leu Ser Asp 290 295 300 atc ctg aga
gtg aac acc gag atc acc aag gcc ccc ctg agc gcc tct 960Ile Leu Arg
Val Asn Thr Glu Ile Thr Lys Ala Pro Leu Ser Ala Ser 305 310 315 320
atg atc aag aga tac gac gag cac cac cag gac ctg acc ctg ctg aaa
1008Met Ile Lys Arg Tyr Asp Glu His His Gln Asp Leu Thr Leu Leu Lys
325 330 335 gct ctc gtg cgg cag cag ctg cct gag aag tac aaa gag att
ttc ttc 1056Ala Leu Val Arg Gln Gln Leu Pro Glu Lys Tyr Lys Glu Ile
Phe Phe 340 345 350 gac cag agc aag aac ggc tac gcc ggc tac att gac
ggc gga gcc agc 1104Asp Gln Ser Lys Asn Gly Tyr Ala Gly Tyr Ile Asp
Gly Gly Ala Ser 355 360 365 cag gaa gag ttc tac aag ttc atc aag ccc
atc ctg gaa aag atg gac 1152Gln Glu Glu Phe Tyr Lys Phe Ile Lys Pro
Ile Leu Glu Lys Met Asp 370 375 380 ggc acc gag gaa ctg ctc gtg aag
ctg aac aga gag gac ctg ctg cgg 1200Gly Thr Glu Glu Leu Leu Val Lys
Leu Asn Arg Glu Asp Leu Leu Arg 385 390 395 400 aag cag cgg acc ttc
gac aac ggc agc atc ccc cac cag atc cac ctg 1248Lys Gln Arg Thr Phe
Asp Asn Gly Ser Ile Pro His Gln Ile His Leu 405 410 415 gga gag ctg
cac gcc att ctg cgg cgg cag gaa gat ttt tac cca ttc 1296Gly Glu Leu
His Ala Ile Leu Arg Arg Gln Glu Asp Phe Tyr Pro Phe 420 425 430 ctg
aag gac aac cgg gaa aag atc gag aag atc ctg acc ttc cgc atc 1344Leu
Lys Asp Asn Arg Glu Lys Ile Glu Lys Ile Leu Thr Phe Arg Ile 435 440
445 ccc tac tac gtg ggc cct ctg gcc agg gga aac agc aga ttc gcc tgg
1392Pro Tyr Tyr Val Gly Pro Leu Ala Arg Gly Asn Ser Arg Phe Ala Trp
450 455 460 atg acc aga aag agc gag gaa acc atc acc ccc tgg aac ttc
gag gaa 1440Met Thr Arg Lys Ser Glu Glu Thr Ile Thr Pro Trp Asn Phe
Glu Glu 465 470 475 480 gtg gtg gac aag ggc gct tcc gcc cag agc ttc
atc gag cgg atg acc 1488Val Val Asp Lys Gly Ala Ser Ala Gln Ser Phe
Ile Glu Arg Met Thr 485 490 495 aac ttc gat aag aac ctg ccc aac gag
aag gtg ctg ccc aag cac agc 1536Asn Phe Asp Lys Asn Leu Pro Asn Glu
Lys Val Leu Pro Lys His Ser 500 505 510 ctg ctg tac gag tac ttc acc
gtg tat aac gag ctg acc aaa gtg aaa 1584Leu Leu Tyr Glu Tyr Phe Thr
Val Tyr Asn Glu Leu Thr Lys Val Lys 515 520 525 tac gtg acc gag gga
atg aga aag ccc gcc ttc ctg agc ggc gag cag 1632Tyr Val Thr Glu Gly
Met Arg Lys Pro Ala Phe Leu Ser Gly Glu Gln 530 535 540 aaa aag gcc
atc gtg gac ctg ctg ttc aag acc aac cgg aaa gtg acc 1680Lys Lys Ala
Ile Val Asp Leu Leu Phe Lys Thr Asn Arg Lys Val Thr 545 550 555 560
gtg aag cag ctg aaa gag gac tac ttc aag aaa atc gag tgc ttc gac
1728Val Lys Gln Leu Lys Glu Asp Tyr Phe Lys Lys Ile Glu Cys Phe Asp
565 570 575 tcc gtg gaa atc tcc ggc gtg gaa gat cgg ttc aac gcc tcc
ctg ggc 1776Ser Val Glu Ile Ser Gly Val Glu Asp Arg Phe Asn Ala Ser
Leu Gly 580 585 590 aca tac cac gat ctg ctg aaa att atc aag gac aag
gac ttc ctg gac 1824Thr Tyr His Asp Leu Leu Lys Ile Ile Lys Asp Lys
Asp Phe Leu Asp 595 600 605 aat gag gaa aac gag gac att ctg gaa gat
atc gtg ctg acc ctg aca 1872Asn Glu Glu Asn Glu Asp Ile Leu Glu Asp
Ile Val Leu Thr Leu Thr 610 615 620 ctg ttt gag gac aga gag atg atc
gag gaa cgg ctg aaa acc tat gcc 1920Leu Phe Glu Asp Arg Glu Met Ile
Glu Glu Arg Leu Lys Thr Tyr Ala 625 630 635 640 cac ctg ttc gac gac
aaa gtg atg aag cag ctg aag cgg cgg aga tac 1968His Leu Phe Asp Asp
Lys Val Met Lys Gln Leu Lys Arg Arg Arg Tyr 645 650 655 acc ggc tgg
ggc agg ctg agc cgg aag ctg atc aac ggc atc cgg gac 2016Thr Gly Trp
Gly Arg Leu Ser Arg Lys Leu Ile Asn Gly Ile Arg Asp 660 665 670 aag
cag tcc ggc aag aca atc ctg gat ttc ctg aag tcc gac ggc ttc 2064Lys
Gln Ser Gly Lys Thr Ile Leu Asp Phe Leu Lys Ser Asp Gly Phe 675 680
685 gcc aac aga aac ttc atg cag ctg atc cac gac gac agc ctg acc ttt
2112Ala Asn Arg Asn Phe Met Gln Leu Ile His Asp Asp Ser Leu Thr Phe
690 695 700 aaa gag gac atc cag aaa gcc cag gtg tcc ggc cag ggc gat
agc ctg 2160Lys Glu Asp Ile Gln Lys Ala Gln Val Ser Gly Gln Gly Asp
Ser Leu 705 710 715 720 cac gag cac att gcc aat ctg gcc ggc agc ccc
gcc att aag aag ggc 2208His Glu His Ile Ala Asn Leu Ala Gly Ser Pro
Ala Ile Lys Lys Gly 725 730 735 atc ctg cag aca gtg aag gtg gtg gac
gag ctc gtg aaa gtg atg ggc 2256Ile Leu Gln Thr Val Lys Val Val Asp
Glu Leu Val Lys Val Met Gly 740 745 750 cgg cac aag ccc gag aac atc
gtg atc gcc atg gcc aga gag aac cag 2304Arg His Lys Pro Glu Asn Ile
Val Ile Ala Met Ala Arg Glu Asn Gln 755 760 765 acc acc cag aag gga
cag aag aac agc cgc gag aga atg aag cgg atc 2352Thr Thr Gln Lys Gly
Gln Lys Asn Ser Arg Glu Arg Met Lys Arg Ile 770 775 780 gaa gag ggc
atc aaa gag ctg ggc agc cag atc ctg aaa gaa cac ccc 2400Glu Glu Gly
Ile Lys Glu Leu Gly Ser Gln Ile Leu Lys Glu His Pro 785 790 795 800
gtg gaa aac acc cag ctg cag aac gag aag ctg tac ctg tac tac ctg
2448Val Glu Asn Thr Gln Leu Gln Asn Glu Lys Leu Tyr Leu Tyr Tyr Leu
805 810 815 cag aat ggg cgg gat atg tac gtg gac cag gaa ctg gac atc
aac cgg 2496Gln Asn Gly Arg Asp Met Tyr Val Asp Gln Glu Leu Asp Ile
Asn Arg 820 825 830 ctg tcc gac tac gat gtg gac gcc atc gtg cct cag
agc ttt ctg aag 2544Leu Ser Asp Tyr Asp Val Asp Ala Ile Val Pro Gln
Ser Phe Leu Lys 835 840 845 gac gac tcc atc gac gcc aag gtg ctg acc
aga agc gac aag gcc cgg 2592Asp Asp Ser Ile Asp Ala Lys Val Leu Thr
Arg Ser Asp Lys Ala Arg 850 855 860 ggc aag agc gac aac gtg ccc tcc
gaa gag gtc gtg aag aag atg aag 2640Gly Lys Ser Asp Asn Val Pro Ser
Glu Glu Val Val Lys Lys Met Lys 865 870 875 880 aac tac tgg cgg cag
ctg ctg aac gcc aag ctg att acc cag aga aag 2688Asn Tyr Trp Arg Gln
Leu Leu Asn Ala Lys Leu Ile Thr Gln Arg Lys 885 890 895 ttc gac aat
ctg acc aag gcc gag aga ggc ggc ctg agc gaa ctg gat 2736Phe Asp Asn
Leu Thr Lys Ala Glu Arg Gly Gly Leu Ser Glu Leu Asp 900 905 910 aag
gcc ggc ttc atc aag aga cag ctg gtg gaa acc cgg cag atc aca 2784Lys
Ala Gly Phe Ile Lys Arg Gln Leu Val Glu Thr Arg Gln Ile Thr 915 920
925 aag cac gtg gca cag atc ctg gac tcc cgg atg aac act aag tac gac
2832Lys His Val Ala Gln Ile Leu Asp Ser Arg Met Asn Thr Lys Tyr Asp
930 935 940 gag aat gac aag ctg atc cgg gaa gtg aaa gtg atc acc ctg
aag tcc 2880Glu Asn Asp Lys Leu Ile Arg Glu Val Lys Val Ile Thr Leu
Lys Ser 945 950 955 960 aag ctg gtg tcc gat ttc cgg aag gat ttc cag
ttt tac aaa gtg cgc 2928Lys Leu Val Ser Asp Phe Arg Lys Asp Phe Gln
Phe Tyr Lys Val Arg 965 970 975 gag atc aac aac tac cac cac gcc cac
gcc gcc tac ctg aac gcc gtc 2976Glu Ile Asn Asn Tyr His His Ala His
Ala Ala Tyr Leu Asn Ala Val 980 985 990 gtg gga acc gcc ctg atc aaa
aag tac cct aag ctg gaa agc gag ttc 3024Val Gly Thr Ala Leu Ile Lys
Lys Tyr Pro Lys Leu Glu Ser Glu Phe 995 1000 1005 gtg tac ggc gac
tac aag gtg tac gac gtg cgg aag atg atc gcc 3069Val Tyr Gly Asp Tyr
Lys Val Tyr Asp Val Arg Lys Met Ile Ala 1010 1015 1020 aag agc gag
cag gaa atc ggc aag gct acc gcc aag tac ttc ttc 3114Lys Ser Glu Gln
Glu Ile Gly Lys Ala Thr Ala Lys Tyr Phe Phe 1025 1030 1035 tac agc
aac atc atg aac ttt ttc aag acc gag att acc ctg gcc 3159Tyr Ser Asn
Ile Met Asn Phe Phe Lys Thr Glu Ile Thr Leu Ala 1040 1045 1050 aac
ggc gag atc cgg aag cgg cct ctg atc gag aca aac ggc gaa 3204Asn Gly
Glu Ile Arg Lys Arg Pro Leu Ile Glu Thr Asn Gly Glu 1055 1060 1065
acc ggg gag atc gtg tgg gat aag ggc cgg gat ttt gcc acc gtg 3249Thr
Gly Glu Ile Val Trp Asp Lys Gly Arg Asp Phe Ala Thr Val 1070 1075
1080 cgg aaa gtg ctg agc atg ccc caa gtg aat atc gtg aaa aag acc
3294Arg Lys Val Leu Ser Met Pro Gln Val Asn Ile Val Lys Lys Thr
1085 1090 1095 gag gtg cag aca ggc ggc ttc agc aaa gag tct atc ctg
ccc aag 3339Glu Val Gln Thr Gly Gly Phe Ser Lys Glu Ser Ile Leu Pro
Lys 1100 1105 1110 agg aac agc gat aag ctg atc gcc aga aag aag gac
tgg gac cct 3384Arg Asn Ser Asp Lys Leu Ile Ala Arg Lys Lys Asp Trp
Asp Pro 1115 1120 1125 aag aag tac ggc ggc ttc gac agc ccc acc gtg
gcc tat tct gtg 3429Lys Lys Tyr Gly Gly Phe Asp Ser Pro Thr Val Ala
Tyr Ser Val 1130 1135 1140 ctg gtg gtg gcc aaa gtg gaa aag ggc aag
tcc aag aaa ctg aag 3474Leu Val Val Ala Lys Val Glu Lys Gly Lys Ser
Lys Lys Leu Lys 1145 1150 1155 agt gtg aaa gag ctg ctg ggg atc acc
atc atg gaa aga agc agc 3519Ser Val Lys Glu Leu Leu Gly Ile Thr Ile
Met Glu Arg Ser Ser 1160 1165 1170 ttc gag aag aat ccc atc gac ttt
ctg gaa gcc aag ggc tac aaa 3564Phe Glu Lys Asn Pro Ile Asp Phe Leu
Glu Ala Lys Gly Tyr Lys 1175 1180 1185 gaa gtg aaa aag gac ctg atc
atc aag ctg cct aag tac tcc ctg 3609Glu Val Lys Lys Asp Leu Ile Ile
Lys Leu Pro Lys Tyr Ser Leu 1190 1195 1200 ttc gag ctg gaa aac ggc
cgg aag aga atg ctg gcc tct gcc ggc 3654Phe Glu Leu Glu Asn Gly Arg
Lys Arg Met Leu Ala Ser Ala Gly 1205 1210 1215 gaa ctg cag aag gga
aac gaa ctg gcc ctg ccc tcc aaa tat gtg 3699Glu Leu Gln Lys Gly Asn
Glu Leu Ala Leu Pro Ser Lys Tyr Val 1220 1225 1230 aac ttc ctg tac
ctg gcc agc cac tat gag aag ctg aag ggc tcc 3744Asn Phe Leu Tyr Leu
Ala Ser His Tyr Glu Lys Leu Lys Gly Ser 1235 1240 1245 ccc gag gat
aat gag cag aaa cag ctg ttt gtg gaa cag cac aag 3789Pro Glu Asp Asn
Glu Gln Lys Gln Leu Phe Val Glu Gln His Lys 1250 1255 1260 cac tac
ctg gac gag atc atc gag cag atc agc gag ttc tcc aag 3834His Tyr Leu
Asp Glu Ile Ile Glu Gln Ile Ser Glu Phe Ser Lys 1265 1270 1275 aga
gtg atc ctg gcc gac gct aat ctg gac aaa gtg ctg tcc gcc 3879Arg Val
Ile Leu Ala Asp Ala Asn Leu Asp Lys Val Leu Ser Ala 1280 1285 1290
tac aac aag cac cgg gat aag ccc atc aga gag cag gcc gag aat 3924Tyr
Asn Lys His Arg Asp Lys Pro Ile Arg Glu Gln Ala Glu Asn 1295 1300
1305 atc atc cac ctg ttt acc ctg acc aat ctg gga gcc cct gcc gcc
3969Ile Ile His Leu Phe Thr Leu Thr Asn Leu Gly Ala Pro Ala Ala
1310 1315 1320 ttc aag tac ttt gac acc acc atc gac cgg aag agg tac
acc agc 4014Phe Lys Tyr Phe Asp Thr Thr Ile Asp Arg Lys Arg Tyr Thr
Ser 1325 1330 1335 acc aaa gag gtg ctg gac gcc acc ctg atc cac cag
agc atc acc 4059Thr Lys Glu Val Leu Asp Ala Thr Leu Ile His Gln Ser
Ile Thr 1340 1345 1350 ggc ctg tac gag aca cgg atc gac ctg tct cag
ctg gga ggc gac 4104Gly Leu Tyr Glu Thr Arg Ile Asp Leu Ser Gln Leu
Gly Gly Asp 1355 1360 1365 5021368PRTHomo sapiens 502Met Asp Lys
Lys Tyr Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val 1 5 10 15 Gly
Trp Ala Val Ile Thr Asp Glu Tyr Lys Val Pro Ser Lys Lys Phe 20 25
30 Lys Val Leu Gly Asn Thr Asp Arg His Ser Ile Lys Lys Asn Leu Ile
35 40 45 Gly Ala Leu Leu Phe Asp Ser Gly Glu Thr Ala Glu Ala Thr
Arg Leu 50 55 60 Lys Arg Thr Ala Arg Arg Arg Tyr Thr Arg Arg Lys
Asn Arg Ile Cys 65 70 75 80 Tyr Leu Gln Glu Ile Phe Ser Asn Glu Met
Ala Lys Val Asp Asp Ser 85 90 95 Phe Phe His Arg Leu Glu Glu Ser
Phe Leu Val Glu Glu Asp Lys Lys 100 105 110 His Glu Arg His Pro Ile
Phe Gly Asn Ile Val Asp Glu Val Ala Tyr 115 120 125 His Glu Lys Tyr
Pro Thr Ile Tyr His Leu Arg Lys Lys Leu
Val Asp 130 135 140 Ser Thr Asp Lys Ala Asp Leu Arg Leu Ile Tyr Leu
Ala Leu Ala His 145 150 155 160 Met Ile Lys Phe Arg Gly His Phe Leu
Ile Glu Gly Asp Leu Asn Pro 165 170 175 Asp Asn Ser Asp Val Asp Lys
Leu Phe Ile Gln Leu Val Gln Thr Tyr 180 185 190 Asn Gln Leu Phe Glu
Glu Asn Pro Ile Asn Ala Ser Gly Val Asp Ala 195 200 205 Lys Ala Ile
Leu Ser Ala Arg Leu Ser Lys Ser Arg Arg Leu Glu Asn 210 215 220 Leu
Ile Ala Gln Leu Pro Gly Glu Lys Lys Asn Gly Leu Phe Gly Asn 225 230
235 240 Leu Ile Ala Leu Ser Leu Gly Leu Thr Pro Asn Phe Lys Ser Asn
Phe 245 250 255 Asp Leu Ala Glu Asp Ala Lys Leu Gln Leu Ser Lys Asp
Thr Tyr Asp 260 265 270 Asp Asp Leu Asp Asn Leu Leu Ala Gln Ile Gly
Asp Gln Tyr Ala Asp 275 280 285 Leu Phe Leu Ala Ala Lys Asn Leu Ser
Asp Ala Ile Leu Leu Ser Asp 290 295 300 Ile Leu Arg Val Asn Thr Glu
Ile Thr Lys Ala Pro Leu Ser Ala Ser 305 310 315 320 Met Ile Lys Arg
Tyr Asp Glu His His Gln Asp Leu Thr Leu Leu Lys 325 330 335 Ala Leu
Val Arg Gln Gln Leu Pro Glu Lys Tyr Lys Glu Ile Phe Phe 340 345 350
Asp Gln Ser Lys Asn Gly Tyr Ala Gly Tyr Ile Asp Gly Gly Ala Ser 355
360 365 Gln Glu Glu Phe Tyr Lys Phe Ile Lys Pro Ile Leu Glu Lys Met
Asp 370 375 380 Gly Thr Glu Glu Leu Leu Val Lys Leu Asn Arg Glu Asp
Leu Leu Arg 385 390 395 400 Lys Gln Arg Thr Phe Asp Asn Gly Ser Ile
Pro His Gln Ile His Leu 405 410 415 Gly Glu Leu His Ala Ile Leu Arg
Arg Gln Glu Asp Phe Tyr Pro Phe 420 425 430 Leu Lys Asp Asn Arg Glu
Lys Ile Glu Lys Ile Leu Thr Phe Arg Ile 435 440 445 Pro Tyr Tyr Val
Gly Pro Leu Ala Arg Gly Asn Ser Arg Phe Ala Trp 450 455 460 Met Thr
Arg Lys Ser Glu Glu Thr Ile Thr Pro Trp Asn Phe Glu Glu 465 470 475
480 Val Val Asp Lys Gly Ala Ser Ala Gln Ser Phe Ile Glu Arg Met Thr
485 490 495 Asn Phe Asp Lys Asn Leu Pro Asn Glu Lys Val Leu Pro Lys
His Ser 500 505 510 Leu Leu Tyr Glu Tyr Phe Thr Val Tyr Asn Glu Leu
Thr Lys Val Lys 515 520 525 Tyr Val Thr Glu Gly Met Arg Lys Pro Ala
Phe Leu Ser Gly Glu Gln 530 535 540 Lys Lys Ala Ile Val Asp Leu Leu
Phe Lys Thr Asn Arg Lys Val Thr 545 550 555 560 Val Lys Gln Leu Lys
Glu Asp Tyr Phe Lys Lys Ile Glu Cys Phe Asp 565 570 575 Ser Val Glu
Ile Ser Gly Val Glu Asp Arg Phe Asn Ala Ser Leu Gly 580 585 590 Thr
Tyr His Asp Leu Leu Lys Ile Ile Lys Asp Lys Asp Phe Leu Asp 595 600
605 Asn Glu Glu Asn Glu Asp Ile Leu Glu Asp Ile Val Leu Thr Leu Thr
610 615 620 Leu Phe Glu Asp Arg Glu Met Ile Glu Glu Arg Leu Lys Thr
Tyr Ala 625 630 635 640 His Leu Phe Asp Asp Lys Val Met Lys Gln Leu
Lys Arg Arg Arg Tyr 645 650 655 Thr Gly Trp Gly Arg Leu Ser Arg Lys
Leu Ile Asn Gly Ile Arg Asp 660 665 670 Lys Gln Ser Gly Lys Thr Ile
Leu Asp Phe Leu Lys Ser Asp Gly Phe 675 680 685 Ala Asn Arg Asn Phe
Met Gln Leu Ile His Asp Asp Ser Leu Thr Phe 690 695 700 Lys Glu Asp
Ile Gln Lys Ala Gln Val Ser Gly Gln Gly Asp Ser Leu 705 710 715 720
His Glu His Ile Ala Asn Leu Ala Gly Ser Pro Ala Ile Lys Lys Gly 725
730 735 Ile Leu Gln Thr Val Lys Val Val Asp Glu Leu Val Lys Val Met
Gly 740 745 750 Arg His Lys Pro Glu Asn Ile Val Ile Ala Met Ala Arg
Glu Asn Gln 755 760 765 Thr Thr Gln Lys Gly Gln Lys Asn Ser Arg Glu
Arg Met Lys Arg Ile 770 775 780 Glu Glu Gly Ile Lys Glu Leu Gly Ser
Gln Ile Leu Lys Glu His Pro 785 790 795 800 Val Glu Asn Thr Gln Leu
Gln Asn Glu Lys Leu Tyr Leu Tyr Tyr Leu 805 810 815 Gln Asn Gly Arg
Asp Met Tyr Val Asp Gln Glu Leu Asp Ile Asn Arg 820 825 830 Leu Ser
Asp Tyr Asp Val Asp Ala Ile Val Pro Gln Ser Phe Leu Lys 835 840 845
Asp Asp Ser Ile Asp Ala Lys Val Leu Thr Arg Ser Asp Lys Ala Arg 850
855 860 Gly Lys Ser Asp Asn Val Pro Ser Glu Glu Val Val Lys Lys Met
Lys 865 870 875 880 Asn Tyr Trp Arg Gln Leu Leu Asn Ala Lys Leu Ile
Thr Gln Arg Lys 885 890 895 Phe Asp Asn Leu Thr Lys Ala Glu Arg Gly
Gly Leu Ser Glu Leu Asp 900 905 910 Lys Ala Gly Phe Ile Lys Arg Gln
Leu Val Glu Thr Arg Gln Ile Thr 915 920 925 Lys His Val Ala Gln Ile
Leu Asp Ser Arg Met Asn Thr Lys Tyr Asp 930 935 940 Glu Asn Asp Lys
Leu Ile Arg Glu Val Lys Val Ile Thr Leu Lys Ser 945 950 955 960 Lys
Leu Val Ser Asp Phe Arg Lys Asp Phe Gln Phe Tyr Lys Val Arg 965 970
975 Glu Ile Asn Asn Tyr His His Ala His Ala Ala Tyr Leu Asn Ala Val
980 985 990 Val Gly Thr Ala Leu Ile Lys Lys Tyr Pro Lys Leu Glu Ser
Glu Phe 995 1000 1005 Val Tyr Gly Asp Tyr Lys Val Tyr Asp Val Arg
Lys Met Ile Ala 1010 1015 1020 Lys Ser Glu Gln Glu Ile Gly Lys Ala
Thr Ala Lys Tyr Phe Phe 1025 1030 1035 Tyr Ser Asn Ile Met Asn Phe
Phe Lys Thr Glu Ile Thr Leu Ala 1040 1045 1050 Asn Gly Glu Ile Arg
Lys Arg Pro Leu Ile Glu Thr Asn Gly Glu 1055 1060 1065 Thr Gly Glu
Ile Val Trp Asp Lys Gly Arg Asp Phe Ala Thr Val 1070 1075 1080 Arg
Lys Val Leu Ser Met Pro Gln Val Asn Ile Val Lys Lys Thr 1085 1090
1095 Glu Val Gln Thr Gly Gly Phe Ser Lys Glu Ser Ile Leu Pro Lys
1100 1105 1110 Arg Asn Ser Asp Lys Leu Ile Ala Arg Lys Lys Asp Trp
Asp Pro 1115 1120 1125 Lys Lys Tyr Gly Gly Phe Asp Ser Pro Thr Val
Ala Tyr Ser Val 1130 1135 1140 Leu Val Val Ala Lys Val Glu Lys Gly
Lys Ser Lys Lys Leu Lys 1145 1150 1155 Ser Val Lys Glu Leu Leu Gly
Ile Thr Ile Met Glu Arg Ser Ser 1160 1165 1170 Phe Glu Lys Asn Pro
Ile Asp Phe Leu Glu Ala Lys Gly Tyr Lys 1175 1180 1185 Glu Val Lys
Lys Asp Leu Ile Ile Lys Leu Pro Lys Tyr Ser Leu 1190 1195 1200 Phe
Glu Leu Glu Asn Gly Arg Lys Arg Met Leu Ala Ser Ala Gly 1205 1210
1215 Glu Leu Gln Lys Gly Asn Glu Leu Ala Leu Pro Ser Lys Tyr Val
1220 1225 1230 Asn Phe Leu Tyr Leu Ala Ser His Tyr Glu Lys Leu Lys
Gly Ser 1235 1240 1245 Pro Glu Asp Asn Glu Gln Lys Gln Leu Phe Val
Glu Gln His Lys 1250 1255 1260 His Tyr Leu Asp Glu Ile Ile Glu Gln
Ile Ser Glu Phe Ser Lys 1265 1270 1275 Arg Val Ile Leu Ala Asp Ala
Asn Leu Asp Lys Val Leu Ser Ala 1280 1285 1290 Tyr Asn Lys His Arg
Asp Lys Pro Ile Arg Glu Gln Ala Glu Asn 1295 1300 1305 Ile Ile His
Leu Phe Thr Leu Thr Asn Leu Gly Ala Pro Ala Ala 1310 1315 1320 Phe
Lys Tyr Phe Asp Thr Thr Ile Asp Arg Lys Arg Tyr Thr Ser 1325 1330
1335 Thr Lys Glu Val Leu Asp Ala Thr Leu Ile His Gln Ser Ile Thr
1340 1345 1350 Gly Leu Tyr Glu Thr Arg Ile Asp Leu Ser Gln Leu Gly
Gly Asp 1355 1360 1365 50315DNAHomo sapiens 503cagaagaaga agggc
1550451DNAHomo sapiens 504ccaatgggga ggacatcgat gtcacctcca
atgactaggg tggtgggcaa c 5150515DNAHomo sapiens 505ctctggccac tccct
1550652DNAHomo sapiens 506acatcgatgt cacctccaat gacaagcttg
ctagcggtgg gcaaccacaa ac 525071733DNAArtificial SequenceDescription
of Artificial Sequence Synthetic polynucleotide 507ccgtttaaac
aattctgcag gaatctagtt attaatagta atcaattacg gggtcattag 60ttcatagccc
atatatggag ttccgcgtta cataacttac ggtaaatggc ccgcctggct
120gaccgcccaa cgacccccgc ccattgacgt caataatgac gtatgttccc
atagtaacgc 180caatagggac tttccattga cgtcaatggg tggagtattt
acggtaaact gcccacttgg 240cagtacatca agtgtatcat atgccaagta
cgccccctat tgacgtcaat gacggtaaat 300ggcccgcctg gcattatgcc
cagtacatga ccttatggga ctttcctact tggcagtaca 360tctacgtatt
agtcatcgct attaccatgg tcgaggtgag ccccacgttc tgcttcactc
420tccccatctc ccccccctcc ccacccccaa ttttgtattt atttattttt
taattatttt 480gtgcagcgat gggggcgggg gggggggggg ggcgcgcgcc
aggcggggcg gggcggggcg 540aggggcgggg cggggcgagg cggagaggtg
cggcggcagc caatcagagc ggcgcgctcc 600gaaagtttcc ttttatggcg
aggcggcggc ggcggcggcc ctataaaaag cgaagcgcgc 660ggcgggcgga
agtcgctgcg cgctgccttc gccccgtgcc ccgctccgcc gccgcctcgc
720gccgcccgcc ccggctctga ctgaccgcgt tactcccaca ggtgagcggg
cgggacggcc 780cttctcctcc gggctgtaat tagcgcttgg tttaatgacg
gcttgtttct tttctgtggc 840tgcgtgaaag ccttgagggg ctccgggagg
gccctttgtg cggggggagc ggctcggggg 900gtgcgtgcgt gtgtgtgtgc
gtggggagcg ccgcgtgcgg ctccgcgctg cccggcggct 960gtgagcgctg
cgggcgcggc gcggggcttt gtgcgctccg cagtgtgcgc gaggggagcg
1020cggccggggg cggtgccccg cggtgcgggg ggggctgcga ggggaacaaa
ggctgcgtgc 1080ggggtgtgtg cgtggggggg tgagcagggg gtgtgggcgc
gtcggtcggg ctgcaacccc 1140ccctgcaccc ccctccccga gttgctgagc
acggcccggc ttcgggtgcg gggctccgta 1200cggggcgtgg cgcggggctc
gccgtgccgg gcggggggtg gcggcaggtg ggggtgccgg 1260gcggggcggg
gccgcctcgg gccggggagg gctcggggga ggggcgcggc ggcccccgga
1320gcgccggcgg ctgtcgaggc gcggcgagcc gcagccattg ccttttatgg
taatcgtgcg 1380agagggcgca gggacttcct ttgtcccaaa tctgtgcgga
gccgaaatct gggaggcgcc 1440gccgcacccc ctctagcggg cgcggggcga
agcggtgcgg cgccggcagg aaggaaatgg 1500gcggggaggg ccttcgtgcg
tcgccgcgcc gccgtcccct tctccctctc cagcctcggg 1560gctgtccgcg
gggggacggc tgccttcggg ggggacgggg cagggcgggg ttcggcttct
1620ggcgtgtgac cggcggctct agagcctctg ctaaccatgt tcatgccttc
ttctttttcc 1680tacagctcct gggcaacgtg ctggttattg tgctgtctca
tcattttggc aaa 17335084269DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 508atggactata
aggaccacga cggagactac aaggatcatg atattgatta caaagacgat 60gacgataaga
tggccccaaa gaagaagcgg aaggtcggta tccacggagt cccagcagcc
120gacaagaagt acagcatcgg cctggacatc ggcaccaact ctgtgggctg
ggccgtgatc 180accgacgagt acaaggtgcc cagcaagaaa ttcaaggtgc
tgggcaacac cgaccggcac 240agcatcaaga agaacctgat cggagccctg
ctgttcgaca gcggcgaaac agccgaggcc 300acccggctga agagaaccgc
cagaagaaga tacaccagac ggaagaaccg gatctgctat 360ctgcaagaga
tcttcagcaa cgagatggcc aaggtggacg acagcttctt ccacagactg
420gaagagtcct tcctggtgga agaggataag aagcacgagc ggcaccccat
cttcggcaac 480atcgtggacg aggtggccta ccacgagaag taccccacca
tctaccacct gagaaagaaa 540ctggtggaca gcaccgacaa ggccgacctg
cggctgatct atctggccct ggcccacatg 600atcaagttcc ggggccactt
cctgatcgag ggcgacctga accccgacaa cagcgacgtg 660gacaagctgt
tcatccagct ggtgcagacc tacaaccagc tgttcgagga aaaccccatc
720aacgccagcg gcgtggacgc caaggccatc ctgtctgcca gactgagcaa
gagcagacgg 780ctggaaaatc tgatcgccca gctgcccggc gagaagaaga
atggcctgtt cggaaacctg 840attgccctga gcctgggcct gacccccaac
ttcaagagca acttcgacct ggccgaggat 900gccaaactgc agctgagcaa
ggacacctac gacgacgacc tggacaacct gctggcccag 960atcggcgacc
agtacgccga cctgtttctg gccgccaaga acctgtccga cgccatcctg
1020ctgagcgaca tcctgagagt gaacaccgag atcaccaagg cccccctgag
cgcctctatg 1080atcaagagat acgacgagca ccaccaggac ctgaccctgc
tgaaagctct cgtgcggcag 1140cagctgcctg agaagtacaa agagattttc
ttcgaccaga gcaagaacgg ctacgccggc 1200tacattgacg gcggagccag
ccaggaagag ttctacaagt tcatcaagcc catcctggaa 1260aagatggacg
gcaccgagga actgctcgtg aagctgaaca gagaggacct gctgcggaag
1320cagcggacct tcgacaacgg cagcatcccc caccagatcc acctgggaga
gctgcacgcc 1380attctgcggc ggcaggaaga tttttaccca ttcctgaagg
acaaccggga aaagatcgag 1440aagatcctga ccttccgcat cccctactac
gtgggccctc tggccagggg aaacagcaga 1500ttcgcctgga tgaccagaaa
gagcgaggaa accatcaccc cctggaactt cgaggaagtg 1560gtggacaagg
gcgcttccgc ccagagcttc atcgagcgga tgaccaactt cgataagaac
1620ctgcccaacg agaaggtgct gcccaagcac agcctgctgt acgagtactt
caccgtgtat 1680aacgagctga ccaaagtgaa atacgtgacc gagggaatga
gaaagcccgc cttcctgagc 1740ggcgagcaga aaaaggccat cgtggacctg
ctgttcaaga ccaaccggaa agtgaccgtg 1800aagcagctga aagaggacta
cttcaagaaa atcgagtgct tcgactccgt ggaaatctcc 1860ggcgtggaag
atcggttcaa cgcctccctg ggcacatacc acgatctgct gaaaattatc
1920aaggacaagg acttcctgga caatgaggaa aacgaggaca ttctggaaga
tatcgtgctg 1980accctgacac tgtttgagga cagagagatg atcgaggaac
ggctgaaaac ctatgcccac 2040ctgttcgacg acaaagtgat gaagcagctg
aagcggcgga gatacaccgg ctggggcagg 2100ctgagccgga agctgatcaa
cggcatccgg gacaagcagt ccggcaagac aatcctggat 2160ttcctgaagt
ccgacggctt cgccaacaga aacttcatgc agctgatcca cgacgacagc
2220ctgaccttta aagaggacat ccagaaagcc caggtgtccg gccagggcga
tagcctgcac 2280gagcacattg ccaatctggc cggcagcccc gccattaaga
agggcatcct gcagacagtg 2340aaggtggtgg acgagctcgt gaaagtgatg
ggccggcaca agcccgagaa catcgtgatc 2400gaaatggcca gagagaacca
gaccacccag aagggacaga agaacagccg cgagagaatg 2460aagcggatcg
aagagggcat caaagagctg ggcagccaga tcctgaaaga acaccccgtg
2520gaaaacaccc agctgcagaa cgagaagctg tacctgtact acctgcagaa
tgggcgggat 2580atgtacgtgg accaggaact ggacatcaac cggctgtccg
actacgatgt ggaccatatc 2640gtgcctcaga gctttctgaa ggacgactcc
atcgacaaca aggtgctgac cagaagcgac 2700aagaaccggg gcaagagcga
caacgtgccc tccgaagagg tcgtgaagaa gatgaagaac 2760tactggcggc
agctgctgaa cgccaagctg attacccaga gaaagttcga caatctgacc
2820aaggccgaga gaggcggcct gagcgaactg gataaggccg gcttcatcaa
gagacagctg 2880gtggaaaccc ggcagatcac aaagcacgtg gcacagatcc
tggactcccg gatgaacact 2940aagtacgacg agaatgacaa gctgatccgg
gaagtgaaag tgatcaccct gaagtccaag 3000ctggtgtccg atttccggaa
ggatttccag ttttacaaag tgcgcgagat caacaactac 3060caccacgccc
acgacgccta cctgaacgcc gtcgtgggaa ccgccctgat caaaaagtac
3120cctaagctgg aaagcgagtt cgtgtacggc gactacaagg tgtacgacgt
gcggaagatg 3180atcgccaaga gcgagcagga aatcggcaag gctaccgcca
agtacttctt ctacagcaac 3240atcatgaact ttttcaagac cgagattacc
ctggccaacg gcgagatccg gaagcggcct 3300ctgatcgaga caaacggcga
aaccggggag atcgtgtggg ataagggccg ggattttgcc 3360accgtgcgga
aagtgctgag catgccccaa gtgaatatcg tgaaaaagac cgaggtgcag
3420acaggcggct tcagcaaaga gtctatcctg cccaagagga acagcgataa
gctgatcgcc 3480agaaagaagg actgggaccc taagaagtac ggcggcttcg
acagccccac cgtggcctat 3540tctgtgctgg tggtggccaa agtggaaaag
ggcaagtcca agaaactgaa gagtgtgaaa 3600gagctgctgg ggatcaccat
catggaaaga agcagcttcg agaagaatcc catcgacttt 3660ctggaagcca
agggctacaa agaagtgaaa aaggacctga tcatcaagct gcctaagtac
3720tccctgttcg agctggaaaa cggccggaag agaatgctgg cctctgccgg
cgaactgcag 3780aagggaaacg aactggccct gccctccaaa tatgtgaact
tcctgtacct ggccagccac 3840tatgagaagc tgaagggctc ccccgaggat
aatgagcaga aacagctgtt tgtggaacag 3900cacaagcact acctggacga
gatcatcgag cagatcagcg agttctccaa gagagtgatc 3960ctggccgacg
ctaatctgga caaagtgctg tccgcctaca acaagcaccg ggataagccc
4020atcagagagc aggccgagaa tatcatccac ctgtttaccc tgaccaatct
gggagcccct 4080gccgccttca agtactttga caccaccatc gaccggaaga
ggtacaccag caccaaagag 4140gtgctggacg ccaccctgat ccaccagagc
atcaccggcc tgtacgagac acggatcgac 4200ctgtctcagc tgggaggcga
caaaaggccg gcggccacga aaaaggccgg ccaggcaaaa 4260aagaaaaag
4269509780DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 509ggaagcggag ccactaactt ctccctgttg
aaacaagcag gggatgtcga agagaatccc 60gggccagtga gcaagggcga ggagctgttc
accggggtgg tgcccatcct ggtcgagctg 120gacggcgacg taaacggcca
caagttcagc gtgtccggcg agggcgaggg cgatgccacc 180tacggcaagc
tgaccctgaa gttcatctgc accaccggca agctgcccgt gccctggccc
240accctcgtga ccaccctgac ctacggcgtg cagtgcttca gccgctaccc
cgaccacatg 300aagcagcacg acttcttcaa gtccgccatg cccgaaggct
acgtccagga gcgcaccatc 360ttcttcaagg acgacggcaa ctacaagacc
cgcgccgagg tgaagttcga gggcgacacc 420ctggtgaacc gcatcgagct
gaagggcatc gacttcaagg aggacggcaa catcctgggg 480cacaagctgg
agtacaacta caacagccac aacgtctata tcatggccga caagcagaag
540aacggcatca aggtgaactt caagatccgc cacaacatcg aggacggcag
cgtgcagctc 600gccgaccact accagcagaa cacccccatc ggcgacggcc
ccgtgctgct gcccgacaac 660cactacctga gcacccagtc cgccctgagc
aaagacccca acgagaagcg cgatcacatg 720gtcctgctgg agttcgtgac
cgccgccggg atcactctcg gcatggacga gctgtacaag 780510597DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
510cgataatcaa cctctggatt acaaaatttg tgaaagattg actggtattc
ttaactatgt 60tgctcctttt acgctatgtg gatacgctgc tttaatgcct ttgtatcatg
ctattgcttc 120ccgtatggct ttcattttct cctccttgta taaatcctgg
ttgctgtctc tttatgagga 180gttgtggccc gttgtcaggc aacgtggcgt
ggtgtgcact gtgtttgctg acgcaacccc 240cactggttgg ggcattgcca
ccacctgtca gctcctttcc gggactttcg ctttccccct 300ccctattgcc
acggcggaac tcatcgccgc ctgccttgcc cgctgctgga caggggctcg
360gctgttgggc actgacaatt ccgtggtgtt gtcggggaaa tcatcgtcct
ttccttggct 420gctcgcctgt gttgccacct ggattctgcg cgggacgtcc
ttctgctacg tcccttcggc 480cctcaatcca gcggaccttc cttcccgcgg
cctgctgccg gctctgcggc ctcttccgcg 540tcttcgcctt cgccctcaga
cgagtcggat ctccctttgg gccgcctccc cgcatcg 597511210DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
511cgacctcgac tgtgccttct agttgccagc catctgttgt ttgcccctcc
cccgtgcctt 60ccttgaccct ggaaggtgcc actcccactg tcctttccta ataaaatgag
gaaattgcat 120cgcattgtct gagtaggtgt cattctattc tggggggtgg
ggtggggcag gacagcaagg 180gggaggattg ggaagacaat ggcaggcatg
210512906DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 512ataacttcgt ataatgtatg ctatacgaag
ttattcgcga tgaataaatg aaagcttgca 60gatctgcgac tctagaggat ctgcgactct
agaggatcat aatcagccnt accacatttt 120gtagaggttt tactngcttt
aaaaaacctc ccacacctcc ccctgaacct gaaacataaa 180atgaatgcaa
ttgttgttgt taacttgttt attgcagctt ataatggtta caaataaagc
240aatagcatca caaatttcac aaataaagca tttttttcac tgcattctag
ttgtggtttg 300tccaaactca tcaatgtatc ttatcatgtc tggatctgcg
actctagagg atcataatca 360gccataccac atttgtagag gttttacttg
ctttaaaaaa cctcccacac ctccccctga 420acctgaaaca taaaatgaat
gcaattgttg ttgttaactt gtttattgca gcttataatg 480gttacaaata
aagcaatagc atcacaaatt tcacaaataa agcatttttt tcactgcatt
540ctagttgtgg tttgtccaaa ctcatcaatg tatcttatca tgtctggatc
tgcgactcta 600gaggatcata atcagccata ccacatttgt agaggtttta
cttgctttaa aaaacctccc 660acacctcccc ctgaacctga aacataaaat
gaatgcaatt gttgttgtta acttgtttat 720tgcagcttat aatggttaca
aataaagcaa tagcatcaca aatttcacaa ataaagcatt 780tttttcactg
cattctagtt gtggtttgtc caaactcatc aatgtatctt atcatgtctg
840gatccccatc aagctgatcc ggaaccctta atataacttc gtataatgta
tgctatacga 900agttat 9065131079DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 513caggccctcc
gagcgtggtg gagccgttct gtgagacagc cgggtacgag tcgtgacgct 60ggaaggggca
agcgggtggt gggcaggaat gcggtccgcc ctgcagcaac cggaggggga
120gggagaaggg agcggaaaag tctccaccgg acgcggccat ggctcggggg
ggggggggca 180gcggaggagc gcttccggcc gacgtctcgt cgctgattgg
cttcttttcc tcccgccgtg 240tgtgaaaaca caaatggcgt gttttggttg
gcgtaaggcg cctgtcagtt aacggcagcc 300ggagtgcgca gccgccggca
gcctcgctct gcccactggg tggggcggga ggtaggtggg 360gtgaggcgag
ctggacgtgc gggcgcggtc ggcctctggc ggggcggggg aggggaggga
420gggtcagcga aagtagctcg cgcgcgagcg gccgcccacc ctccccttcc
tctgggggag 480tcgttttacc cgccgccggc cgggcctcgt cgtctgattg
gctctcgggg cccagaaaac 540tggcccttgc cattggctcg tgttcgtgca
agttgagtcc atccgccggc cagcgggggc 600ggcgaggagg cgctcccagg
ttccggccct cccctcggcc ccgcgccgca gagtctggcc 660gcgcgcccct
gcgcaacgtg gcaggaagcg cgcgctgggg gcggggacgg gcagtagggc
720tgagcggctg cggggcgggt gcaagcacgt ttccgacttg agttgcctca
agaggggcgt 780gctgagccag acctccatcg cgcactccgg ggagtggagg
gaaggagcga gggctcagtt 840gggctgtttt ggaggcagga agcacttgct
ctcccaaagt cgctctgagt tgttatcagt 900aagggagctg cagtggagta
ggcggggaga aggccgcacc cttctccgga ggggggaggg 960gagtgttgca
atacctttct gggagttctc tgctgcctcc tggcttctga ggaccgccct
1020gggcctggga gaatcccttc cccctcttcc ctcgtgatct gcaactccag
tctttctag 10795144336DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 514agatgggcgg
gagtcttctg ggcaggctta aaggctaacc tggtgtgtgg gcgttgtcct 60gcaggggaat
tgaacaggtg taaaattgga gggacaagac ttcccacaga ttttcggttt
120tgtcgggaag ttttttaata ggggcaaata aggaaaatgg gaggataggt
agtcatctgg 180ggttttatgc agcaaaacta caggttatta ttgcttgtga
tccgcctcgg agtattttcc 240atcgaggtag attaaagaca tgctcacccg
agttttatac tctcctgctt gagatcctta 300ctacagtatg aaattacagt
gtcgcgagtt agactatgta agcagaattt taatcatttt 360taaagagccc
agtacttcat atccatttct cccgctcctt ctgcagcctt atcaaaaggt
420attttagaac actcatttta gccccatttt catttattat actggcttat
ccaaccccta 480gacagagcat tggcattttc cctttcctga tcttagaagt
ctgatgactc atgaaaccag 540acagattagt tacatacacc acaaatcgag
gctgtagctg gggcctcaac actgcagttc 600ttttataact ccttagtaca
ctttttgttg atcctttgcc ttgatcctta attttcagtg 660tctatcacct
ctcccgtcag gtggtgttcc acatttgggc ctattctcag tccagggagt
720tttacaacaa tagatgtatt gagaatccaa cctaaagctt aactttccac
tcccatgaat 780gcctctctcc tttttctcca tttataaact gagctattaa
ccattaatgg tttccaggtg 840gatgtctcct cccccaatat tacctgatgt
atcttacata ttgccaggct gatattttaa 900gacattaaaa ggtatatttc
attattgagc cacatggtat tgattactgc ttactaaaat 960tttgtcattg
tacacatctg taaaaggtgg ttccttttgg aatgcaaagt tcaggtgttt
1020gttgtctttc ctgacctaag gtcttgtgag cttgtatttt ttctatttaa
gcagtgcttt 1080ctcttggact ggcttgactc atggcattct acacgttatt
gctggtctaa atgtgatttt 1140gccaagcttc ttcaggacct ataattttgc
ttgacttgta gccaaacaca agtaaaatga 1200ttaagcaaca aatgtatttg
tgaagcttgg tttttaggtt gttgtgttgt gtgtgcttgt 1260gctctataat
aatactatcc aggggctgga gaggtggctc ggagttcaag agcacagact
1320gctcttccag aagtcctgag ttcaattccc agcaaccaca tggtggctca
caaccatctg 1380taatgggatc tgatgccctc ttctggtgtg tctgaagacc
acaagtgtat tcacattaaa 1440taaataaatc ctccttcttc ttcttttttt
tttttttaaa gagaatactg tctccagtag 1500aatttactga agtaatgaaa
tactttgtgt ttgttccaat atggtagcca ataatcaaat 1560tactctttaa
gcactggaaa tgttaccaag gaactaattt ttatttgaag tgtaactgtg
1620gacagaggag ccataactgc agacttgtgg gatacagaag accaatgcag
actttaatgt 1680cttttctctt acactaagca ataaagaaat aaaaattgaa
cttctagtat cctatttgtt 1740taaactgcta gctttactta acttttgtgc
ttcatctata caaagctgaa agctaagtct 1800gcagccatta ctaaacatga
aagcaagtaa tgataatttt ggatttcaaa aatgtagggc 1860cagagtttag
ccagccagtg gtggtgcttg cctttatgcc tttaatccca gcactctgga
1920ggcagagaca ggcagatctc tgagtttgag cccagcctgg tctacacatc
aagttctatc 1980taggatagcc aggaatacac acagaaaccc tgttggggag
gggggctctg agatttcata 2040aaattataat tgaagcattc cctaatgagc
cactatggat gtggctaaat ccgtctacct 2100ttctgatgag atttgggtat
tattttttct gtctctgctg ttggttgggt cttttgacac 2160tgtgggcttt
ctttaaagcc tccttcctgc catgtggtct cttgtttgct actaacttcc
2220catggcttaa atggcatggc tttttgcctt ctaagggcag ctgctgagat
ttgcagcctg 2280atttccaggg tggggttggg aaatctttca aacactaaaa
ttgtccttta attttttttt 2340taaaaaatgg gttatataat aaacctcata
aaatagttat gaggagtgag gtggactaat 2400attaaatgag tccctcccct
ataaaagagc tattaaggct ttttgtctta tacttaactt 2460tttttttaaa
tgtggtatct ttagaaccaa gggtcttaga gttttagtat acagaaactg
2520ttgcatcgct taatcagatt ttctagtttc aaatccagag aatccaaatt
cttcacagcc 2580aaagtcaaat taagaatttc tgacttttaa tgttaatttg
cttactgtga atataaaaat 2640gatagctttt cctgaggcag ggtctcacta
tgtatctctg cctgatctgc aacaagatat 2700gtagactaaa gttctgcctg
cttttgtctc ctgaatacta aggttaaaat gtagtaatac 2760ttttggaact
tgcaggtcag attcttttat aggggacaca ctaagggagc ttgggtgata
2820gttggtaaat gtgtttaagt gatgaaaact tgaattatta tcaccgcaac
ctacttttta 2880aaaaaaaaag ccaggcctgt tagagcatgc ttaagggatc
cctaggactt gctgagcaca 2940caagagtagt tacttggcag gctcctggtg
agagcatatt tcaaaaaaca aggcagacaa 3000ccaagaaact acagttaagg
ttacctgtct ttaaaccatc tgcatataca cagggatatt 3060aaaatattcc
aaataatatt tcattcaagt tttcccccat caaattggga catggatttc
3120tccggtgaat aggcagagtt ggaaactaaa caaatgttgg ttttgtgatt
tgtgaaattg 3180ttttcaagtg atagttaaag cccatgagat acagaacaaa
gctgctattt cgaggtctct 3240tggtttatac tcagaagcac ttctttgggt
ttccctgcac tatcctgatc atgtgctagg 3300cctaccttag gctgattgtt
gttcaaataa acttaagttt cctgtcaggt gatgtcatat 3360gatttcatat
atcaaggcaa aacatgttat atatgttaaa catttgtact taatgtgaaa
3420gttaggtctt tgtgggtttg atttttaatt ttcaaaacct gagctaaata
agtcattttt 3480acatgtctta catttggtgg aattgtataa ttgtggtttg
caggcaagac tctctgacct 3540agtaacccta cctatagagc actttgctgg
gtcacaagtc taggagtcaa gcatttcacc 3600ttgaagttga gacgttttgt
tagtgtatac tagtttatat gttggaggac atgtttatcc 3660agaagatatt
caggactatt tttgactggg ctaaggaatt gattctgatt agcactgtta
3720gtgagcattg agtggccttt aggcttgaat tggagtcact tgtatatctc
aaataatgct 3780ggcctttttt aaaagccctt gttctttatc accctgtttt
ctacataatt tttgttcaaa 3840gaaatacttg tttggatctc cttttgacaa
caatagcatg ttttcaagcc atattttttt 3900tccttttttt tttttttttt
ggtttttcga gacagggttt ctctgtatag ccctggctgt 3960cctggaactc
actttgtaga ccaggctggc ctcgaactca gaaatccgcc tgcctctgcc
4020tcctgagtgc cgggattaaa ggcgtgcacc accacgcctg gctaagttgg
atattttgtt 4080atataactat aaccaatact aactccactg ggtggatttt
taattcagtc agtagtctta 4140agtggtcttt attggccctt cattaaaatc
tactgttcac tctaacagag gctgttggta 4200ctagtggcac ttaagcaact
tcctacggat atactagcag attaagggtc agggatagaa 4260actagtctag
cgttttgtat acctaccagc tttatactac cttgttctga tagaaatatt
4320tcaggacatc tagctt 43365151846DNAArtificial SequenceDescription
of Artificial Sequence Synthetic polynucleotide 515aattctaccg
ggtaggggag gcgcttttcc caaggcagtc tggagcatgc gctttagcag 60ccccgctggg
cacttggcgc tacacaagtg gcctctggcc tcgcacacat tccacatcca
120ccggtaggcg ccaaccggct ccgttctttg gtggcccctt cgcgccacct
tctactcctc 180ccctagtcag gaagttcccc cccgccccgc agctcgcgtc
gtgcaggacg tgacaaatgg 240aagtagcacg tctcactagt ctcgtgcaga
tggacagcac cgctgagcaa tggaagcggg 300taggcctttg gggcagcggc
caatagcagc tttgctcctt cgctttctgg gctcagaggc 360tgggaagggg
tgggtccggg ggcgggctca ggggcgggct caggggcggg gcgggcgccc
420gaaggtcctc cggaggcccg gcattctgca cgcttcaaaa gcgcacgtct
gccgcgctgt 480tctcctcttc ctcatctccg ggcctttcga cctgcaatcg
ccgctagcga agttcctatt 540ctctagaaag tataggaact tcgccaccat
gggatcggcc attgaacaag atggattgca 600cgcaggttct ccggccgctt
gggtggagag gctattcggc tatgactggg cacaacagac 660aatcggctgc
tctgatgccg ccgtgttccg gctgtcagcg caggggcgcc cggttctttt
720tgtcaagacc gacctgtccg gtgccctgaa tgaactgcag gacgaggcag
cgcggctatc 780gtggctggcc acgacgggcg ttccttgcgc agctgtgctc
gacgttgtca ctgaagcggg 840aagggactgg ctgctattgg gcgaagtgcc
ggggcaggat ctcctgtcat ctcaccttgc 900tcctgccgag aaagtatcca
tcatggctga tgcaatgcgg cggctgcata cgcttgatcc 960ggctacctgc
ccattcgacc accaagcgaa acatcgcatc gagcgagcac gtactcggat
1020ggaagccggt cttgtcgatc aggatgatct ggacgaagag catcaggggc
tcgcgccagc 1080cgaactgttc gccaggctca aggcgcgcat gcccgacggc
gatgatctcg tcgtgaccca 1140tggcgatgcc tgcttgccga atatcatggt
ggaaaatggc cgcttttctg gattcatcga 1200ctgtggccgg ctgggtgtgg
cggaccgcta tcaggacata gcgttggcta cccgtgatat 1260tgctgaagag
cttggcggcg aatgggctga ccgcttcctc gtgctttacg gtatcgccgc
1320tcccgattcg cagcgcatcg ccttctatcg ccttcttgac gagttcttct
gaggggatcc 1380gctgtaagtc tgcagaaatt gatgatctat taaacaataa
agatgtccac taaaatggaa 1440gtttttcctg tcatactttg ttaagaaggg
tgagaacaga gtacctacat tttgaatgga 1500aggattggag ctacgggggt
gggggtgggg tgggattaga taaatgcctg ctctttactg 1560aaggctcttt
actattgctt tatgataatg tttcatagtt ggatatcata atttaaacaa
1620gcaaaaccaa attaagggcc agctcattcc tcccactcat gatctataga
tctatagatc 1680tctcgtggga tcattgtttt tctcttgatt cccactttgt
ggttctaagt actgtggttt 1740ccaaatgtgt cagtttcata gcctgaagaa
cgagatcagc agcctctgtt ccacatacac 1800ttcattctca gtattgtttt
gccaagttct aattccatca gaaagc 18465161519DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
516taccgggtag gggaggcgct tttcccaagg cagtctggag catgcgcttt
agcagccccg 60ctgggcactt ggcgctacac aagtggcctc tggcctcgca cacattccac
atccaccggt 120aggcgccaac cggctccgtt ctttggtggc cccttcgcgc
caccttctac tcctccccta 180gtcaggaagt tcccccccgc cccgcagctc
gcgtcgtgca ggacgtgaca aatggaagta 240gcacgtctca ctagtctcgt
gcagatggac agcaccgctg agcaatggaa gcgggtaggc 300ctttggggca
gcggccaata gcagctttgc tccttcgctt tctgggctca gaggctggga
360aggggtgggt ccgggggcgg gctcaggggc gggctcaggg gcggggcggg
cgcccgaagg 420tcctccggag gcccggcatt ctgcacgctt caaaagcgca
cgtctgccgc gctgttctcc 480tcttcctcat ctccgggcct ttcgacctgc
aggtcctcgc catggatcct gatgatgttg 540ttgattcttc taaatctttt
gtgatggaaa acttttcttc gtaccacggg actaaacctg 600gttatgtaga
ttccattcaa aaaggtatac aaaagccaaa atctggtaca caaggaaatt
660atgacgatga ttggaaaggg ttttatagta ccgacaataa atacgacgct
gcgggatact 720ctgtagataa tgaaaacccg ctctctggaa aagctggagg
cgtggtcaaa gtgacgtatc 780caggactgac gaaggttctc gcactaaaag
tggataatgc cgaaactatt aagaaagagt 840taggtttaag tctcactgaa
ccgttgatgg agcaagtcgg aacggaagag tttatcaaaa 900ggttcggtga
tggtgcttcg cgtgtagtgc tcagccttcc cttcgctgag gggagttcta
960gcgttgaata tattaataac tgggaacagg cgaaagcgtt aagcgtagaa
cttgagatta 1020attttgaaac ccgtggaaaa cgtggccaag atgcgatgta
tgagtatatg gctcaagcct 1080gtgcaggaaa tcgtgtcagg cgatctcttt
gtgaaggaac cttacttctg tggtgtgaca 1140taattggaca aactacctac
agagatttaa agctctaagg taaatataaa atttttaagt 1200gtataatgtg
ttaaactact gattctaatt gtttgtgtat tttagattcc aacctatgga
1260actgatgaat gggagcagtg gtggaatgca gatcctagag ctcgctgatc
agcctcgact 1320gtgccttcta gttgccagcc atctgttgtt tgcccctccc
ccgtgccttc cttgaccctg 1380gaaggtgcca ctcccactgt cctttcctaa
taaaatgagg aaattgcatc gcattgtctg 1440agtaggtgtc attctattct
ggggggtggg gtggggcagg acagcaaggg ggaggattgg 1500gaagacaata
gcaggcatg 151951723DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 517gagggcctat ttcccatgat tcc
2351822DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 518cttgtggaaa ggacgaaaca cc
2251945DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 519aacnnnnnnn nnnnnnnnnn nnnggtgttt
cgtcctttcc acaag 4552028DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 520cctgagtgtt
gaggccccag tggctgct 2852137DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 521acgagggcag
agtgctgctt gctgctggcc aggcccc 3752268DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 522catcaggctc tcagctcagc ctgagtgttg aggccctgct
ggccaggccc ctgcgtgggc 60ccaagctg 6852327DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 523gagggcctat ttcccatgat tccttca
27524125DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 524aaaaaaagca ccgactcggt gccacttttt
caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa aacnnnnnnn
nnnnnnnnnn nnnggtgttt cgtcctttcc 120acaag 125525111DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
525gaaacaccnn nnnnnnnnnn nnnnnnnngt tttagagcta gaaatagcaa
gttaaaataa 60ggctagtccg ttatcaactt gaaaaagtgg caccgagtcg gtgctttttt
t 11152620DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 526agctgtttta ctggtcggct
2052720DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 527aatggataca cctggtcgaa
2052820DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 528caatggatac acctggtcga 2052968DNAHomo
sapiens 529accatgtata ccacttgggc tttggcagta gctaactgca ctaaatataa
tataaggagg 60gttttatg 6853023DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 530nnnnnnnnnn
nnnnnnnnnn ngg 2353115DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 531nnnnnnnnnn nnngg
1553223DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 532nnnnnnnnnn nnnnnnnnnn ngg
2353314DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 533nnnnnnnnnn nngg 1453425DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 534nnnnnnnnnn nnnnnnnnnn nggng 2553517DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 535nnnnnnnnnn nnnggng 1753625DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 536nnnnnnnnnn nnnnnnnnnn nggng
2553716DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 537nnnnnnnnnn nnggng 16
* * * * *