U.S. patent application number 15/230025 was filed with the patent office on 2016-11-24 for engineering of systems, methods and optimized guide compositions for sequence manipulation.
The applicant listed for this patent is THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGE. Invention is credited to Le Cong, Patrick Hsu, Fei Ran, Feng Zhang.
Application Number | 20160340662 15/230025 |
Document ID | / |
Family ID | 49920627 |
Filed Date | 2016-11-24 |
United States Patent
Application |
20160340662 |
Kind Code |
A1 |
Zhang; Feng ; et
al. |
November 24, 2016 |
ENGINEERING OF SYSTEMS, METHODS AND OPTIMIZED GUIDE 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) ; Cong; Le; (Cambridge, MA) ; Hsu;
Patrick; (San Diego, CA) ; Ran; Fei; (Boston,
MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
THE BROAD INSTITUTE, INC.
MASSACHUSETTS INSTITUTE OF TECHNOLOGY
PRESIDENT AND FELLOWS OF HARVARD COLLEGE |
Cambridge
Cambridge
Cambridge |
MA
MA
MA |
US
US
US |
|
|
Family ID: |
49920627 |
Appl. No.: |
15/230025 |
Filed: |
August 5, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14104990 |
Dec 12, 2013 |
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15230025 |
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61748427 |
Jan 2, 2013 |
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61758468 |
Jan 30, 2013 |
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61769046 |
Feb 25, 2013 |
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61791409 |
Mar 15, 2013 |
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61802174 |
Mar 15, 2013 |
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61806375 |
Mar 28, 2013 |
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61814263 |
Apr 20, 2013 |
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61819803 |
May 6, 2013 |
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61828130 |
May 28, 2013 |
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61835931 |
Jun 17, 2013 |
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61836127 |
Jun 17, 2013 |
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61736527 |
Dec 12, 2012 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 15/1082 20130101;
C12N 15/907 20130101; C12Y 301/00 20130101; C12N 15/79 20130101;
C12N 2810/50 20130101; C12N 15/52 20130101; C12N 15/902 20130101;
C12N 15/63 20130101; C12N 9/16 20130101; C12N 15/85 20130101; C12N
2800/10 20130101; C12N 15/01 20130101; C12N 15/86 20130101; C12N
9/22 20130101; C12Q 1/6806 20130101 |
International
Class: |
C12N 9/22 20060101
C12N009/22; C12N 15/86 20060101 C12N015/86 |
Goverment Interests
STATEMENT AS TO FEDERALLY SPONSORED RESEARCH
[0004] This invention was made with government support under grant
number DP1MH100706 awarded by the National Institutes of Health.
The government has certain rights in the invention.
Claims
1. An engineered, non-naturally occurring Clustered Regularly
Interspersed Short Palindromic Repeats (CRISPR)-CRISPR associated
(Cas) (CRISPR-Cas) vector system comprising one or more vectors
comprising: a) a first regulatory element operably linked to one or
more nucleotide sequences encoding one or more CRISPR-Cas system
guide RNAs that hybridize with target sequences in polynucleotide
loci in a eukaryotic cell, the guide RNA comprising a guide
sequence, a tracr sequence, and a tracr mate sequence, b) a second
regulatory element operably linked to a nucleotide sequence
encoding a Type II Cas9 protein, said protein comprising a nuclear
localization signal (NLS); wherein components (a) and (b) are
located on same or different vectors of the system, wherein the
tracr sequence is 30 or more nucleotides in length, and whereby the
one or more guide RNAs target the polynucleotide loci in a
eukaryotic cell and the Cas9 protein cleaves the polynucleotide
loci, whereby sequence of the polynucleotide loci is modified; and,
wherein the Cas9 protein and the one or more guide RNAs do not
naturally occur together.
2. An engineered, non-naturally occurring Type II CRISPR-Cas vector
system according to claim 1, wherein the Cas9 protein comprises one
or more mutations in a catalytic domain, such that the mutated Cas9
protein lacks the ability to cleave one strand of the
polynucleotide loci, and is a nickase.
3. The system of claim 1 or 2, wherein the vectors are viral
vectors.
4. The system of claim 3, wherein the viral vectors are retroviral,
lentiviral, adenoviral, adeno-associated or herpes simplex viral
vectors.
5. The system of claim 2 wherein the Cas9 protein comprises one or
more mutations in the RuvC I, RuvC II or RuvC III catalytic
domains.
6. The system of claim 2 wherein the Cas9 protein comprises a
mutation selected from the group consisting of D10A, H840A, N854A
and N863A with reference to the position numbering of a
Streptococcus pyogenes Cas9 (SpCas9) protein.
7. The system of claim 1 or 2, wherein the guide RNA is a chimeric
RNA comprising the guide sequence, the tracr sequence, and a tracr
mate sequence.
8. The system of claim 7 wherein hybridization between the tracr
sequence and the tracr mate sequence produces a transcript having a
secondary structure.
9. The system of claim 8, wherein the secondary structure is a
hairpin.
10. The system of claim 1 or 2, wherein the eukaryotic cell is a
mammalian cell or a human cell.
11. The system of claim 1 or 2, wherein the nucleotide sequence
encoding the Cas9 protein is codon optimized for expression in a
eukaryotic cell.
12. The system of claim 1 or 2, wherein a repair template is
inserted into the cleaved polynucleotide loci.
Description
RELATED APPLICATIONS AND INCORPORATION BY REFERENCE
[0001] This application is a continuation of U.S. application Ser.
No. 14/104,990, filed Dec. 12, 2013 and which claims priority to
U.S. provisional patent application 61/836,127 entitled ENGINEERING
OF SYSTEMS, METHODS AND OPTIMIZED COMPOSITIONS FOR SEQUENCE
MANIPULATION filed on Jun. 17, 2013. This application also claims
priority 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. Priority is also
claimed to U.S. provisional patent applications 61/736,527 and
61/748,427, both entitled SYSTEMS METHODS AND COMPOSITIONS FOR
SEQUENCE MANIPULATION filed on Dec. 12, 2012 and Jan. 2, 2013,
respectively. Priority is also claimed to U.S. provisional patent
applications 61/791,409 and 61/835,931 both entitled
BI-2011/008/44790.02.2003 and BI-2011/008/44790.03.2003 filed on
Mar. 15, 2013 and Jun. 17, 2013 respectively.
[0002] Reference is also made to U.S. provisional patent
applications 61/835,936, 61/836,101, 61/836,080, 61/836,123 and
61/835,973 each filed Jun. 17, 2013.
[0003] 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 44790.00.2047_SL.txt and is 181,665
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 cell, e.g., 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%, 90%, 95%, or 99% of sequence complementarity along the length
of the tracr mate sequence when optimally aligned.
[0010] 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.
[0011] Aspects of the invention comprehend one or more of the
guide, tracr and tracr mate sequences are modified to improve
stability in the CRISPR-Cas system chiRNA or CRISPR enzyme system.
In an embodiment of the invention, the modification may comprise
sequence optimization. In another embodiment, the modification may
comprise reduction in polyT sequences in the tracr and/or tracr
mate sequence. The invention provides that one or more Ts present
in a poly-T sequence of the relevant wild type sequence have been
substituted with a non-T nucleotide. The modified sequence may not
comprise any polyT sequence having more than 4 contiguous Ts. In a
further aspect of the invention the modification may comprise
altering loops and/or hairpins. Embodiments of the invention
encompass providing a minimum of two hairpins in the guide sequence
or providing a hairpin formed by complementation between the tracr
and tracr mate sequence or providing one or more further hairpin(s)
at the 3' end of the tracrRNA sequence. Further embodiments of the
invention encompass providing one or more additional hairpin(s)
added to the 3' of the guide sequence or extending the 5' end of
the guide sequence or providing one or more hairpins in the 5' end
of the guide sequence. In a preferred embodiment, the modification
comprises two hairpins or three hairpins or at most five
hairpins.
[0012] 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.
[0013] 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).
[0014] 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 III 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.).
[0015] Advantageous vectors include lentiviruses and
adeno-associated viruses, and types of such vectors can also be
selected for targeting particular types of cells.
[0016] 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.
[0017] 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.
[0018] 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.
[0019] 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% 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.
[0020] 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.
[0021] 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.
[0022] 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 with 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.
[0023] 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 with 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.
[0024] 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.
[0025] 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 polynuceltide
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.
[0026] In some aspects the invention provides a non-naturally
occurring or engineered composition comprising a CRISPR-Cas system
chimeric RNA (chiRNA) polynucleotide sequence, wherein the
polynucleotide sequence comprises (a) a guide sequence capable of
hybridizing to a target sequence in a eukaryotic cell, (b) a tracr
mate sequence, and (c) a tracr sequence wherein (a), (b) and (c)
are arranged in a 5' to 3' orientation, wherein when transcribed,
the tracr mate sequence hybridizes to the tracr sequence and the
guide sequence directs sequence-specific binding of a CRISPR
complex to the target sequence, 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,
[0027] or
[0028] a CRISPR enzyme system, wherein the system is encoded by a
vector system comprising one or more vectors comprising I. a first
regulatory element operably linked to a CRISPR-Cas system chimeric
RNA (chiRNA) polynucleotide sequence, wherein the polynucleotide
sequence comprises (a) one or more guide sequences capable of
hybridizing to one or more target sequences in a eukaryotic cell,
(b) a tracr mate sequence, and (c) one or more tracr sequences, and
II. a second regulatory element operably linked to an enzyme-coding
sequence encoding a CRISPR enzyme comprising at least one or more
nuclear localization sequences, wherein (a), (b) and (c) are
arranged in a 5' to 3'orientation, wherein components I and II are
located on the same or different vectors of the system, wherein
when transcribed, the tracr mate sequence hybridizes to the tracr
sequence and the guide sequence directs sequence-specific binding
of a CRISPR complex to the target sequence, wherein the CRISPR
complex comprises the 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, or a
multiplexed CRISPR enzyme system, wherein the system is encoded by
a vector system comprising one or more vectors comprising I. a
first regulatory element operably linked to (a) one or more guide
sequences capable of hybridizing to a target sequence in a cell,
and (b) at least one or more tracr mate sequences, II. a second
regulatory element operably linked to an enzyme-coding sequence
encoding a CRISPR enzyme, and III. a third regulatory element
operably linked to a tracr sequence, wherein components I, II and
III are located on the same or different vectors of the system,
wherein when transcribed, the tracr mate sequence hybridizes to the
tracr sequence and the guide sequence directs sequence-specific
binding of a CRISPR complex to the target sequence, wherein the
CRISPR complex comprises the 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 wherein in the multiplexed system multiple guide sequences and
a single tracr sequence is used; and wherein one or more of the
guide, tracr and tracr mate sequences are modified to improve
stability.
[0029] In aspects of the invention, the modification comprises an
engineered secondary structure. For example, the modification can
comprise a reduction in a region of hybridization between the tracr
mate sequence and the tracr sequence. For example, the modification
also may comprise fusing the tracr mate sequence and the tracr
sequence through an artificial loop. The modification may comprise
the tracr sequence having a length between 40 and 120 bp. In
embodiments of the invention, the tracr sequence is between 40 bp
and full length of the tracr. In certain embodiments, the length of
tracRNA includes at least nucleotides 1-67 and in some embodiments
at least nucleotides 1-85 of the wild type tracRNA. In some
embodiments, at least nucleotides corresponding to nucleotides 1-67
or 1-85 of wild type S. pyogenes Cas9 tracRNA may be used. Where
the CRISPR system uses enzymes other than Cas9, or other than
SpCas9, then corresponding nucleotides in the relevant wild type
tracRNA may be present. In some embodiments, the length of tracRNA
includes no more than nucleotides 1-67 or 1-85 of the wild type
tracRNA. The modification may comprise sequence optimization. In
certain aspects, sequence optimization may comprise reducing the
incidence of polyT sequences in the tracr and/or tracr mate
sequence. Sequence optimization may be combined with reduction in
the region of hybridization between the tracr mate sequence and the
tracr sequence; for example, a reduced length tracr sequence.
[0030] In an aspect the invention provides the CRISPR-Cas system or
CRISPR enzyme system wherein the modification comprises reduction
in polyT sequences in the tracr and/or tracr mate sequence. In some
aspects of the invention, one or more Ts present in a poly-T
sequence of the relevant wild type sequence (that is, a stretch of
more than 3, 4, 5, 6, or more contiguous T bases; in some
embodiments, a stretch of no more than 10, 9, 8, 7, 6 contiguous T
bases) may be substituted with a non-T nucleotide, e.g., an A, so
that the string is broken down into smaller stretches of Ts with
each stretch having 4, or fewer than 4 (for example, 3 or 2)
contiguous Ts. Bases other than A may be used for substitution, for
example C or G, or non-naturally occuring nucleotides or modified
nucleotides. If the string of Ts is involved in the formation of a
hairpin (or stem loop), then it is advantageous that the
complementary base for the non-T base be changed to complement the
non-T nucleotide. For example, if the non-T base is an A, then its
complement may be changed to a T, e.g., to preserve or assist in
the preservation of secondary structure. For instance, 5'-TTTTT can
be altered to become 5'-TTTAT and the complementary 5'-AAAAA can be
changed into 5'-ATAAA.
[0031] In an aspect the invention provides the CRISPR-Cas system or
CRISPR enzyme system wherein the modification comprises adding a
polyT terminator sequence. In an aspect the invention provides the
CRISPR-Cas system or CRISPR enzyme system wherein the modification
comprises adding a polyT terminator sequence in tracr and/or tracr
mate sequences. In an aspect the invention provides the CRISPR-Cas
system or CRISPR enzyme system wherein the modification comprises
adding a polyT terminator sequence in the guide sequence. The polyT
terminator sequence may comprise 5 contiguous T bases, or more than
5.
[0032] In an aspect the invention provides the CRISPR-Cas system or
CRISPR enzyme system wherein the modification comprises altering
loops and/or hairpins. In an aspect the invention provides the
CRISPR-Cas system or CRISPR enzyme system wherein the modification
comprises providing a minimum of two hairpins in the guide
sequence. In an aspect the invention provides the CRISPR-Cas system
or CRISPR enzyme system wherein the modification comprises
providing a hairpin formed by complementation between the tracr and
tracr mate (direct repeat) sequence. In an aspect the invention
provides the CRISPR-Cas system or CRISPR enzyme system wherein the
modification comprises providing one or more further hairpin(s) at
or towards the 3' end of the tracrRNA sequence. For example, a
hairpin may be formed by providing self complementary sequences
within the tracRNA sequence joined by a loop such that a hairpin is
formed on self folding. In an aspect the invention provides the
CRISPR-Cas system or CRISPR enzyme system wherein the modification
comprises providing additional hairpins added to the 3' of the
guide sequence. In an aspect the invention provides the CRISPR-Cas
system or CRISPR enzyme system wherein the modification comprises
extending the 5' end of the guide sequence. In an aspect the
invention provides the CRISPR-Cas system or CRISPR enzyme system
wherein the modification comprises providing one or more hairpins
in the 5' end of the guide sequence. In an aspect the invention
provides the CRISPR-Cas system or CRISPR enzyme system wherein the
modification comprises appending the sequence (5'-AGGACGAAGTCCTAA)
(SEQ ID NO: 1) to the 5' end of the guide sequence. Other sequences
suitable for forming hairpins will be known to the skilled person,
and may be used in certain aspects of the invention. In some
aspects of the invention, at least 2, 3, 4, 5, or more additional
hairpins are provided. In some aspects of the invention, no more
than 10, 9, 8, 7, 6 additional hairpins are provided. In an aspect
the invention provides the CRISPR-Cas system or CRISPR enzyme
system wherein the modification comprises two hairpins. In an
aspect the invention provides the CRISPR-Cas system or CRISPR
enzyme system wherein the modification comprises three hairpins. In
an aspect the invention provides the CRISPR-Cas system or CRISPR
enzyme system wherein the modification comprises at most five
hairpins.
[0033] In an aspect the invention provides the CRISPR-Cas system or
CRISPR enzyme system wherein the modification comprises providing
cross linking, or providing one or more modified nucleotides in the
polynucleotide sequence. Modified nucleotides and/or cross linking
may be provided in any or all of the tracr, tracr mate, and/or
guide sequences, and/or in the enzyme coding sequence, and/or in
vector sequences. Modifications may include inclusion of at least
one non naturally occurring nucleotide, or a modified nucleotide,
or analogs thereof. Modified nucleotides may be modified at the
ribose, phosphate, and/or base moiety. Modified nucleotides may
include 2'-O-methyl analogs, 2'-deoxy analogs, or 2'-fluoro
analogs. The nucleic acid backbone may be modified, for example, a
phosphorothioate backbone may be used. The use of locked nucleic
acids (LNA) or bridged nucleic acids (BNA) may also be possible.
Further examples of modified bases include, but are not limited to,
2-aminopurine, 5-bromo-uridine, pseudouridine, inosine,
7-methylguanosine.
[0034] It will be understood that any or all of the above
modifications may be provided in isolation or in combination in a
given CRISPR-Cas system or CRISPR enzyme system. Such a system may
include one, two, three, four, five, or more of said
modifications.
[0035] In an aspect the invention provides the CRISPR-Cas system or
CRISPR enzyme system wherein the CRISPR enzyme is a type II CRISPR
system enzyme, e.g., a Cas9 enzyme. In an aspect the invention
provides the CRISPR-Cas system or CRISPR enzyme system wherein the
CRISPR enzyme is comprised of less than one thousand amino acids,
or less than four thousand amino acids. In an aspect the invention
provides the CRISPR-Cas system or CRISPR enzyme system wherein the
Cas9 enzyme is StCas9 or StlCas9, or the Cas9 enzyme is a Cas9
enzyme from an organism selected from the group consisting of genus
Streptococcus, Campylobacter, Nitratifractor, Staphylococcus,
Parvibaculum, Roseburia, Neisseria, Gluconacetobacter,
Azospirillum, Sphaerochaeta, Lactobacillus, Eubacterium or
Corynebacter. In an aspect the invention provides the CRISPR-Cas
system or CRISPR enzyme system wherein the CRISPR enzyme is a
nuclease directing cleavage of both strands at the location of the
target sequence.
[0036] In an aspect the invention provides the CRISPR-Cas system or
CRISPR enzyme system wherein the first regulatory element is a
polymerase III promoter. In an aspect the invention provides the
CRISPR-Cas system or CRISPR enzyme system wherein the second
regulatory element is a polymerase II promoter.
[0037] In an aspect the invention provides the CRISPR-Cas system or
CRISPR enzyme system wherein the guide sequence comprises at least
fifteen nucleotides.
[0038] In an aspect the invention provides the CRISPR-Cas system or
CRISPR enzyme system wherein the modification comprises optimized
tracr sequence and/or optimized guide sequence RNA and/or co-fold
structure of tracr sequence and/or tracr mate sequence(s) and/or
stabilizing secondary structures of tracr sequence and/or tracr
sequence with a reduced region of base-pairing and/or tracr
sequence fused RNA elements; and/or, in the multiplexed system
there are two RNAs comprising a tracer and comprising a plurality
of guides or one RNA comprising a plurality of chimerics.
[0039] In aspects of the invention the chimeric RNA architecture is
further optimized according to the results of mutagenesis studies.
In chimeric RNA with two or more hairpins, mutations in the
proximal direct repeat to stabilize the hairpin may result in
ablation of CRISPR complex activity. Mutations in the distal direct
repeat to shorten or stabilize the hairpin may have no effect on
CRISPR complex activity. Sequence randomization in the bulge region
between the proximal and distal repeats may significantly reduce
CRISPR complex activity. Single base pair changes or sequence
randomization in the linker region between hairpins may result in
complete loss of CRISPR complex activity. Hairpin stabilization of
the distal hairpins that follow the first hairpin after the guide
sequence may result in maintenance or improvement of CRISPR complex
activity. Accordingly, in preferred embodiments of the invention,
the chimeric RNA architecture may be further optimized by
generating a smaller chimeric RNA which may be beneficial for
therapeutic delivery options and other uses and this may be
achieved by altering the distal direct repeat so as to shorten or
stabilize the hairpin. In further preferred embodiments of the
invention, the chimeric RNA architecture may be further optimized
by stabilizing one or more of the distal hairpins. Stabilization of
hairpins may include modifying sequences suitable for forming
hairpins. In some aspects of the invention, at least 2, 3, 4, 5, or
more additional hairpins are provided. In some aspects of the
invention, no more than 10, 9, 8, 7, 6 additional hairpins are
provided. In some aspects of the invention stabilization may be
cross linking and other modifications. Modifications may include
inclusion of at least one non naturally occurring nucleotide, or a
modified nucleotide, or analogs thereof. Modified nucleotides may
be modified at the ribose, phosphate, and/or base moiety. Modified
nucleotides may include 2'-O-methyl analogs, 2'-deoxy analogs, or
2'-fluoro analogs. The nucleic acid backbone may be modified, for
example, a phosphorothioate backbone may be used. The use of locked
nucleic acids (LNA) or bridged nucleic acids (BNA) may also be
possible. Further examples of modified bases include, but are not
limited to, 2-aminopurine, 5-bromo-uridine, pseudouridine, inosine,
7-methylguanosine.
[0040] In an aspect the invention provides the CRISPR-Cas system or
CRISPR enzyme system wherein the CRISPR enzyme is codon-optimized
for expression in a eukaryotic cell.
[0041] Accordingly, in some aspects of the invention, the length of
tracRNA required in a construct of the invention, e.g., a chimeric
construct, need not necessarily be fixed, and in some aspects of
the invention it can be between 40 and 120 bp, and in some aspects
of the invention up to the full length of the tracr, e.g., in some
aspects of the invention, until the 3' end of tracr as punctuated
by the transcription termination signal in the bacterial genome. In
certain embodiments, the length of tracRNA includes at least
nucleotides 1-67 and in some embodiments at least nucleotides 1-85
of the wild type tracRNA. In some embodiments, at least nucleotides
corresponding to nucleotides 1-67 or 1-85 of wild type S. pyogenes
Cas9 tracRNA may be used. Where the CRISPR system uses enzymes
other than Cas9, or other than SpCas9, then corresponding
nucleotides in the relevant wild type tracRNA may be present. In
some embodiments, the length of tracRNA includes no more than
nucleotides 1-67 or 1-85 of the wild type tracRNA With respect to
sequence optimization (e.g., reduction in polyT sequences), e.g.,
as to strings of Ts internal to the tracr mate (direct repeat) or
tracrRNA, in some aspects of the invention, one or more Ts present
in a poly-T sequence of the relevant wild type sequence (that is, a
stretch of more than 3, 4, 5, 6, or more contiguous T bases; in
some embodiments, a stretch of no more than 10, 9, 8, 7, 6
contiguous T bases) may be substituted with a non-T nucleotide,
e.g., an A, so that the string is broken down into smaller
stretches of Ts with each stretch having 4, or fewer than 4 (for
example, 3 or 2) contiguous Ts. If the string of Ts is involved in
the formation of a hairpin (or stem loop), then it is advantageous
that the complementary base for the non-T base be changed to
complement the non-T nucleotide. For example, if the non-T base is
an A, then its complement may be changed to a T, e.g., to preserve
or assist in the preservation of secondary structure. For instance,
5'-TTTTT can be altered to become 5'-TTTAT and the complementary
5'-AAAAA can be changed into 5'-ATAAA. As to the presence of polyT
terminator sequences in tracr+tracr mate transcript, e.g., a polyT
terminator (TTTTT or more), in some aspects of the invention it is
advantageous that such be added to end of the transcript, whether
it is in two RNA (tracr and tracr mate) or single guide RNA form.
Concerning loops and hairpins in tracr and tracr mate transcripts,
in some aspects of the invention it is advantageous that a minimum
of two hairpins be present in the chimeric guide RNA. A first
hairpin can be the hairpin formed by complementation between the
tracr and tracr mate (direct repeat) sequence. A second hairpin can
be at the 3' end of the tracrRNA sequence, and this can provide
secondary structure for interaction with Cas9. Additional hairpins
may be added to the 3' of the guide RNA, e.g., in some aspects of
the invention to increase the stability of the guide RNA.
Additionally, the 5' end of the guide RNA, in some aspects of the
invention, may be extended. In some aspects of the invention, one
may consider 20 bp in the 5' end as a guide sequence. The .kappa.'
portion may be extended. One or more hairpins can be provided in
the 5' portion, e.g., in some aspects of the invention, this may
also improve the stability of the guide RNA. In some aspects of the
invention, the specific hairpin can be provided by appending the
sequence (5'-AGGACGAAGTCCTAA) (SEQ ID NO: 1) to the 5' end of the
guide sequence, and, in some aspects of the invention, this may
help improve stability. Other sequences suitable for forming
hairpins will be known to the skilled person, and may be used in
certain aspects of the invention. In some aspects of the invention,
at least 2, 3, 4, 5, or more additional hairpins are provided. In
some aspects of the invention, no more than 10, 9, 8, 7, 6
additional hairpins are provided. The foregoing also provides
aspects of the invention involving secondary structure in guide
sequences. In some aspects of the invention there may be cross
linking and other modifications, e.g., to improve stability.
Modifications may include inclusion of at least one non naturally
occurring nucleotide, or a modified nucleotide, or analogs thereof.
Modified nucleotides may be modified at the ribose, phosphate,
and/or base moiety. Modified nucleotides may include 2'-O-methyl
analogs, 2'-deoxy analogs, or 2'-fluoro analogs. The nucleic acid
backbone may be modified, for example, a phosphorothioate backbone
may be used. The use of locked nucleic acids (LNA) or bridged
nucleic acids (BNA) may also be possible. Further examples of
modified bases include, but are not limited to, 2-aminopurine,
5-bromo-uridine, pseudouridine, inosine, 7-methylguanosine. Such
modifications or cross linking may be present in the guide sequence
or other sequences adjacent the guide sequence.
[0042] 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.
[0043] 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
[0044] 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:
[0045] 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).
[0046] FIG. 2A-F illustrates an exemplary CRISPR system, a possible
mechanism of action, an example adaptation for expression in
eukaryotic cells, and results of tests assessing nuclear
localization and CRISPR activity. FIG. 2C discloses SEQ ID NOS
103-104, respectively, in order of appearance. FIG. 2E discloses
SEQ ID NOS 105-107, respectively, in order of appearance. FIG. 2F
discloses SEQ ID NOS 108-112, respectively, in order of
appearance.
[0047] FIG. 3A-C illustrates an exemplary expression cassette for
expression of CRISPR system elements in eukaryotic cells, predicted
structures of example guide sequences, and CRISPR system activity
as measured in eukaryotic and prokaryotic cells. FIG. 3A discloses
SEQ ID NO: 113. FIG. 3B discloses SEQ ID NOS 114-122, respectively,
in order of appearance.
[0048] FIG. 4A-D illustrates results of an evaluation of SpCas9
specificity for an example target. FIG. 4A discloses SEQ ID NOS
123, 106 and 124-134, respectively, in order of appearance. FIG. 4C
discloses SEQ ID NO: 123.
[0049] FIG. 5A-G illustrates an exemplary vector system and results
for its use in directing homologous recombination in eukaryotic
cells. FIG. 5E discloses SEQ ID NO: 135. FIG. 5F discloses SEQ ID
NOS 136 and 137, respectively, in order of appearance. FIG. 5G
discloses SEQ ID NOS 138-142, respectively, in order of
appearance.
[0050] FIG. 6A-C illustrates a comparison of different tracrRNA
transcripts for Cas9-mediated gene targeting. FIG. 6A discloses SEQ
ID NOS 143 and 144, respectively, in order of appearance.
[0051] FIG. 7A-D illustrates an exemplary CRISPR system, an example
adaptation for expression in eukaryotic cells, and results of tests
assessing CRISPR activity. FIG. 7B discloses SEQ ID NOS 145 and
146, respectively, in order of appearance. FIG. 7C discloses SEQ ID
NO: 147.
[0052] FIG. 8A-C illustrates exemplary manipulations of a CRISPR
system for targeting of genomic loci in mammalian cells. FIG. 8A
discloses SEQ ID NO: 148. FIG. 8B discloses SEQ ID NOS 149-151,
respectively, in order of appearance.
[0053] FIG. 9A-B illustrates the results of a Northern blot
analysis of crRNA processing in mammalian cells. FIG. 9A discloses
SEQ ID NO: 152.
[0054] FIG. 10A-C illustrates a schematic representation of
chimeric RNAs and results of SURVEYOR assays for CRISPR system
activity in eukaryotic cells. FIG. 10A discloses SEQ ID NO: 153
[0055] FIG. 11A-B illustrates a graphical representation of the
results of SURVEYOR assays for CRISPR system activity in eukaryotic
cells.
[0056] FIG. 12 illustrates predicted secondary structures for
exemplary chimeric RNAs comprising a guide sequence, tracr mate
sequence, and tracr sequence. FIG. 12 discloses SEQ ID NOS 83-102,
respectively, in order of appearance.
[0057] FIG. 13A-D is a phylogenetic tree of Cas genes
[0058] FIG. 14A-F shows 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).
[0059] FIG. 15 shows a graph depicting the function of different
optimized guide RNAs.
[0060] FIG. 16 shows the sequence and structure of different guide
chimeric RNAs.
[0061] FIG. 16 discloses SEQ ID NOS 154-165, respectively, in order
of appearance.
[0062] FIG. 17 shows the co-fold structure of the tracrRNA and
direct repeat. FIG. 17 discloses SEQ ID NO: 166.
[0063] FIGS. 18 A and B shows data from the St1Cas9 chimeric guide
RNA optimization in vitro. FIG. 18A discloses SEQ ID NOS 167-172,
respectively, in order of appearance. FIG. 18B discloses SEQ ID NOS
173-178, respectively, in order of appearance.
[0064] FIG. 19A-B shows cleavage of either unmethylated or
methylated targets by SpCas9 cell lysate. FIG. 19A discloses SEQ ID
NOS 179, 179, 180 and 180, respectively, in order of
appearance.
[0065] FIG. 20A-G shows the optimization of guide RNA architecture
for SpCas9-mediated mammalian genome editing. (a) Schematic of
bicistronic expression vector (PX330) for U6 promoter-driven single
guide RNA (sgRNA) and CBh promoter-driven human codon-optimized
Streptococcus pyogenes Cas9 (hSpCas9) used for all subsequent
experiments. The sgRNA consists of a 20-nt guide sequence (blue)
and scaffold (red), truncated at various positions as indicated.
(b) SURVEYOR assay for SpCas9-mediated indels at the human EMX1 and
PVALB loci. Arrows indicate the expected SURVEYOR fragments (n=3).
(c) Northern blot analysis for the four sgRNA truncation
architectures, with UI as loading control. (d) Both wildtype (wt)
or nickase mutant (D10A) of SpCas9 promoted insertion of a HindIII
site into the human EMX1 gene. Single stranded oligonucleotides
(ssODNs), oriented in either the sense or antisense direction
relative to genome sequence, were used as homologous recombination
templates. (e) Schematic of the human SERPINB5 locus. sgRNAs and
PAMs are indicated by colored bars above sequence; methylcytosine
(Me) are highlighted (pink) and numbered relative to the
transcriptional start site (TSS, +1). (f) Methylation status of
SERPINB5 assayed by bisulfite sequencing of 16 clones. Filled
circles, methylated CpG; open circles, unmethylated CpG. (g)
Modification efficiency by three sgRNAs targeting the methylated
region of SERPINB5, assayed by deep sequencing (n=2). Error bars
indicate Wilson intervals (Online Methods). FIG. 20A discloses SEQ
ID NO: 153. FIG. 20E discloses SEQ ID NO: 181.
[0066] FIG. 21A-B shows the further optimization of CRISPR-Cas
sgRNA architecture. (a) Schematic of four additional sgRNA
architectures, I-IV. Each consists of a 20-nt guide sequence (blue)
joined to the direct repeat (DR, grey), which hybridizes to the
tracrRNA (red). The DR-tracrRNA hybrid is truncated at +12 or +22,
as indicated, with an artificial GAAA stem loop. tracrRNA
truncation positions are numbered according to the previously
reported transcription start site for tracrRNA. sgRNA architectures
II and IV carry mutations within their poly-U tracts, which could
serve as premature transcriptional terminators. (b) SURVEYOR assay
for SpCas9-mediated indels at the human EMX1 locus for target sites
1-3. Arrows indicate the expected SURVEYOR fragments (n=3). FIG.
21A discloses SEQ ID NOS 153 and 182-184, respectively, in order of
appearance.
[0067] FIG. 22 illustrates visualization of some target sites in
the human genome. FIG. 22 discloses SEQ ID NOS 185-263,
respectively, in order of appearance.
[0068] FIG. 23A-B shows (A) a schematic of the sgRNA and (B) the
SURVEYOR analysis of five sgRNA variants for SaCas9 for an optimal
truncated architecture with highest cleavage efficiency. FIG. 23A
discloses SEQ ID NO: 264.
[0069] The figures herein are for illustrative purposes only and
are not necessarily drawn to scale.
DETAILED DESCRIPTION OF THE INVENTION
[0070] 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.
[0071] 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)".
[0072] 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.
[0073] 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.
[0074] 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.
[0075] "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.
[0076] 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 I,
Second Chapter "Overview of principles of hybridization and the
strategy of nucleic acid probe assay", Elsevier, N.Y.
[0077] "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.
[0078] As used herein, "stabilization" or "increasing stability"
with respect to components of the CRISPR system relate to securing
or steadying the structure of the molecule. This may be
accomplished by introduction of one or mutations, including single
or multiple base pair changes, increasing the number of hair pins,
cross linking, breaking up particular stretches of nucleotides and
other modifications. Modifications may include inclusion of at
least one non naturally occurring nucleotide, or a modified
nucleotide, or analogs thereof. Modified nucleotides may be
modified at the ribose, phosphate, and/or base moiety. Modified
nucleotides may include 2'-O-methyl analogs, 2'-deoxy analogs, or
2'-fluoro analogs. The nucleic acid backbone may be modified, for
example, a phosphorothioate backbone may be used. The use of locked
nucleic acids (LNA) or bridged nucleic acids (BNA) may also be
possible. Further examples of modified bases include, but are not
limited to, 2-aminopurine, 5-bromo-uridine, pseudouridine, inosine,
7-methylguanosine. These modifications may apply to any component
of the CRSIPR system. In a preferred embodiment these modifications
are made to the RNA components, e.g. the guide RNA or chimeric
polynucleotide sequence.
[0079] 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.
[0080] 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.
[0081] 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. In some
embodiments, a subject may be an invertebrate animal, for example,
an insect or a nematode; while in others, a subject may be a plant
or a fungus.
[0082] 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.
[0083] 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.
[0084] 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.
[0085] 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)).
[0086] 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.
[0087] 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.
[0088] Examples of suitable inducible non-fusion E. coli expression
vectors include pTrc (Amrann et al., (1988) Gene 69:301-315) and
pET 11d (Studier et al., GENE EXPRESSION TECHNOLOGY: METHODS IN
ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990)
60-89).
[0089] In some embodiments, a vector is a yeast expression vector.
Examples of vectors for expression in yeast Saccharomyces cerivisae
include pYepSec1 (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.).
[0090] 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).
[0091] 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.
[0092] 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 .alpha.-fetoprotein promoter (Campes and Tilghman, 1989.
Genes Dev. 3: 537-546).
[0093] 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,
Mycobacterium, Streptomyces, Aquifex. Porphyromonas, Chlorobium,
Thermus, Bacillus, Listeria, Staphylococcus, Clostridium,
Thermoanaerobacter, Mycoplasma, Fusobacterium, Azarcus,
Chromobacterium, Neisseria, Nitrosomonas, Desulfovibrio, Geobacter,
Myrococcus, Campylobacter, Wolinella, Acinetobacter, Erwinia,
Esrcherihia, Legionella, Methylococcus, Pasteurella,
Photobacterium, Salmonella, Xanthomonas, Yersinia, Treponema, and
Thermotoga.
[0094] 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 hybridisation 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.
[0095] 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 hybridise 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%, 70%, 80%, 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.
[0096] 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.
[0097] 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 I 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 500/a of nuclease (i.e., regular Cas9 without
D10 mutation) in hESCs.
[0098] As a further example, two or more catalytic domains of Cas9
(RuvC I, 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.
[0099] 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, Pa.), 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.
[0100] 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: 2); the NLS from nucleoplasmin (e.g. the
nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ
ID NO: 3)); the c-myc NLS having the amino acid sequence PAAKRVKLD
(SEQ ID NO: 4) or RQRRNELKRSP (SEQ ID NO: 5); the hRNPA1 M9 NLS
having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID
NO: 6); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV
(SEQ ID NO: 7) of the IBB domain from importin-alpha; the sequences
VSRKRPRP (SEQ ID NO: 8) and PPKKARED (SEQ ID NO: 9) of the myoma T
protein; the sequence PQPKKKPL (SEQ ID NO: 10) of human p53; the
sequence SALIKKKKKMAP (SEQ ID NO: 11) of mouse c-abl IV; the
sequences DRLRR (SEQ ID NO: 12) and PKQKKRK (SEQ ID NO: 13) of the
influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO: 14) of the
Hepatitis virus delta antigen; the sequence REKKKFLKRR (SEQ ID NO:
15) of the mouse M.times.1 protein; the sequence
KRKGDEVDGVDEVAKKKSKK (SEQ ID NO: 16) of the human poly(ADP-ribose)
polymerase; and the sequence RKCLQAGMNLEARKTKK (SEQ ID NO: 17) of
the steroid hormone receptors (human) glucocorticoid.
[0101] 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.
[0102] 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%, 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.
[0103] 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 nnnnnnnnNNNNNNNNNNNNXGG (SEQ ID NO:
265) where NNNNNNNNNNNNXGG (SEQ ID NO: 266) (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 nnnnnnnnnNNNNNNNNNNNXGG (SEQ ID NO: 267)
where NNNNNNNNNNNXGG (SEQ ID NO: 268) (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 nnnnnnnnNNNNNNNNNNNNXXAGAAW
(SEQ ID NO: 18) where NNNNNNNNNNNNXXAGAAW (SEQ ID NO: 19) (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
nnnnnnnnnNNNNNNNNNNNXXAGAAW (SEQ ID NO: 20) where
NNNNNNNNNNNXXAGAAW (SEQ ID NO: 21) (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 nnnnnnnnNNNNNNNNNNNNXGGXG
(SEQ ID NO: 269) where NNNNNNNNNNNNXGGXG (SEQ ID NO: 270) (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 nnnnnnnnnNNNNNNNNNNNXGGXG
(SEQ ID NO: 271) where NNNNNNNNNNNXGGXG (SEQ ID NO: 272) (N is A,
G, T, or C; and X can be anything) has a single occurrence in the
genome. In each of these sequences "n" may be A, G, T, or C, and
need not be considered in identifying a sequence as unique.
[0104] 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 P A Carr and G M Church, 2009,
Nature Biotechnology 27(12): 1151-62). Further algorithms may be
found in U.S. application Ser. No. TBA (Broad Reference BI-2012/084
44790.11.2022); incorporated herein by reference.
[0105] 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)
NNNNNNNNNNNNNNNNNNgtttttgtactctcaagatttaGAAAtaaatcttgcagaagctacaaagataagg-
ctt catgccgaaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT
(SEQ ID NO: 22); (2)
NNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaaatca
acaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (SEQ ID NO: 23); (3)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaa-
atca acaccctgtcattttatggcagggtgtTTTTTT (SEQ ID NO: 24); (4)
NNNNNNNNNNNNNNNgttttagagctaGAAAtagcaagttaaaataaggctagtccgttatcaacttgaaaa
agtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 25); (5)
NNNNNNNNNNNNNNNNNNgttttagagctaGAAATAGcaagttaaaataaggctagtccgttatcaacttgaa
aaagtgTTTTTTT (SEQ ID NO: 26); and (6)
NNNNNNNNNNNNNNNNNNNNgttttagagctagAAATAGcaagttaaaataaggctagtccgttatcaTTTTT
TTT (SEQ ID NO: 27). 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).
[0106] 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.
[0107] 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, GAL4 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.
[0108] 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).
[0109] 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.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).
[0110] 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).
[0111] 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.
[0112] 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).
[0113] 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).
[0114] 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 .psi.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 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.
[0115] 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, C1R, 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/AR1,
EMT6/AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, HEK-293, HeLa,
Hepa1c1c7, HL-60, HMEC, HT-29, Jurkat, JY cells, K562 cells, Ku812,
KCL22, KG1, KYO1, 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.
[0116] 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. Transgenic animals are
also provided, as are transgenic plants, especially crops and
algae. The transgenic animal or plant may be useful in applications
outside of providing a disease model. These may include food or
feed production through expression of, for instance, higher
protein, carbohydrate, nutrient or vitamins levels than would
normally be seen in the wildtype. In this regard, transgenic
plants, especially pulses and tubers, and animals, especially
mammals such as livestock (cows, sheep, goats and pigs), but also
poultry and edible insects, are preferred.
[0117] Transgenic algae or other plants such as rape may be
particularly useful in the production of vegetable oils or biofuels
such as alcohols (especially methanol and ethanol), for instance.
These may be engineered to express or overexpress high levels of
oil or alcohols for use in the oil or biofuel industries.
[0118] 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.
[0119] 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.
[0120] 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 14). Accordingly, reference
herein to animal cells may also apply, mutatis mutandis, to plant
cells unless otherwise apparent.
[0121] 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).
[0122] 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 provide individually or in combinations, and may 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.
[0123] 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.
[0124] 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.
[0125] 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 recognised 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.
[0126] 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.
[0127] 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.
[0128] 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.
[0129] 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.
[0130] 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
applications 61/736,527 and 61/748,427. Such genes, proteins and
pathways may be the target polynucleotide of a CRISPR
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 Macular Abcr; Ccl2; Cc2; cp
(ceruloplasmin); Timp3; cathepsinD; Degeneration Vldlr; Ccr2
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 Repeat HTT (Huntington's Dx); SBMA/SMAX1/AR
(Kennedy's Disorders 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
Fragile X Syndrome FMR2; FXR1; FXR2; mGLUR5 Secretase Related APH-1
(alpha and beta); Presenilin (Psen1); nicastrin Disorders (Ncstn);
PEN-2 Others Nos1; Parp1; Nat1; Nat2 Prion - related disorders Prp
ALS SOD1; ALS2; STEX; FUS; TARDBP; VEGF (VEGF-a; VEGF-b; VEGF-c)
Drug addiction Prkce (alcohol); Drd2; Drd4; ABAT (alcohol); GRIA2;
Grm5; Grin1; Htr1b; Grin2a; Drd3; Pdyn; Gria1 (alcohol) Autism
Mecp2; BZRAP1; MDGA2; Sema5A; Neurexin 1; Fragile X (FMR2 (AFF2);
FXR1; FXR2; Mglur5) Alzheimer's Disease E1; CHIP; UCH; UBB; Tau;
LRP; PICALM; Clusterin; PS1; SORL1; CR1; Vldlr; Uba1; 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 Disease
x-Synuclein; DJ-1; LRRK2; Parkin; PINK1
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, FANCF, 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, GBE1, 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, CATF1,
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, PAXIP1L,
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, TRP, 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), Atrophin1 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, PITX3, BFSP2,
CP49, CP47, CRYAA, CRYA1, 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; HSP90AA1; 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; BRAF; 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; ABL1; 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;
CARNS1; 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; PIK2; 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; TRAF8; 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; TP53INP1; 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 Signaling NCOR2; SP1; ARNT; CDKN1B;
FOS; CHEK1; 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;
TNT; RAF1; CREBBP; MAP2K2; PIK3R1; PPP2R5C; MAP2K1; NFTKB1; 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; PDPKI; 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; P1K3C3; 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- I Signaling IGF1; PRKCZ; ELK1; MAPK1;
PTPN11; NEDD4; AKT2; PIK3CA; PRKCI; PTK2; FOS; PIK3CB; PIK3C3;
MAPK8; IGF1R; IRS1; MAPK3; IGFBP7; KRAS; PIK3C2A; YWHAZ; PXN; RAF1;
CASP9; MAP2K2; AKT1; PIK3R1; PDPK1; MAP2K1; IGFBP2; SFN; JUN;
CYR61; AKT3; FOXO1; SRF; CTGF; RPS6KB1 NRF2-mediated PRKCE; EP300;
SOD2; PRKCZ; MAPK1; SQSTM1; Oxidative Stress Response NQO1; PIK3CA;
PRKCI; FOS; PIK3CB; PIK3C3; MAPK8; 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; VAV3; PRKCA G-Protein Coupled PRKCE; RAP1A;
RGS16; MAPK1; GNAS; AKT2; IKBKB; Receptor Signaling PIK3CA; CREB1;
GNAQ; NFKB2; CAMK2A; PIK3CB; PIK3C3; MAPK3; KRAS; RELA; SRC;
PIK3C2A; RAF1; IKBKG; RELB; FYN; MAP2K2; AKT1; 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;
HDACS; CDKN1B; BTRC; Checkpoint Regulation ATR; ABL1; E2F1; HDAC2;
HDAC7A; 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 Metabolism PLK1; AKT2;
CDK8; MAPK8; MAPK3; PRKCD; PRKAA1; 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; HSP90AA1; 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; MAPP2K2; 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 Function MAPK8; ALDH1A1; GSTP1; MAPK9; ABCB1;
TRAF2; 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; IRS1; 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
in the KDR; FLT1; PGF; AKT2; PIK3CA; PIK3CB; PIK3C3; Cardiovascular
System CAV1; PRKCD; NOS3; PIK3C2A; AKT1; PIK3R1; 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; PARK2; 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;
SPHK1; 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; GYP1B1 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; Otx2; Gbx2; FGF-8; Reelin; Dab1;
unc-86 (Pou4f1 or Brn3a); Numb; Reln
[0131] 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.cndot.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.
[0132] 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 sytem 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).
[0133] In yet another aspect of the invention, the CRISPR-Cas
system may be C1 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.
[0134] 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.
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.
[0135] 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 asn
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.
[0136] Examples of proteins associated with Parkinson's disease
include but are not limited to .alpha.-synuclein, DJ-1, LRRK2, PINK
1, Parkin, UCHL1, Synphilin-1, and NURR1.
[0137] Examples of addiction-related proteins may include ABAT for
example.
[0138] Examples of inflammation-related proteins may include the
monocyte chemoattractant protein-1 (MCP1) 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.
[0139] 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), IL4 (interleukin 4), ANGPT1
(angiopoietin 1), ABCG8 (ATP-binding cassette, sub-family G
(WHITE), member 8), or CTSK (cathepsin K), for example.
[0140] 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 (UBE1C) encoded by the UBA3
gene, for example.
[0141] Examples of proteins associated with 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.
[0142] Examples of proteins associated with 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.
[0143] Examples of proteins associated with Schizophrenia may
include NRG1, ErbB4, CPLX1, TPH1, TPH2, NRXN1, GSK3A, BDNF, DISC1,
GSK3B, and combinations thereof.
[0144] 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.
[0145] 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), APH1B (anterior pharynx defective 1 homolog B
(C. elegans)), PSEN2 (presenilin 2 (Alzheimer disease 4)), or BACE1
(beta-site APP-cleaving enzyme 1), for example.
[0146] Examples of proteins associated with Amyotrophic Lateral
Sclerosis may include SOD1 (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.
[0147] Examples of proteins associated with prion diseases may
include SOD1 (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.
[0148] 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 ADRA1D (Alpha-1D adrenergic receptor for Alpha-1D
adrenoreceptor), for example.
[0149] 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.
[0150] 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.
[0151] 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.
[0152] 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.
[0153] 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
[COFS1]; 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.
[0154] Chronic administration of protein therapeutics may elicit
unacceptable immune responses to the specific protein. The
immunogenicity of protein drugs can be ascribed to a few
immunodominant helper T lymphocyte (HTL) epitopes. Reducing the MHC
binding affinity of these HTL epitopes contained within these
proteins can generate drugs with lower immunogenicity (Tangri S, et
al. ("Rationally engineered therapeutic proteins with reduced
immunogenicity" J Immunol. 2005 Mar. 15; 174(6):3187-96.) In the
present invention, the immunogenicity of the CRISPR enzyme in
particular may be reduced following the approach first set out in
Tangri et al with respect to erythropoietin and subsequently
developed. Accordingly, directed evolution or rational design may
be used to reduce the immunogenicity of the CRISPR enzyme (for
instance a Cas9) in the host species (human or other species).
[0155] 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.
[0156] 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
[0157] 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
[0158] 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.
[0159] 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: 3), and
the C-terminal NLS was that of the SV40 large T-antigen (PKKKRKV)
(SEQ ID NO: 2). Of the versions of SpCas9 tested, only
2.times.NLS-SpCas9 exhibited nuclear localization (FIG. 2B).
[0160] 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 171nt that are subsequently processed into
identical 75nt mature tracrRNAs. The shorter 89nt tracrRNA was
selected for expression in mammalian cells (expression constructs
illustrated in FIG. 6, with functionality as determined by results
of Surveryor assay shown in FIG. 6B). 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.
[0161] 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 EMX1
locus (FIG. 2C), a key gene in the development of the cerebral
cortex.
[0162] 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 EM XI locus (see e.g.
Guschin et 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. 4-8,
10 and 11). These results define a three-component system for
efficient CRISPR-mediated genome modification in mammalian
cells.
[0163] 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. 9 provides an additional Northern blot
analysis of crRNA processing in mammalian cells. FIG. 9A
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 and the direct
repeat sequences are shown in the sequence beneath FIG. 9A. The
line indicates the region whose reverse-complement sequence was
used to generate Northern blot probes for EMX1(1) crRNA detection.
FIG. 9B 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.
[0164] 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
a promoter and tracrRNA and pre-crRNA array (DR-Spacer-DR) driven
by the RNA Pol3 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.
[0165] 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).
[0166] Guide sequences can be inserted between BbsI sites using
annealed oligonucleotides. 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 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 (FIGS. 4 and 5).
[0167] FIG. 5 provides a further illustration that SpCas9 can be
reprogrammed to target multiple genomic loci in mammalian cells.
FIG. 5A provides a schematic of the human EMX1 locus showing the
location of five protospacers, indicated by the underlined
sequences. FIG. 5B 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.
5C. Each protospacer is targeted using either processed
pre-crRNA/tracrRNA complex (crRNA) or chimeric RNA (chiRNA).
[0168] 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.
[0169] 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. 3A, including 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.
[0170] 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. 3C). 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. 3C). In the
bacterial assay, all spacers facilitated efficient CRISPR
interference (FIG. 3C). These results suggest that there may be
additional factors affecting the efficiency of CRISPR activity in
mammalian cells.
[0171] 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).
[0172] 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 I catalytic domain of SpCas9 was
engineered to convert the nuclease into a nickase (SpCas9n;
illustrated in FIG. 5A) (see e.g. Sapranausaks et al., 2011,
Cucleic Acis 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.
[0173] 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. 5G) was detected.
This demonstrates that the CRISPR system can mediate multiplexed
editing within a single genome.
Example 2
CRISPR System Modifications and Alternatives
[0174] 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. 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. 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. 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. 7.
Example 3
Sample Target Sequence Selection Algorithm
[0175] 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.sub.x-NNAGAAW-3' 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.sub.x-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.
[0176] 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).
[0177] Further details of methods and algorithms to optimize
sequence selection can be found in U.S. application Ser. No. TBA
(Broad Reference BI-2012/084 44790.11.2022); incorporated herein by
reference.
Example 4
Evaluation of Multiple Chimeric crRNA-tracrRNA Hybrids
[0178] 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: 28) 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. 11a
and 11b, corresponding to FIGS. 10b and 10c, 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 protospacer genomic SEQ ID target
protospacer sequence (5' to 3') PAM Strand ID NO: 1 EMX1
GGACATCGATGTCACCTCCAATGACTAGGG TGG + 29 2 EMX1
CATTGGAGGTGACATCGATGTCCTCCCCAT TGG - 30 3 EMX1
GGAAGGGCCTGAGTCCGAGCAGAAGAAGAA GGG + 31 4 PVALB
GGTGGCGAGAGGGGCCGAGATTGGGTGTTC AGG + 32 5 PVALB
ATGCAGGAGGGTGGCGAGAGGGGCCGAGAT TGG + 33
Cell Culture and Transfection
[0179] 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 .mu.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.
SURVEYOR Assay for Genome Modification
[0180] 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, 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.
TABLE-US-00005 TABLE E genomic SEQ primer name target primer
sequence (5' to 3') ID NO Sp-EMX1-F EMX1 AAAACCACCCTTCTCTCTGGC 34
Sp-EMX1-R EMX1 GGAGATTGGAGACACGGAGAG 35 Sp-PVALB-F PVALB
CTGGAAAGCCAATGCCTGAC 36 Sp-PVALB-R PVALB GGCAGCAAACTCCTTGTCCT
37
Computational Identification of Unique CRISPR Target Sites
[0181] 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. 22.
[0182] 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.
10b and 10a). 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.
10c and 10b).
[0183] 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 (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) 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.
[0184] FIGS. 11 and 21 illustrate exemplary bicistronic expression
vectors 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
(tracr mate sequence GTTTTAGAGCTA (SEQ ID NO: 38), 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".
[0185] Sequences described 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: 39)
GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGGCTGTTAGAGAGATAATTGGAATTAA-
TT
TGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCAGTT-
TT
AAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGATTTCTTGGCTTTATATA-
TC
TTGTGGAAAGGACGAAACACCGGAACCATTCAAAACAGCATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC-
TT GAAAAAGTGGCACCGAGTCGGTGCTTTTTTT (bold = tracrRNA sequence;
underline = terminator sequence) U6-long tracrRNA (Streptococcus
pyogenes SF370): (SEQ ID NO: 40)
GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGGCTGTTAGAGAGATAATTGGAATTAA-
TT
TGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCAGTT-
TT
AAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGATTTCTTGGCTTTATATA-
TC
TTGTGGAAAGGACGAAACACCGGTAGTATTAAGTATTGTTTTATGGCTGATAAATTTCTTTGAATTTCTCCTTG-
AT
TATTTGTTATAAAAGTTATAAAATAATCTTGTTGGAACCATTCAAAACAGCATAGCAAGTTAAAATAAGGCTAG-
TC CGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT U6-DR-BbsI
backbone-DR (Streptococcus pyogenes SF370): (SEQ ID NO: 41)
GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGGCTGTTAGAGAGATAATTGGAATTAA-
TT
TGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCAGTT-
TT
AAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGATTTCTTGGCTTTATATA-
TC
TTGTGGAAAGGACGAAACACCGGGTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAACGGGTCTTCGAGAAGA-
CG TTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC U6-chimeric RNA-BbsI
backbone (Streptococcus pyogenes SF370) (SEQ ID NO: 42)
GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGGCTGTTAGAGAGATAATTGGAATTAA-
TT
TGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCAGTT-
TT
AAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGATTTCTTGGCTTTATATA-
TC
TTGTGGAAAGGACGAAACACCGGGTCTTCGAGAAGACCTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGC-
TA GTCCG NLS-SpCas9-EGFP: (SEQ ID NO: 43)
MDYKDHDGYKDHDIDYKDDDDKMAPKKKRKVGIHGVPAADKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLG-
NT
DRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKK-
HE
RHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQL-
VQ
TYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKL-
QL
SKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVR-
QQ
LPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHL-
GE
LHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFI-
ER
MTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDY-
FK
KIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFD-
DK
VMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDLSTFKEDIQKAQVSGQGDSL-
HE
HIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQIL-
KE
HPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPE-
EV
VKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKL-
IR
EVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKS-
EQ
EIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQ-
TG
GFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKN-
PI
DFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNE-
QK
QLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDT-
TI
DRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDAAAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGE-
GD
ATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRA-
EV
KGEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNT-
PI GDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK
SpCas9-EGFP-NLS: (SEQ ID NO: 44)
MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTR-
RK
NRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKAD-
LR
LIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLI-
AQ
LPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILL-
SD
ILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKP-
IL
EKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVVG-
PL
ARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKY-
VT
EGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKD-
FL
DNEEDNEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTIL-
DF
LKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKP-
EN
IVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINR-
LS
DYDVDHIVPQSFLKKSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLS-
EL
DKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAH-
DA
YLNAVVGTALIKKYPKLESEFVYGDYKVYDVRMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPL-
IE
TNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPT-
VA
YSVLVVAKEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLEFELENGRKRML-
AS
AGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKV-
LS
AYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLG-
GD
AAAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCF-
SR
YPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNS-
HN
VYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEF-
VT AAGITLGMDELYKKRPAATKKAGQAKKKK NLS-SpCas9-EGFP-NLS: (SEQ ID NO:
45)
MDYKDHDGYKDHDIDYKDDDDKMAPKKKRKVGIHGVPAADKKYSIGLDIGTNSVGWAVITDYEKVPSKKFKVLG-
NT
DRHSIKKNLIGALLFDSGETAEATRLKTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKH-
ER
HPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLV-
QT
YNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQ-
LS
KDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDIRLVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQ-
QL
PEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLG-
EL
HAILRRQEDFYPFLKDNREKIEKLILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFI-
ER
MTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDY-
FK
KIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFD-
DK
VMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL-
HE
HIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQIL-
KE
HPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPS-
EE
VVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDK-
LI
REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAK-
SE
QEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEV-
QT
GGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEK-
NP
IDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDN-
EQ
KQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFD-
TT
IDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDAAAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEG-
EG
DATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTR-
AE
VKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQN-
TP
IGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKKRPAATKKAGQAKKKK
NLS-SpCas9-NLS: (SEQ ID NO: 46)
MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGIHGVPAADKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVL-
GN
TDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDK-
KH
ERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQ-
LV
QTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAK-
LQ
LSKDYTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDIRLVNTEITKAPLSASMIKRYDEHHQDLTLLKAL-
VR
QQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQI-
HL
GELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQS-
FI
ERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKE-
DY
FKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEKTILDFLKSDGFANRNFMQLIHDDS-
LT
FKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNS-
RE
RMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSID-
NK
VLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITK-
HV
AQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLE-
SE
FVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFA-
TV
RKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKL-
KS
VKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYV-
NF
LYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENI-
IH
LFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDKRPAATKKAGQAKKKK
NLS-mCherry-SpRNase3: (SEQ ID NO: 47)
MFLFSLTSFLSSSRTLVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPL-
PF
AWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFP-
SD
GPVMQKKTMGWEASSSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHN-
ED
YTIVEQYERAEGRHSTGGMDELYKGSKQLEELLSTSFDIQFNDLTLLETAFTHTSYANEHRLLNVSHNERLEFL-
GD
AVLQLIISEYLFAKYPKKTEGDMSKLRSMIVREESLAGFSRFCSFDAYIKLGKGEEKSGGRRRDTILGDLFEAF-
LG
ALLLDKGIDAVRRFLKQVMIPQVEKGNFERVKDYKTCLQEFLQTKGDVAIDYQVISEKGPAHAKQFEVSIVVNG-
AV LSKGLGKSKKALEQDAAKNALALQLSEV SpRNase3-mCherry-NLS: (SEQ ID NO:
48)
MKQLEELLSTSFDIQFNDLTLLETAFTHTSYANEHRLLNVSHNERLEFLGDAVLQLIISEYLFAKYPKKTEGDM-
SK
LRSMIVREESLAGFSRFCSFDAYIKLGKGEEKSGGRRRDTILGDLFEAFLGALLLDKGIDAVRRFLKQVMIPQV-
EK
GNFERVKDYKTCLQEFLQTKGDVAIDYQVISEKGPAHAKQFEVSIVVNGAVLSKGLGKSKKLAEQDAAKNALAQ-
LS
EVGSVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFM-
YG
SKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMG-
WE
ASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAE-
GR HSTGGMDELYKKRPAATKKAGQAKKKK NLS-SpCas9n-NLS (the D10A nickase
mutation is lowercase): (SEQ ID NO: 49)
MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGIHGVPAADKKYSIGLaIGTNSVGWAVITDEYKVPSKKFKVL-
GN
TDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDK-
KH
ERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQ-
LV
QTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAK-
LQ
LSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALV-
RQ
QLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIH-
LG
ELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSF-
IE
RMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKED-
YF
KKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEEDEDILEDIVLTLTLFEDREMIEERLKTYAHLF-
DD
KVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDS-
LH
EHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKSRERMKRIEEGIKELGSQIL-
KE
HPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPS-
EE
VVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDK-
LI
REVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAK-
SE
QEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEV-
QT
GGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEK-
NP
IDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDN-
EQ
KQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFD-
TT IDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDKRPAATKKAGQAKKKK hEMX1-HR
Template-HindIII-NheI: (SEQ ID NO: 50)
GAATGCTGCCCTCAGACCCGCTTCCTCCCTGTCCTTGTCTGTCCAAGGAGAATGAGGTCTCACTGGTGGATTTC-
GG
ACTACCCTGAGGAGCTGGCACCTGAGGGACAAGGCCCCCCACCTGCCCAGCTCCAGCCTCTGATGAGGGGTGGG-
AG
AGAGCTACATGAGGTTGCTAAGAAAGCCTCCCCTGAAGGAGACCACACAGTGTGTGAGGTTGGAGTCTCTAGCA-
GC
GGGTTCTGTGCCCCCAGGGATAGTCTGGCTGTCCAGGCACTGCTCTTGATATAAACACCACCTCCTAGTTATGA-
AA
CCATGCCCATTCTGCCTCTCTGTATGGAAAAGAGCATGGGGCTGGCCCGTGGGGTGGTGTCCACTTTAGGCCCT-
GT
GGGAGATCATGGGAACCCACGCAGTGGGTCATAGGCTCTCTCATTTACTACTCACATCCACTCTGTGAAGAAGC-
GA
TTATGATCTCTCCTCTAGAAACTCGTAGAGTCCCATGTCTGCCGGCTTCCAGAGCCTGCACTCCTCCACCTTGG-
CT
TGGCTTTGCTGGGGCTAGAGGAGCTAGGATGCACAGCAGCTCTGTGACCCTTTGTTTGAGAGGAACAGGAAAAC-
CA
CCCTTCTCTCTGGCCCACTGTGTCCTCTTCCTGCCCTGCCATCCCCTTCTGTGAATGTTAGACCCATGGGAGCA-
GC
TGGTCAGAGGGGACCCCGGCCTGGGGCCCCTAACCCTATGTAGCCTCAGTCTTCCCATCAGGCTCTCAGCTCAG-
CC
TGAGTGTTGAGGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCA-
GG
TGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTACAAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAG-
CA
GAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATGGGGAGGACATCGATG-
TC
ACCTCCAATGACaagcttgctagcGGTGGGCAACCACAAACCCACGAGGGCAGAGTGCTGCTTGCTGCTGGCCA-
GG
CCCCTGCGTGGGCCCAAGCTGGACTCTGGCCACTCCCTGGCCAGGCTTTGGGGAGGCCTGGAGTCATGGCCCCA-
CA
GGGCTTGAAGCCCGGGGCCGCCATTGACAGAGGGACAAGCAATGGGCTGGCTGAGGCCTGGGACCACTTGGCCT-
TC
TCCTCGGAGAGCCTGCCTGCCTGGGCGGGCCCGCCCGCCACCGCAGCCTCCCAGCTGCTCTCCGTGTCTCCAAT-
CT
CCCTTTTGTTTTGATGCATTTCTGTTTTAATTTATTTTCCAGGCACCACTGTAGTTTAGTGATCCCCAGTGTCC-
CC
CTTCCCTATGGGAATAATAAAAGTCTCTCTCTTAATGACACGGGCATCCAGCTCCAGCCCCAGAGCCTGGGGTG-
GT
AGATTCCGGCTCTGAGGGCCAGTGGGGGCTGGTAGAGCAAACGCGTTCAGGGCCTGGGAGCCTGGGGTGGGGTA-
CT
GGTGGAGGGGGTCAAGGGTAATTCATTAACTCCTCTCTTTTGTTGGGGGACCCTGGTCTCTACCTCCAGCTCCA-
CA
GCAGGAGAAACAGGCTAGACATAGGGAAGGGCCATCCTGTATCTTGAGGGAGGACAGGCCCAGGTCTTTCTTAA-
CG
TATTGAGAGGTGGGAATCAGGCCCAGGTAGTTCAATGGGAGAGGGAGAGTGCTTCCCTCTGCCTAGAGACTCTG-
GT
GGCTTCTCCAGTTGAGGAGAAACCAGAGGAAAGGGGAGGATTGGGGTCTGGGGGAGGGAACACCATTCACAAAG-
GC
TGACGGTTCCAGTCCGAAGTCGTGGGCCCACCAGGATGCTCACCTGTCCTTGGAGAACCGCTGGGCAGGTTGAG-
AC
TGCAGAGACAGGGCTTAAGGCTGAGCCTGCAACCAGTCCCCAGTGACTCAGGGCCTCCTCAGCCCAAGAAAGAG-
CA ACGTGCCAGGGCCCGCTGAGCTCTTGTGTTCACCTG NLS-StCsn1-NLS: (SEQ ID NO:
51)
MKRPAATKKAGQAKKKKSDLVLGLDIGIGSVGVGILNKVTGEIIHKNSRIFPAAQAENNLVRRTNRQGRRLARR-
KK
HRRVRLNRLFEESGLITDFTKISINLNPYQLRVKGLTDELSNEELFIALKNMVKHRGISYLDDASDDGNSSVGD-
YA
QIVKENSKQLETKTPGQIQLERYQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSEALRILQTQQEFNPQITDE-
FI
NRYLEILTGKRKYYHGPGNEKSRTDYGRYRTSGETLDNIFGILIGKCRFYPDEFRAAKASYTAQEFNLLNDLNN-
LT
VPTETKKLSKEQKNQIINYVKNEKAMGPAKLFKYIAKLLSCDVADIKGYRIDKSGKAEIHTFEAYRKMKTLETL-
DI
EQMDRETLDKLAYVLTLNTEREGIQEALEHEFADGSFSQKQVDELVQFRKANSSIFGKGWHNFSVKLMMELIPE-
LY
ETSEEQMTILTRLGKQKTTSSSNKTKYIDEKLLTEEIYNPVVAKSVRQAIKIVNAAIKEYGDFDNIVIEMARET-
NE
DDEKKAIQKIQKANKDEKDAAMLKAANQYNGKAELPHSVFHGHKQLATKIRLWHQQGERCLYTGKTISIHDLIN-
NS
QFEVDHILPLSITFDDSLANKVLVYATANQEKGQRTPYQALDSMDDAWSFRELKAFVRESKTLSNKKKEYLLTE-
ED
ISKFDVRKKFIERNLVDTRYASRVVLNALQEHFRAHKIDTKVSVVRGQFTSQLRRHWGIEKTRDTYHHHAVDAL-
II
AASSQLNLWKKQKNTLVSYSEDQLLDIETGELISDDEYKESVFKAPYQHFVDTLKSKEFEDSILFSYQVDSKFN-
RK
ISDATIYATRQAKVGKDKADETYVLGKIKDIYTQDGYDAFMKIYKKDKSKFLMYRHDPQTFEKVIEPILENYPN-
KQ
INEKGKEVPCNPFLKYKEEHGYIRKYSKKGNGPEIKSLKYYDSKLGNHIDITPKDSNNKVVLQSVSPWRADVYF-
NK
TTGKYEILGLKYADLQFEKGTGTYKISQEKYNDIKKKEGVDSDSEFKFTLYKNDLLLVKDTETKEQQLFRFLSR-
TM
PKQKHYVELKPYDKQKFEGGEALIKVLGNVANSGQCKKGLGKSNISIYKVRTDVLGNQHIIKNEGDKPKLDFKR-
PA ATKKAGQAKKKK U6-St_tracrRNA(7-97): (SEQ ID NO: 52)
GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGGCTGTTAGAGAGATAATTGGAATTAA-
TT
TGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGGTAGTTTGCAGTT-
TT
AAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGATTTCTTGGCTTTATATA-
TC
TTGTGGAAAGGACGAAACACCGTTACTTAAATCTTGCAGAAGCTACAAAGATAAGGCTTCATGCCGAAATCAAC-
AC CCTGTCATTTTATGGCAGGGTGTTTTCGTTATTTAA U6-DR-spacer-DR (S.
pyogenes SF370) (SEQ ID NO: 53)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattggaattaa-
tt
tgactgtaaacacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagtt-
tt
aaaattatgttttaaaatggactatcatatgcttaccgtaacttgaaagtatttcgatttcttggctttatata-
tc
ttgtggaaaggacgaaacaccgggttttagagctatgctgttttgaatggtcccaaaacNNNNNNNNNNNNNNN-
NN NNNNNNNNNNNNNgttttagagctatgctgttttgaatggtcccaaaacTTTTTTT
(lowercase underline = direct repeat; N = guide sequence; bold =
terminator) Chimeric RNA containing +48 tracr RNA (S. pyogenes
SF370) (SEQ ID NO: 54)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattggaattaa-
tt
tgactgtaaacacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagtt-
tt
aaaattatgttttaaaatggactatcatatgcttaccgtaacttgaaagtatttcgatttcttggctttatata-
tc
ttgtggaaaggacgaaacaccNNNNNNNNNNNNNNNNNNNNgttttagagctagaaatagcaagttaaaataag-
gc tagtccgTTTTTTT (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: 55)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattggaattaa-
tt
tgactgtaaacacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagtt-
tt
aaaattatgttttaaaatggactatcatatgcttaccgtaacttgaaagtatttcgatttcttggctttatata-
tc
ttgtggaaaggacgaaacaccNNNNNNNNNNNNNNNNNNNNgttttagagctagaaatagcaagttaaaataag-
gc tagtccgttatcaTTTTTTT (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: 56)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattggaattaa-
tt
tgactgtaaacacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagtt-
tt
aaaattatgttttaaaatggactatcatatgcttaccgtaacttgaaagtatttcgatttcttggctttatata-
tc
ttgtggaaaggacgaaacaccNNNNNNNNNNNNNNNNNNNNgttttagagctagaaatagcaagttaaaataag-
gc tagtccgttatcaacttgaaaaagtgTTTTTTT (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: 57)
gagggcctatttcccatgattccttcatatttgcatatacgatacaaggctgttagagagataattggaattaa-
tt
tgactgtaaacacaaagatattagtacaaaatacgtgacgtagaaagtaataatttcttgggtagtttgcagtt-
tt
aaaattatgttttaaaatggactatcatatgcttaccgtaacttgaaagtatttcgatttcttggctttatata-
tc
ttgtggaaaggacgaaacaccNNNNNNNNNNNNNNNNNNNNgttttagagctagaaatagcaagttaaaataag-
gc tagtccgttatcaacttgaaaaagtggcaccgagtcggtgcTTTTTTT (N = guide
sequence; first underline = tracr mate sequence; second underline =
tracr sequence; bold = terminator) CBh-NLS-SpCas9-NLS (SEQ ID NO:
58)
CGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCAACGACCCCCGCCCATTGACGTCAATAATGA-
CG
TATGTTCCCATAGTAACGCCAATAGGGACTTTCCATTGACGTCAATGGGTGGAGTATTTACGGTAAACTGCCCA-
CT
TGGCAGTACATCAAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCTGG-
CA
TTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTATTAGTCATCGCTATTACCA-
TG
GTCGAGGTGAGCCCCACGTTCTGCTTCACTCTCCCCATCTCCCCCCCCTCCCCACCCCCAATTTTGTATTTATT-
TA
TTTTTTAATTATTTTGTGCAGCGATGGGGGCGGGGGGGGGGGGGGGGCGCGCGCCAGGCGGGGCGGGGCGGGGC-
GA
GGGGCGGGGCGGGGCGAGGCGGAGAGGTGCGGCGGCAGCCAATCAGAGCGGCGCGCAGCGCGCGGCGGGCGGGA-
GT
CGCTGCGACGCTGCCTTCGCCCCGTGCCCCGCTCCGCCGCCGCCTCGCGCCGCCCGCCCCGGCTCTGACTGACC-
GC
GTTACTCCCACAGGTGAGCGGGCGGGACGGCCCTTCTCCTCCGGGCTGTAATTAGCTGAGCAAGAGGTAAGGGT-
TT
AAGGGATGGTTGGTTGGTGGGGTATTAATGTTTAATTACCTGGAGCACCTGCCTGAAATCACTTTTTTTCAGGT-
TG
GaccggtgccaccATGGACTATAAGGACCACGACGGAGACTACAAGGATCATGATATTGATTACAAAGACGATG-
AC
GATAAGATGGCCCCAAAGAAGAAGCGGAAGGTCGGTATCCACGGAGTCCCAGCAGCCGACAAGAAGTACAGCAT-
CG
GCCTGGACATCGGCACCAACTCTGTGGGCTGGGCCGTGATCACCGACGAGTACAAGGTGCCCAGCAAGAAATTC-
AA
GGTGCTGGGCAACACCGACCGGCACAGCATCAAGAAGAACCTGATCGGAGCCCTGCTGTTCGACAGCGGCGAAA-
CA
GCCGAGGCCACCCGGCTGAAGAGAACCGCCAGAAGAAGATACACCAGACGGAAGAACCGGATCTGCTATCTGCA-
AG
AGATCTTCAGCAACGAGATGGCCAAGGTGGACGACAGCTTCTTCCACAGACTGGAAGAGTCCTTCCTGGTGGAA-
GA
GGATAAGAAGCACGAGCGGCACCCCATCTTCGGCAACATCGTGGACGAGGTGGCCTACCACGAGAAGTACCCCA-
CC
ATCTACCACCTGAGAAAGAAACTGGTGGACAGCACCGACAAGGCCGACCTGCGGCTGATCTATCTGGCCCTGGC-
CC
ACATGATCAAGTTCCGGGGCCACTTCCTGATCGAGGGCGACCTGAACCCCGACAACAGCGACGTGGACAAGCTG-
TT
CATCCAGCTGGTGCAGACCTACAACCAGCTGTTCGAGGAAAACCCCATCAACGCCAGCGGCGTGGACGCCAAGG-
CC
ATCCTGTCTGCCAGACTGAGCAAGAGCAGACGGCTGGAAAATCTGATCGCCCAGCTGCCCGGCGAGAAGAAGAA-
TG
GCCTGTTCGGCAACCTGATTGCCCTGAGCCTGGGCCTGACCCCCAACTTCAAGAGCAACTTCGACCTGGCCGAG-
GA
TGCCAAACTGCAGCTGAGCAAGGACACCTACGACGACGACCTGGACAACCTGCTGGCCCAGATCGGCGACCAGT-
AC
GCCGACCTGTTTCTGGCCGCCAAGAACCTGTCCGACGCCATCCTGCTGAGCGACATCCTGAGAGTGAACACCGA-
GA
TCACCAAGGCCCCCCTGAGCGCCTCTATGATCAAGAGATACGACGAGCACCACCAGGACCTGACCCTGCTGAAA-
GC
TCTCGTGCGGCAGCAGCTGCCTGAGAAGTACAAAGAGATTTTCTTCGACCAGAGCAAGAACGGCTACGCCGGCT-
AC
ATTGACGGCGGAGCCAGCCAGGAAGAGTTCTACAAGTTCATCAAGCCCATCCTGGAAAAGATGGACGGCACCGA-
GG
AACTGCTCGTGAAGCTGAACAGAGAGGACCTGCTGCGGAAGCAGCGGACCTTCGACAACGGCAGCATCCCCCAC-
CA
GATCCACCTGGGAGAGCTGCACGCCATTCTGCGGCGGCAGGAAGATTTTTACCCATTCCTGAAGGACAACCGGG-
AA
AAGATCGAGAAGATCCTGACCTTCCGCATCCCCTACTACGTGGGCCCTCTGGCCAGGGGAAACAGCAGATTCGC-
CT
GGATGACCAGAAAGAGCGAGGAAACCATCACCCCCTGGAACTTCGAGGAAGTGGTGGACAAGGGCGCTTCCGCC-
CA
GAGCTTCATCGAGCGGATGACCAACTTCGATAAGAACCTGCCCAACGAGAAGGTGCTGCCCAAGCACAGCCTGC-
TG
TACGAGTACTTCACCGTGTATAACGAGCTGACCAAAGTGAAATACGTGACCGAGGGAATGAGAAAGCCCGCCTT-
CC
TGAGCGGCGAGCAGAAAAAGGCCATCGTGGACCTGCTGTTCAAGACCAACCGGAAAGTGACCGTGAAGCAGCTG-
AA
AGAGGACTACTTCAAGAAAATCGAGTGCTTCGACTCCGTGGAAATCTCCGGCGTGGAAGATCGGTTCAACGCCT-
CC
CTGGGCACATACCACGATCTGCTAAAATTATCAAGGACAAGGACTTCCTGGACAATGAGGAAAACGAGGACATT-
CT
GGAAGATATCGTGCTGACCCTGACACTGTTTGAGGACAGAGAGATGATCGAGGAACGGCTGAAAACCTATGCCC-
AC
CTGTTCGACGACAAAGTGATGAAGCAGCTGAAGCGGCGGAGATACACCGGCTGGGGCAGGCTGAGCCGGAAGCT-
GA
TCAACGGCATCCGGGACAAGCAGTCCGGCAAGACAATCCTGGATTTCCTGAAGTCCGACGGCTTCGCCAACAGA-
AA
CTTCATGCAGCTGATCCACGACGACAGCCTGACCTTTAAAGAGGACATCCAGAAAGCCCAGGTGTCCGGCCAGG-
GC
GATAGCCTGCACGAGCACATTGCCAATCTGGCCGGCAGCCCCGCCATTAAGAAGGGCATCCTGCAGACAGTGAA-
GG
TGGTGGACGAGCTCGTGAAAGTGATGGGCCGGCACAAGCCCGAGAACATCGTGATCGAAATGGCCAGAGAGAAC-
CA
GACCACCCAGAAGGGACAGAAGAACAGCCGCGAGAGAATGAAGCGGATCGAAGAGGGCATCAAAGAGCTGGGCA-
GC
CAGATCCTGAAAGAACACCCCGTGGAAAACACCCAGCTGCAGAACGAGAAGCTGTACCTGTACTACCTGCAGAA-
TG
GGCGGGATATGTACGTGGACCAGGAACTGGACATCAACCGGCTGTCCGACTACGATGTGGACCATATCGTGCCT-
CA
GAGCTTTCTGAAGGACGACTCCATCGACAACAAGGTGCTGACCAGAAGCGACAAGAACCGGGGCAAGAGCGACA-
AC
GTGCCCTCCGAAGAGGTCGTGAAGAAGATGAAGAACTACTGGCGGCAGCTGCTGAACGCCAAGCTGATTACCCA-
GA
GAAAGTTCGACAATCTGACCAAGGCCGAGAGAGGCGGCCTGAGCGAACTGGATAAGGCCGGCTTCATCAAGAGA-
CA
GCTGGTGGAAACCCGGCAGATCACAAAGCACGTGGCACAGATCCTGGACTCCCGGATGAACACTAAGTACGACG-
AG
AATGACAAGCTGATCCGGGAAGTGAAAGTGATCACCCTGAAGTCCAAGCTGGTGTCCGATTTCCGGAAGGATTT-
CC
AGTTTTACAAAGTGCGCGAGATCAACAACTACCACCACGCCCACGACGCCTACCTGAACGCCGTCGTGGGAACC-
GC
CTGATCAAAAAGTACCCTAAGCTGGAAAGCGAGTTCGTGTACGGCGACTACAAGGTGTACGACGTGCGGAAGAT-
GA
TCGCCAAGAGCGAGCAGGAAATCGGCAAGGCTACCGCCAAGTACTTCTTCTACAGCAACATCATGAACTTTTTC-
AA
GACCGAGATTACCCTGGCCAACGGCGAGATCCGGAAGCGGCCTCTGATCGAGACAAACGGCGAAACCGGGGAGA-
TC
GTGTGGGATAAGGGCCGGGATTTTGCCACCGTGCGGAAAGTGCTGAGCATGCCCCAAGTGAATATCGTGAAAAA-
GA
CCGAGGTGCAGACAGGCGGCTTCAGCAAAGAGTCTATCCTGCCCAAGAGGAACAGCGATAAGCTGATCGCCAGA-
AA
GAAGGACTGGGACCCTAAGAAGTACGGCGGCTTCGACAGCCCCACCGTGGCCTATTCTGTGCTGGTGGTGGCCA-
AA
GTGGAAAAGGGCAAGTCCAAGAAACTGAAGAGTGTGAAAGAGCTGCTGGGGATCACCATCATGGAAAGAAGCAG-
CT
TCGAGAAGAATCCCATCGACTTTCTGGAAGCCAAGGGCTACAAAGAAGTGAAAAAGGACCTGATCATCAAGCTG-
CC
TAAGTACTCCCTGTTCGAGCTGGAAAACGGCCGGAAGAGAATGCTGGCCTCTGCCGGCGAACTGCAGAAGGGAA-
AC
GAACTGGCCCTGCCCTCCAAATATGTGAACTTCCTGTACCTGGCCAGCCACTATGAGAAGCTGAAGGGCTCCCC-
CG
AGGATAATGAGCAGAAACAGCTGTTTGTGGAACAGCACAAGCACTACCTGGACGAGATCATCGAGCAGATCAGC-
GA
GTTCTCCAAGAGAGTGATCCTGGCCGACGCTAATCTGGACAAAGTGCTGTCCGCCTACAACAAGCACCGGGATA-
AG
CCCATCAGAGAGCAGGCCGAGAATATCATCCACCTGTTTACCCTGACCAATCTGGGAGCCCCTGCCGCCTTCAA-
GT
ACTTTGACACCACCATCGACCGGAAGAGGTACACCAGCACCAAAGAGGTGCTGGACGCCACCCTGATCCACCAG-
AG
CATCACCGGCCTGTACGAGACACGGATCGACCTGTCTCAGCTGGGAGGCGACTTTCTTTTTCTTAGCTTGACCA-
GC TTTCTTAGTAGCAGCAGGACGCTTTAA Example chimeric RNA for S.
thermophilus LMD-9 CRISPR1 Cas9 (with PAM of NNAGAAW) (SEQ ID NO:
59)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaagatttaGAAAtaaatcttgcagaagctacaaagataag-
gc ttcatgccgaaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (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)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaaa-
tc aacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (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)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaaa-
tc aacaccctgtcattttatggcagggtgtTTTTTT (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)
NNNNNNNNNNNNNNNNNNNNgttattgtactctcaagatttaGAAAtaaatcttgcagaagctacaaagataag-
gc ttcatgccgaaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (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)
NNNNNNNNNNNNNNNNNNNNgttattgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaaa-
tc aacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (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)
NNNNNNNNNNNNNNNNNNNNgttattgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaaa-
tc aacaccctgtcattttatggcagggtgtTTTTTT (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)
NNNNNNNNNNNNNNNNNNNNgttattgtactctcaagatttaGAAAtaaatcttgcagaagctacaatgataag-
gc ttcatgccgaaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (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: 66)
NNNNNNNNNNNNNNNNNNNNgttattgtactctcaGAAAtgcagaagctacaatgataaggcttcatgccgaaa-
tc aacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (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:
67)
NNNNNNNNNNNNNNNNNNNNgttattgtactctcaGAAAtgcagaagctacaatgataaggcttcatgccgaaa-
tc aacaccctgtcattttatggcagggtgtTTTTTT (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: 68)
NNNNNNNNNNNNNNNNNNNNgttttagagctgtgGAAAcacagcgagttaaaataaggcttagtccgtactcaa-
ct tgaaaaggtggcaccgattcggtgtTTTTTT (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 NLS at both 5' and 3' ends) (SEQ ID NO: 69)
ATGAAAAGGCCGGCGGCCACGAAAAAGGCCGGCCAGGCAAAAAAGAAAAAGACCAAGCCCTACAGCATCGGCCT-
GG
ACATCGGCACCAATAGCGTGGGCTGGGCCGTGACCACCGACAACTACAAGGTGCCCAGCAAGAAAATGAAGGTG-
CT
GGGCAACACCTCCAAGAAGTACATCAAGAAAAACCTGCTGGGCGTGCTGCTGTTCGACAGCGGCATTACAGCCG-
AG
GGCAGACGGCTGAAGAGAACCGCCAGACGGCGGTACACCCGGCGGAGAAACAGAATCCTGTATCTGCAAGAGAT-
CT
TCAGCACCGAGATGGCTACCCTGGACGACGCCTTCTTCCAGCGGCTGGACGACAGCTTCCTGGTGCCCGACGAC-
AA
GCGGGACAGCAAGTACCCCATCTTCGGCAACCTGGTGGAAGAGAAGGCCTACCACGACGAGTTCCCCACCATCT-
AC
CACCTGAGAAAGTACCTGGCCGACAGCACCAAGAAGGCCGACCTGAGACTGGTGTATCTGGCCCTGGCCCACAT-
GA
TCAAGTACCGGGGCCACTTCCTGATCGAGGGCGAGTTCAACAGCAAGAACAACGACATCCAGAAGAACTTCCAG-
GA
CTTCCTGGACACCTACAACGCCATCTTCGAGAGCGACCTGTCCCTGGAAAACAGCAAGCAGCTGGAAGAGATCG-
TG
AAGGACAAGATCAGCAAGCTGGAAAAGAAGGACCGCATCCTGAAGCTGTTCCCCGGCGAGAAGAACAGCGGAAT-
CT
TCAGCGAGTTTCTGAAGCTGATCGTGGGCAACCAGGCCGACTTCAGAAAGTGCTTCAACCTGGACGAGAAAGCC-
AG
CCTGCACTTCAGCAAAGAGAGCTACGACGAGGACCTGGAAACCCTGCTGGGATATATCGGCGACGACTACAGCG-
AC
GTGTTCCTGAAGGCCAAGAAGCTGTACGACGCTATCCTGCTGAGCGGCTTCCTGACCGTGACCGACAACGAGAC-
AG
AGGCCCCACTGAGCAGCGCCATGATTAAGCGGTACAACGAGCACAAAGAGGATCTGGCTCTGCTGAAAGAGTAC-
AT
CCGGAACATCAGCCTGAAAACCTACAATGAGGTGTTCAAGGACGACACCAAGAACGGCTACGCCGGCTACATCG-
AC
GGCAAGACCAACCAGGAAGATTTCTATGTGTACCTGAAGAAGCTGCTGGCCGAGTTCGAGGGGGCCGACTACTT-
TC
TGGAAAAAATCGACCGCGAGGATTTCCTGCGGAAGCAGCGGACCTTCGACAACGGCAGCATCCCCTACCAGATC-
CA
TCTGCAGGAAATGCGGGCCATCCTGGACAAGCAGGCCAAGTTCTACCCTTCCTGGCCAAGAACAAAGAGCGGAT-
CG
AGAAGATCCTGACCTTCCGCATCCCTTACTACGTGGGCCCCCTGGCCAGAGGCAACAGCGATTTTGCCTGGTCC-
AT
CCGGAAGCGCAATGAGAAGATCACCCCCTGGAACTTCGAGGACGTGATCGACAAAGAGTCCAGCGCCGAGGCCT-
TC
ATCAACCGGATGACCAGCTTCGACCTGTACCTGCCCGAGGAAAAGGTGCTGCCCAAGCACAGCCTGCTGTACGA-
GA
CATTCAATGTGTATAACGAGCTGACCAAAGTGCGGTTTATCGCCGAGTCTATGCGGGACTACCAGTTCCTGGAC-
TC
CAAGCAGAAAAAGGACATCGTGCGGCTGTACTTCAAGGACAAGCGGAAAGTGACCGATAAGGACATCATCGAGT-
AC
CTGCACGCCATCTACGGCTACGATGGCATCGAGCTGAAGGGCATCGAGAAGCAGTTCAACTCCAGCCTGAGCAC-
AT
ACCACGACCTGCTGAACATTATCAACGACAAAGAATTTCTGGACGACTCCAGCAACGAGGCCATCATCGAAGAG-
AT
CATCCACACCCTGACCATCTTTGAGGACCGCGAGATGATCAAGCAGCGGCTGAGCAAGTTCGAGAACATCTTCG-
AC
AAGAGCGTGCTGAAAAAGCTGAGCAGACGGCACTACACCGGCTGGGGCAAGCTGAGCGCCAAGCTGATCAACGG-
CA
TCCGGGACGAGAAGTCCGGCAACACAATCCTGGACTACCTGATCGACGACGGCATCAGCAACCGGAACTTCATG-
CA
GCTGATCCACGACGACGCCCTGAGCTTCAAGAAGAAGATCCAGAAGGCCCAGATCATCGGGGACGAGGACAAGG-
GC
AACATCAAAGAAGTCGTGAAGTCCCTGCCCGGCAGCCCCGCCATCAAGAAGGGAATCCTGCAGAGCATCAAGAT-
CG
TGGACGAGCTCGTGAAAGTGATGGGCGGCAGAAAGCCCGAGAGCATCGTGGTGGAAATGGCTAGAGAGAACCAG-
TA
CACCAATCAGGGCAAGAGCAACAGCCAGCAGAGACTGAAGAGACTGGAAAAGTCCCTGAAAGAGCTGGGCAGCA-
AG
ATTCTGAAAGAGAATATCCCTGCCAAGCTGTCCAAGATCGACAACAACGCCCTGCAGAACGACCGGCTGTACCT-
GT
ACTACCTGCAGAATGGCAAGGACATGTATACAGGCGACGACCTGGATATCGACCGCCTGAGCAACTACGACATC-
GA
CCATATTATCCCCCAGGCCTTCCTGAAAGACAACAGCATTGACAACAAAGTGCTGGTGTCCTCCGCCAGCAACC-
GC
GGCAAGTCCGATGATGTGCCCAGCCTGGAAGTCGTGAAAAAGAGAAAGACCTTCTGGTATCAGCTGCTGAAAAG-
CA
AGCTGATTAGCCAGAGGAAGTTCGACAACCTGACCAAGGCCGAGAGAGGCGGCCTGAGCCCTGAAGATAAGGCC-
GG
CTTCATCCAGAGACAGCTGGTGGAAACCCGGCAGATCACCAAGCACGTGGCCAGACTGCTGGATGAGAAGTTTA-
AC
AACAAGAAGGACGAGAACAACCGGGCCGTGCGGACCGTGAAGATCATCACCCTGAAGTCCACCCTGGTGTCCCA-
GT
TCCGGAAGGACTTCGAGCTGTATAAAGTGCGCGAGATCAATGACTTTCACCACGCCCACGACGCCTACCTGAAT-
GC
CGTGGTGGCTTCCGCCCTGCTGAAGAAGTACCCTAAGCTGGAACCCGAGTTCGTGTACGGCGACTACCCCAAGT-
AC
AACTCCTTCAGAGAGCGGAAGTCCGCCACGAGAAGGTGTACTTCTACTCCAACATCATGAATATCTTTAAGAAG-
TC
CATCTCCCTGGCCGATGGCAGAGTGATCGAGCGGCCCCTGATCGAAGTGAACGAAGAGACAGGCGAGAGCGTGT-
GG
AACAAAGAAAGCGACCTGGCCACCGTGCGGCGGGTGCTGAGTTATCCTCAAGTGAATGTCGTGAAGAAGGTGGA-
AG
AACAGAACCACGGCCTGGATCGGGGCAAGCCCAAGGGCCTGTTCAACGCCAACCTGTCCAGCAAGCCTAAGCCC-
AA
CTCCAACGAGAATCTCGTGGGGGCCAAAGAGTACCTGGACCCTAAGAAGTACGGCGGATACGCCGGCATCTCCA-
AT
AGCTTCACCGTGCTCGTGAAGGGCACAATCGAGAAGGGCGCTAAGAAAAAGATCACAAACGTGCTGGAATTTCA-
GG
GGATCTCTATCCTGGACCGGATCAACTACCGGAAGGATAAGCTGAACTTTCTGCTGGAAAAAGGCTACAAGGAC-
AT
TGAGCTGATTATCGAGCTGCCTAAGTACTCCCTGTTCGAACTGAGCGACGGCTCCAGACGGATGCTGGCCTCCA-
TC
CTGTCCACCAACAACAAGCGGGGCGAGATCCACAAGGGAAACCAGATCTTCCTGAGCCAGAAATTTGTGAAACT-
GC
TGTACCACGCCAAGCGGATCTCCAACACCATCAATGAGAACCACCGGAAATACGTGGAAAACCACAAGAAAGAG-
TT
TGAGGAACTGTTCTACTACATCCTGGAGTTCAACGAGAACTATGTGGGAGCCAAGAAGAACGGCAAACTGCTGA-
AC
TCCGCCTTCCAGAGCTGGCAGAACCACAGCATCGACGAGCTGTGCAGCTCCTTCATCGGCCCTACCGGCAGCGA-
GC
GGAAGGGACTGTTTGAGCTGACCTCCAGAGGCTCTGCCGCCGACTTTGAGTTCCTGGGAGTGAAGATCCCCCGG-
TA
CAGAGACTACACCCCCTCTAGTCTGCTGAAGGACGCCACCCTGATCCACCAGAGCGTGACCGGCCTGTACGAAA-
CC
CGGATCGACCTGGCTAAGCTGGGCGAGGGAAAGCGTCCTGCTGCTACTAAGAAAGCTGGTCAAGCTAAGAAAAA-
GA AATAA
Example 5
Optimization of the Guide RNA for Streptococcus pyogenes Cas9
(Referred to as SpCas9)
[0186] Applicants mutated the tracrRNA and direct repeat sequences,
or mutated the chimeric guide RNA to enhance the RNAs in cells.
[0187] 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-00007 Optimized tracrRNA 1 (mutation underlined): (SEQ ID
NO: 70) GGAACCATTCAtAACAGCATAGCAAGTTAtAATAAGGCTAGTCCGTTA
TCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTT Optimized direct repeat 1
(mutation underlined): (SEQ ID NO: 71)
GTTaTAGAGCTATGCTGTTaTGAATGGTCCCAAAAC Optimized tracrRNA 2 (mutation
underlined): (SEQ ID NO: 72)
GGAACCATTCAAtACAGCATAGCAAGTTAAtATAAGGCTAGTCCGTTA
TCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTT Optimized direct repeat 2
(mutation underlined): (SEQ ID NO: 73)
GTaTTAGAGCTATGCTGTaTTGAATGGTCCCAAAAC Applicants also optimized the
chimeric guideRNA for optimal activity in eukaryotic cells.
Original guide RNA: (SEQ ID NO: 74)
NNNNNNNNNNNNNNNNNNNNGTTTTAGAGCTAGAAATAGCAAGTTAAA
ATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGC TTTTTTT Optimized
chimeric guide RNA sequence 1: (SEQ ID NO: 75)
NNNNNNNNNNNNNNNNNNNNGTATTAGAGCTAGAAATAGCAAGTTAAT
ATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGC TTTTTTT Optimized
chimeric guide RNA sequence 2: (SEQ ID NO: 76)
NNNNNNNNNNNNNNNNNNNNGTTTTAGAGCTATGCTGTTTTGGAAACA
AAACAGCATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAA
AAGTGGCACCGAGTCGGTGCTTTTTTT Optimized chimeric guide RNA sequence
3: (SEQ ID NO: 77) NNNNNNNNNNNNNNNNNNNNGTATTAGAGCTATGCTGTATTGGAAACA
ATACAGCATAGCAAGTTAATATAAGGCTAGTCCGTTATCAACTTGAAA
AAGTGGCACCGAGTCGGTGCTTTTTTT
[0188] Applicants showed that optimized chimeric guide RNA works
better as indicated in FIG. 9. 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: 78)
Example 6
Optimization of Streptococcus thermophilus LMD-9 CRISPR1 Cas9
(Referred to as St1Cas9)
[0189] Applicants designed guide chimeric RNAs as shown in FIG.
12.
[0190] The St1Cas9 guide RNAs can under go the same type of
optimization as for SpCas9 guide RNAs, by breaking the stretches of
poly thymines (Ts).
Example 7
Improvement of the Cas9 System for In Vivo Application
[0191] Applicants conducted a Metagenomic search for a Cas9 with
small molecular weight. Most Cas9 homologs are fairly large. For
example the SpCas9 is around 1368aa long, which is too large to be
easily packaged into viral vectors for delivery. Some of the
sequences may have been mis-annotated and therefore the exact
frequency for each length may not necessarily be accurate.
Nevertheless it provides a glimpse at distribution of Cas9 proteins
and suggest that there are shorter Cas9 homologs.
[0192] Through computational analysis, Applicants found that in the
bacterial strain Campylobacter, there are two Cas9 proteins with
less than 1000 amino acids. The sequence for one Cas9 from
Campylobacter jejuni is presented below. At this length, CjCas9 can
be easily packaged into AAV, lentiviruses, Adenoviruses, and other
viral vectors for robust delivery into primary cells and in vivo in
animal models.
TABLE-US-00008 >Campylobacter jejuni Cas9 (CjCas91) (SEQ ID NO:
79) MARILAFDIGISSIGWAFSENDILKGCGVRIFTKVENPKTGESLALPRR
LARSARKRLARRKARLNHLKHLIANEFKLNYEDYQSFDESLAKAYKGSL
ISPYELRFRALNELLSKQDFARVILHIAKRRGYDDIKNSDDKEKGAILK
AIKQNEEKLANYQSVGEYLYKEYFQKFKENSKEFTNVRNKKESYERCIA
QSFLKDELKLIFKKQREFGFSFSKKFEEEVLSVAFYKRALKDFSHLVGN
CSFFTDEKRAPKNSPLAFMFVALTRIINLLNNLKNTEGILYTKDDLNAL
LENEVLKNGTLTYKQTKKLLGLSDDYEFKGEKGTYFIEFKKYKEFIKAL
GEHNLSQDDLNEIAKDITLIKDEIKLKKALAKYDLNQNQIDSLSKLEFK
DHLNISFKALKLVTPLMLEGKKYDEACNELNLKVAINEDKKDFLPAFNE
TYYKDEVTNPVVLRAIKEYRKVLNALLKKYGKVHKINIELAREVGKNHS
QRAKIEKEQNENYKAKKDAELECEKLGLKINSKNILKLRLFKEQKEFCA
YSGEKIKISDLQDEKMLEIDHIYPYSRSFDDSYMNKVLVFTKQNQEKLN
QTPFEAFGNDSAKWQKIEVLKNLPTKKQKRILDKNYKDKEQKNFKDNLN
DTRYIARLVLNYTKDYLDFLPLSDDENTKLNDTQKGSKVHVEAKSGMLT
SALRHTWGFSAKDRNNHLHHAIDAVIIAYANNSIVKAFSDFKKEQESNS
AELYAKKISELDYKNKRKFFEPFSGFRQKVLDKIDEIFVSKPERKKPSG
ALHEETFRKEEEFYQSYGGKEGVLKALELGKIRKVNGKIVKNGDMFRVD
IFKHKKTNKFYAVPIYTMDFALKVLPNKAVARSKKGEIKDWILMDENYE
FCFSLYKDSLILIQTKDMQEPEFVYYNAFTSSTVSLIVSKHDNKFETLS
KNQKILFKNANEKEVIAKSIGIQNLKVFEKYIVSALGEVTKAEFRQRED FKK
[0193] The putative tracrRNA element for this CjCas9 is:
TABLE-US-00009 (SEQ ID NO: 80)
TATAATCTCATAAGAAATTTAAAAAGGGACTAAAATAAAGAGTTTGCGG
GACTCTGCGGGGTTACAATCCCCTAAAACCGCTTTTAAAATT
[0194] The Direct Repeat sequence is:
TABLE-US-00010 (SEQ ID NO: 81)
ATTTTACCATAAAGAAATTTAAAAAGGGACTAAAAC
[0195] The co-fold structure of the tracrRNA and direct repeat is
provided in FIG. 6.
[0196] An example of a chimeric guide RNA for CjCas9 is:
TABLE-US-00011 (SEQ ID NO: 82)
NNNNNNNNNNNNNNNNNNNNGUUUUAGUCCCGAAAGGGACUAAAAUAAA
GAGUUUGCGGGACUCUGCGGGGUUACAAUCCCCUAAAACCGCUUUU
[0197] Applicants have also optimized Cas9 guide RNA using in vitro
methods. FIG. 18 shows data from the St1Cas9 chimeric guide RNA
optimization in vitro.
[0198] 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.
Example 8
Sa sgRNA Optimization
[0199] Applicants designed five sgRNA variants for SaCas9 for an
optimal truncated architecture with highest cleavage efficiency. In
addition, the native direct repeat:tracr duplex system was tested
alongside sgRNAs. Guides with indicated lengths were co-transfected
with SaCas9 and tested in HEK 293FT cells for activity. A total of
100 ng sgRNA U6-PCR amplicon (or 50 ng of direct repeat and 50 ng
of tracrRNA) and 400 ng of SaCas9 plasmid were co-transfected into
200,000 Hepa1-6 mouse hepatocytes, and DNA was harvested 72-hours
post-transfection for SURVEYOR analysis. The results are shown in
FIG. 23.
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[0246] 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.
Sequence CWU 1
1
272115DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 1aggacgaagt cctaa 1527PRTSimian virus 40
2Pro Lys Lys Lys Arg Lys Val 1 5 316PRTUnknownDescription of
Unknown Nucleoplasmin bipartite NLS sequence 3Lys Arg Pro Ala Ala
Thr Lys Lys Ala Gly Gln Ala Lys Lys Lys Lys 1 5 10 15
49PRTUnknownDescription of Unknown C-myc NLS sequence 4Pro Ala Ala
Lys Arg Val Lys Leu Asp 1 5 511PRTUnknownDescription of Unknown
C-myc NLS sequence 5Arg Gln Arg Arg Asn Glu Leu Lys Arg Ser Pro 1 5
10 638PRTHomo sapiens 6Asn 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
742PRTUnknownDescription of Unknown IBB domain from importin-alpha
sequence 7Arg 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 88PRTUnknownDescription of Unknown Myoma T protein sequence 8Val
Ser Arg Lys Arg Pro Arg Pro 1 5 98PRTUnknownDescription of Unknown
Myoma T protein sequence 9Pro Pro Lys Lys Ala Arg Glu Asp 1 5
108PRTHomo sapiens 10Pro Gln Pro Lys Lys Lys Pro Leu 1 5 1112PRTMus
musculus 11Ser Ala Leu Ile Lys Lys Lys Lys Lys Met Ala Pro 1 5 10
125PRTInfluenza virus 12Asp Arg Leu Arg Arg 1 5 137PRTInfluenza
virus 13Pro Lys Gln Lys Lys Arg Lys 1 5 1410PRTHepatitus delta
virus 14Arg Lys Leu Lys Lys Lys Ile Lys Lys Leu 1 5 10 1510PRTMus
musculus 15Arg Glu Lys Lys Lys Phe Leu Lys Arg Arg 1 5 10
1620PRTHomo sapiens 16Lys Arg Lys Gly Asp Glu Val Asp Gly Val Asp
Glu Val Ala Lys Lys 1 5 10 15 Lys Ser Lys Lys 20 1717PRTHomo
sapiens 17Arg Lys Cys Leu Gln Ala Gly Met Asn Leu Glu Ala Arg Lys
Thr Lys 1 5 10 15 Lys 1827DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 18nnnnnnnnnn
nnnnnnnnnn nnagaaw 271919DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 19nnnnnnnnnn
nnnnagaaw 192027DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 20nnnnnnnnnn nnnnnnnnnn nnagaaw
272118DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 21nnnnnnnnnn nnnagaaw
1822137DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 22nnnnnnnnnn nnnnnnnnnn gtttttgtac
tctcaagatt tagaaataaa tcttgcagaa 60gctacaaaga taaggcttca tgccgaaatc
aacaccctgt cattttatgg cagggtgttt 120tcgttattta atttttt
13723123DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 23nnnnnnnnnn nnnnnnnnnn gtttttgtac
tctcagaaat gcagaagcta caaagataag 60gcttcatgcc gaaatcaaca ccctgtcatt
ttatggcagg gtgttttcgt tatttaattt 120ttt 12324110DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
24nnnnnnnnnn nnnnnnnnnn gtttttgtac tctcagaaat gcagaagcta caaagataag
60gcttcatgcc gaaatcaaca ccctgtcatt ttatggcagg gtgttttttt
11025102DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 25nnnnnnnnnn nnnnnnnnnn gttttagagc
tagaaatagc aagttaaaat aaggctagtc 60cgttatcaac ttgaaaaagt ggcaccgagt
cggtgctttt tt 1022688DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 26nnnnnnnnnn
nnnnnnnnnn gttttagagc tagaaatagc aagttaaaat aaggctagtc 60cgttatcaac
ttgaaaaagt gttttttt 882776DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 27nnnnnnnnnn
nnnnnnnnnn gttttagagc tagaaatagc aagttaaaat aaggctagtc 60cgttatcatt
tttttt 762812RNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 28guuuuagagc ua 122933DNAHomo
sapiens 29ggacatcgat gtcacctcca atgactaggg tgg 333033DNAHomo
sapiens 30cattggaggt gacatcgatg tcctccccat tgg 333133DNAHomo
sapiens 31ggaagggcct gagtccgagc agaagaagaa ggg 333233DNAHomo
sapiens 32ggtggcgaga ggggccgaga ttgggtgttc agg 333333DNAHomo
sapiens 33atgcaggagg gtggcgagag gggccgagat tgg 333421DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
34aaaaccaccc ttctctctgg c 213521DNAArtificial SequenceDescription
of Artificial Sequence Synthetic primer 35ggagattgga gacacggaga g
213620DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 36ctggaaagcc aatgcctgac 203720DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
37ggcagcaaac tccttgtcct 203812DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 38gttttagagc ta
1239335DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 39gagggcctat 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
33540423DNAArtificial 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 gtagtattaa gtattgtttt atggctgata aatttctttg
aatttctcct 300tgattatttg ttataaaagt tataaaataa tcttgttgga
accattcaaa acagcatagc 360aagttaaaat aaggctagtc cgttatcaac
ttgaaaaagt ggcaccgagt cggtgctttt 420ttt 42341339DNAArtificial
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 ggttttagag ctatgctgtt
ttgaatggtc ccaaaacggg tcttcgagaa 300gacgttttag agctatgctg
ttttgaatgg tcccaaaac 33942309DNAArtificial 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 ggtcttcgag aagacctgtt
ttagagctag aaatagcaag ttaaaataag 300gctagtccg
309431648PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 43Met 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 44 1625PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
44Met 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 451664PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
45Met 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 461423PRTArtificial
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 Lys Arg Pro Ala Ala Thr 1400 1405 1410 Lys Lys Ala Gly Gln Ala
Lys Lys Lys Lys 1415 1420 47483PRTArtificial SequenceDescription of
Artificial Sequence Synthetic polypeptide 47Met 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 48483PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
48Met 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
491423PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 49Met 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
502012DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 50gaatgctgcc 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 2012511153PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
51Met 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 52340DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
52gagggcctat 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 34053360DNAArtificial 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 ggttttagag ctatgctgtt
ttgaatggtc ccaaaacnnn nnnnnnnnnn 300nnnnnnnnnn nnnnnnngtt
ttagagctat gctgttttga atggtcccaa aacttttttt 36054318DNAArtificial
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 240cgaaacaccn nnnnnnnnnn nnnnnnnnng
ttttagagct agaaatagca agttaaaata 300aggctagtcc gttttttt
31855325DNAArtificial 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 gttatcattt ttttt 32556337DNAArtificial
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 gttatcaact
tgaaaaagtg ttttttt 33757352DNAArtificial 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 gcaccgagtc ggtgcttttt tt 352585101DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
58cgttacataa 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 510159137DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
59nnnnnnnnnn nnnnnnnnnn gtttttgtac tctcaagatt tagaaataaa tcttgcagaa
60gctacaaaga taaggcttca tgccgaaatc aacaccctgt cattttatgg cagggtgttt
120tcgttattta atttttt 13760123DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 60nnnnnnnnnn
nnnnnnnnnn gtttttgtac tctcagaaat gcagaagcta caaagataag 60gcttcatgcc
gaaatcaaca ccctgtcatt ttatggcagg gtgttttcgt tatttaattt 120ttt
12361110DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 61nnnnnnnnnn nnnnnnnnnn gtttttgtac
tctcagaaat gcagaagcta caaagataag 60gcttcatgcc gaaatcaaca ccctgtcatt
ttatggcagg gtgttttttt 11062137DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 62nnnnnnnnnn
nnnnnnnnnn gttattgtac tctcaagatt tagaaataaa tcttgcagaa 60gctacaaaga
taaggcttca tgccgaaatc aacaccctgt cattttatgg cagggtgttt
120tcgttattta atttttt 13763123DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 63nnnnnnnnnn
nnnnnnnnnn gttattgtac tctcagaaat gcagaagcta caaagataag 60gcttcatgcc
gaaatcaaca ccctgtcatt ttatggcagg gtgttttcgt tatttaattt 120ttt
12364110DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 64nnnnnnnnnn nnnnnnnnnn gttattgtac
tctcagaaat gcagaagcta caaagataag 60gcttcatgcc gaaatcaaca ccctgtcatt
ttatggcagg gtgttttttt 11065137DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 65nnnnnnnnnn
nnnnnnnnnn gttattgtac tctcaagatt tagaaataaa tcttgcagaa 60gctacaatga
taaggcttca tgccgaaatc aacaccctgt cattttatgg cagggtgttt
120tcgttattta atttttt 13766123DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 66nnnnnnnnnn
nnnnnnnnnn gttattgtac tctcagaaat gcagaagcta caatgataag 60gcttcatgcc
gaaatcaaca ccctgtcatt ttatggcagg gtgttttcgt tatttaattt 120ttt
12367110DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 67nnnnnnnnnn nnnnnnnnnn gttattgtac
tctcagaaat gcagaagcta caatgataag 60gcttcatgcc gaaatcaaca ccctgtcatt
ttatggcagg gtgttttttt 11068107DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 68nnnnnnnnnn
nnnnnnnnnn gttttagagc tgtggaaaca cagcgagtta aaataaggct 60tagtccgtac
tcaacttgaa aaggtggcac cgattcggtg ttttttt 107694263DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
69atgaaaaggc 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
42637084DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 70ggaaccattc ataacagcat agcaagttat
aataaggcta gtccgttatc aacttgaaaa 60agtggcaccg agtcggtgct tttt
847136DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 71gttatagagc tatgctgtta tgaatggtcc caaaac
367284DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 72ggaaccattc aatacagcat agcaagttaa
tataaggcta gtccgttatc aacttgaaaa 60agtggcaccg agtcggtgct tttt
847336DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 73gtattagagc tatgctgtat tgaatggtcc caaaac
3674103DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 74nnnnnnnnnn nnnnnnnnnn gttttagagc
tagaaatagc aagttaaaat aaggctagtc 60cgttatcaac ttgaaaaagt ggcaccgagt
cggtgctttt ttt 10375103DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 75nnnnnnnnnn
nnnnnnnnnn gtattagagc tagaaatagc aagttaatat aaggctagtc 60cgttatcaac
ttgaaaaagt ggcaccgagt cggtgctttt ttt 10376123DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
76nnnnnnnnnn nnnnnnnnnn gttttagagc tatgctgttt tggaaacaaa acagcatagc
60aagttaaaat aaggctagtc cgttatcaac ttgaaaaagt ggcaccgagt cggtgctttt
120ttt 12377123DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 77nnnnnnnnnn nnnnnnnnnn
gtattagagc tatgctgtat tggaaacaat acagcatagc 60aagttaatat aaggctagtc
cgttatcaac ttgaaaaagt ggcaccgagt cggtgctttt 120ttt 1237820DNAHomo
sapiens 78gtcacctcca atgactaggg 2079984PRTCampylobacter jejuni
79Met Ala Arg Ile Leu Ala Phe Asp Ile Gly Ile Ser Ser Ile Gly Trp 1
5 10 15 Ala Phe Ser Glu Asn Asp Glu Leu Lys Asp Cys Gly Val Arg Ile
Phe 20 25 30 Thr Lys Val Glu Asn Pro Lys Thr Gly Glu Ser Leu Ala
Leu Pro Arg 35 40 45 Arg Leu Ala Arg Ser Ala Arg Lys Arg Leu Ala
Arg Arg Lys Ala Arg 50 55 60 Leu Asn His Leu Lys His Leu Ile Ala
Asn Glu Phe Lys Leu Asn Tyr 65 70 75 80 Glu Asp Tyr Gln Ser Phe Asp
Glu Ser Leu Ala Lys Ala Tyr Lys Gly 85 90 95 Ser Leu Ile Ser Pro
Tyr Glu Leu Arg Phe Arg Ala Leu Asn Glu Leu 100 105 110 Leu Ser Lys
Gln Asp Phe Ala Arg Val Ile Leu His Ile Ala Lys Arg 115 120 125 Arg
Gly Tyr Asp Asp Ile Lys Asn Ser Asp Asp Lys Glu Lys Gly Ala 130 135
140 Ile Leu Lys Ala Ile Lys Gln Asn Glu Glu Lys Leu Ala Asn Tyr Gln
145 150 155 160 Ser Val Gly Glu Tyr Leu Tyr Lys Glu Tyr Phe Gln Lys
Phe Lys Glu 165 170 175 Asn Ser Lys Glu Phe Thr Asn Val Arg Asn Lys
Lys Glu Ser Tyr Glu 180 185 190 Arg Cys Ile Ala Gln Ser Phe Leu Lys
Asp Glu Leu Lys Leu Ile Phe 195 200 205 Lys Lys Gln Arg Glu Phe Gly
Phe Ser Phe Ser Lys Lys Phe Glu Glu 210 215 220 Glu Val Leu Ser Val
Ala Phe Tyr Lys Arg Ala Leu Lys Asp Phe Ser 225 230 235 240 His Leu
Val Gly Asn Cys Ser Phe Phe Thr Asp Glu Lys Arg Ala Pro 245 250 255
Lys Asn Ser Pro Leu Ala Phe Met Phe Val Ala Leu Thr Arg Ile Ile 260
265 270 Asn Leu Leu Asn Asn Leu Lys Asn Thr Glu Gly Ile Leu Tyr Thr
Lys 275 280 285 Asp Asp Leu Asn Ala Leu Leu Asn Glu Val Leu Lys Asn
Gly Thr Leu 290 295 300 Thr Tyr Lys Gln Thr Lys Lys Leu Leu Gly Leu
Ser Asp Asp Tyr Glu 305 310 315 320 Phe Lys Gly Glu Lys Gly Thr Tyr
Phe Ile Glu Phe Lys Lys Tyr Lys 325 330 335 Glu Phe Ile Lys Ala Leu
Gly Glu His Asn Leu Ser Gln Asp Asp Leu 340 345 350 Asn Glu Ile Ala
Lys Asp Ile Thr Leu Ile Lys Asp Glu Ile Lys Leu 355 360 365 Lys Lys
Ala Leu Ala Lys Tyr Asp Leu Asn Gln Asn Gln Ile Asp Ser 370 375 380
Leu Ser Lys Leu Glu Phe Lys Asp His Leu Asn Ile Ser Phe Lys Ala 385
390 395 400 Leu Lys Leu Val Thr Pro Leu Met Leu Glu Gly Lys Lys Tyr
Asp Glu 405 410 415 Ala Cys Asn Glu Leu Asn Leu Lys Val Ala Ile Asn
Glu Asp Lys Lys 420 425 430 Asp Phe Leu Pro Ala Phe Asn Glu Thr Tyr
Tyr Lys Asp Glu Val Thr 435 440 445 Asn Pro Val Val Leu Arg Ala Ile
Lys Glu Tyr Arg Lys Val Leu Asn 450 455 460 Ala Leu Leu Lys Lys Tyr
Gly Lys Val His Lys Ile Asn Ile Glu Leu 465 470 475 480 Ala Arg Glu
Val Gly Lys Asn His Ser Gln Arg Ala Lys Ile Glu Lys 485 490 495 Glu
Gln Asn Glu Asn Tyr Lys Ala Lys Lys Asp Ala Glu Leu Glu Cys 500 505
510 Glu Lys Leu Gly Leu Lys Ile Asn Ser Lys Asn Ile Leu Lys Leu Arg
515 520 525 Leu Phe Lys Glu Gln Lys Glu Phe Cys Ala Tyr Ser Gly Glu
Lys Ile 530 535 540 Lys Ile Ser Asp Leu Gln Asp Glu Lys Met Leu Glu
Ile Asp His Ile 545 550 555 560 Tyr Pro Tyr Ser Arg Ser Phe Asp Asp
Ser Tyr Met Asn Lys Val Leu 565 570 575 Val Phe Thr Lys Gln Asn Gln
Glu Lys Leu Asn Gln Thr Pro Phe Glu 580 585 590 Ala Phe Gly Asn Asp
Ser Ala Lys Trp Gln Lys Ile Glu Val Leu Ala 595 600 605 Lys Asn Leu
Pro Thr Lys Lys Gln Lys Arg Ile Leu Asp Lys Asn Tyr 610 615 620 Lys
Asp Lys Glu Gln Lys Asn Phe Lys Asp Arg Asn Leu Asn Asp Thr 625 630
635 640 Arg Tyr Ile Ala Arg Leu Val Leu Asn Tyr Thr Lys Asp Tyr Leu
Asp 645 650 655 Phe Leu Pro Leu Ser Asp Asp Glu Asn Thr Lys Leu Asn
Asp Thr Gln 660 665 670 Lys Gly Ser Lys Val His Val Glu Ala Lys Ser
Gly Met Leu Thr Ser 675 680 685 Ala Leu Arg His Thr Trp Gly Phe Ser
Ala Lys Asp Arg Asn Asn His 690 695 700 Leu His His Ala Ile Asp Ala
Val Ile Ile Ala Tyr Ala Asn Asn Ser 705 710 715 720 Ile Val Lys Ala
Phe Ser Asp Phe Lys Lys Glu Gln Glu Ser Asn Ser 725 730 735 Ala Glu
Leu Tyr Ala Lys Lys Ile Ser Glu Leu Asp Tyr Lys Asn Lys 740 745 750
Arg Lys Phe Phe Glu Pro Phe Ser Gly Phe Arg Gln Lys Val Leu Asp 755
760 765 Lys Ile Asp Glu Ile Phe Val Ser Lys Pro Glu Arg Lys Lys Pro
Ser 770 775 780 Gly Ala Leu His Glu Glu Thr Phe Arg Lys Glu Glu Glu
Phe Tyr Gln 785 790 795 800 Ser Tyr Gly Gly Lys Glu Gly Val Leu Lys
Ala Leu Glu Leu Gly Lys 805 810 815 Ile Arg Lys Val Asn Gly Lys Ile
Val Lys Asn Gly Asp Met Phe Arg 820 825 830 Val Asp Ile Phe Lys His
Lys Lys Thr Asn Lys Phe Tyr Ala Val Pro 835 840 845 Ile Tyr Thr Met
Asp Phe Ala Leu Lys Val Leu Pro Asn Lys Ala Val 850 855 860 Ala Arg
Ser Lys Lys Gly Glu Ile Lys Asp Trp Ile Leu Met Asp Glu 865 870 875
880 Asn Tyr Glu Phe Cys Phe Ser Leu Tyr Lys Asp Ser Leu Ile Leu Ile
885 890 895 Gln Thr Lys Asp Met Gln Glu Pro Glu Phe Val Tyr Tyr Asn
Ala Phe 900 905 910 Thr Ser Ser Thr Val Ser Leu Ile Val Ser Lys His
Asp Asn Lys Phe 915 920 925 Glu Thr Leu Ser Lys Asn Gln Lys Ile Leu
Phe Lys Asn Ala Asn Glu 930 935 940 Lys Glu Val Ile Ala Lys Ser Ile
Gly Ile Gln Asn Leu Lys Val Phe 945 950 955 960 Glu Lys Tyr Ile Val
Ser Ala Leu Gly Glu Val Thr Lys Ala Glu Phe 965 970 975 Arg Gln Arg
Glu Asp Phe Lys Lys 980 8091DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 80tataatctca
taagaaattt aaaaagggac taaaataaag agtttgcggg actctgcggg 60gttacaatcc
cctaaaaccg cttttaaaat t 918136DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 81attttaccat
aaagaaattt aaaaagggac taaaac 368295RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 82nnnnnnnnnn nnnnnnnnnn guuuuagucc cgaaagggac
uaaaauaaag aguuugcggg 60acucugcggg guuacaaucc ccuaaaaccg cuuuu
958369RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 83gucaccucca augacuaggg guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuuuuuu 698469RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 84gacaucgaug uccuccccau guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuuuuuu 698569RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 85gaguccgagc agaagaagaa guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuuuuuu 698669RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 86ggggccgaga uuggguguuc guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuuuuuu 698769RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 87guggcgagag gggccgagau guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuuuuuu 698876RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 88gucaccucca augacuaggg guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucauu uuuuuu 768976RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 89gacaucgaug uccuccccau guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucauu uuuuuu 769076RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 90gaguccgagc agaagaagaa guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucauu uuuuuu 769176RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 91ggggccgaga uuggguguuc guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucauu uuuuuu 769276RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 92guggcgagag gggccgagau guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucauu uuuuuu 769388RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 93gucaccucca augacuaggg guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu guuuuuuu
889488RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 94gacaucgaug uccuccccau guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu guuuuuuu
889588RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 95gaguccgagc agaagaagaa guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu guuuuuuu
889688RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 96ggggccgaga uuggguguuc guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu guuuuuuu
889788RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 97guggcgagag gggccgagau guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu guuuuuuu
8898103RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 98gucaccucca augacuaggg guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu ggcaccgagu
cggugcuuuu uuu 10399103RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 99gacaucgaug
uccuccccau guuuuagagc uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac
uugaaaaagu ggcaccgagu cggugcuuuu uuu 103100103RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 100gaguccgagc agaagaagaa guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu ggcaccgagu cggugcuuuu
uuu 103101103RNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 101ggggccgaga uuggguguuc
guuuuagagc uagaaauagc aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu
ggcaccgagu cggugcuuuu uuu 103102103RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 102guggcgagag gggccgagau guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu ggcaccgagu cggugcuuuu
uuu 103103102DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 103gttttagagc tatgctgttt
tgaatggtcc caaaacggaa gggcctgagt ccgagcagaa 60gaagaagttt tagagctatg
ctgttttgaa tggtcccaaa ac 102104100DNAHomo sapiens 104cggaggacaa
agtacaaacg gcagaagctg gaggaggaag ggcctgagtc cgagcagaag 60aagaagggct
cccatcacat caaccggtgg cgcattgcca 10010550DNAHomo sapiens
105agctggagga ggaagggcct gagtccgagc agaagaagaa gggctcccac
5010630RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 106gaguccgagc agaagaagaa guuuuagagc
3010749DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 107agctggagga ggaagggcct gagtccgagc
agaagagaag ggctcccat 4910853DNAHomo sapiens 108ctggaggagg
aagggcctga gtccgagcag aagaagaagg gctcccatca cat 5310952DNAHomo
sapiens 109ctggaggagg aagggcctga gtccgagcag aagagaaggg ctcccatcac
at 5211054DNAHomo sapiens 110ctggaggagg aagggcctga gtccgagcag
aagaaagaag ggctcccatc acat 5411150DNAHomo sapiens 111ctggaggagg
aagggcctga gtccgagcag aagaagggct cccatcacat 5011247DNAHomo sapiens
112ctggaggagg aagggcctga gcccgagcag aagggctccc atcacat
4711366DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 113nnnnnnnnnn nnnnnnnnnn guuuuagagc
uagaaauagc aaguuaaaau aaggctagtc 60cguuuu 6611420RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 114gaguccgagc agaagaagaa 2011520RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 115gacaucgaug uccuccccau 2011620RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 116gucaccucca augacuaggg 2011720RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 117auuggguguu cagggcagag 2011820RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 118guggcgagag gggccgagau 2011920RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 119ggggccgaga uuggguguuc 2012020RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 120gugccauuag cuaaaugcau 2012120RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 121guaccaccca caggugccag 2012220RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 122gaaagccucu gggccaggaa 2012348DNAHomo sapiens
123ctggaggagg aagggcctga gtccgagcag aagaagaagg gctcccat
4812420RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 124gaguccgagc agaagaagau
2012520RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 125gaguccgagc agaagaagua
2012620RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 126gaguccgagc agaagaacaa
2012720RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 127gaguccgagc agaagaugaa
2012820RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 128gaguccgagc agaaguagaa
2012920RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 129gaguccgagc agaugaagaa
2013020RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 130gaguccgagc acaagaagaa
2013120RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 131gaguccgagg agaagaagaa
2013220RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 132gaguccgugc agaagaagaa
2013320RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 133gagucggagc agaagaagaa
2013420RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 134gagaccgagc agaagaagaa
2013524DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 135aatgacaagc ttgctagcgg tggg
2413639DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 136aaaacggaag ggcctgagtc cgagcagaag
aagaagttt 3913739DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 137aaacaggggc cgagattggg
tgttcagggc agaggtttt 3913838DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 138aaaacggaag
ggcctgagtc cgagcagaag aagaagtt 3813940DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 139aacggaggga ggggcacaga tgagaaactc agggttttag
4014038DNAHomo sapiens 140agcccttctt cttctgctcg gactcaggcc cttcctcc
3814140DNAHomo sapiens 141cagggaggga ggggcacaga tgagaaactc
aggaggcccc 4014280DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 142ggcaatgcgc caccggttga
tgtgatggga gcccttctag gaggccccca gagcagccac 60tggggcctca acactcaggc
8014398DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 143ggacgaaaca ccggaaccat tcaaaacagc
atagcaagtt aaaataaggc tagtccgtta 60tcaacttgaa aaagtggcac cgagtcggtg
cttttttt 98144186DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 144ggacgaaaca ccggtagtat
taagtattgt tttatggctg ataaatttct ttgaatttct 60ccttgattat ttgttataaa
agttataaaa taatcttgtt ggaaccattc aaaacagcat 120agcaagttaa
aataaggcta gtccgttatc aacttgaaaa agtggcaccg agtcggtgct 180tttttt
18614546RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 145nnnnnnnnnn nnnnnnnnng uuauuguacu
cucaagauuu auuuuu 4614691RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 146guuacuuaaa
ucuugcagaa gcuacaaaga uaaggcuuca ugccgaaauc aacacccugu 60cauuuuaugg
caggguguuu ucguuauuua a 9114770DNAHomo sapiens 147ttttctagtg
ctgagtttct gtgactcctc tacattctac ttctctgtgt ttctgtatac 60tacctcctcc
70148122DNAHomo sapiens 148ggaggaaggg cctgagtccg agcagaagaa
gaagggctcc catcacatca accggtggcg 60cattgccacg aagcaggcca atggggagga
catcgatgtc acctccaatg actagggtgg 120gc 12214948RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 149acnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnguuuuaga
gcuaugcu 4815067DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 150agcauagcaa guuaaaauaa
ggctaguccg uuaucaacuu gaaaaagugg caccgagucg 60gugcuuu
6715162RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 151nnnnnnnnnn nnnnnnnnnn guuuuagagc
uagaaauagc aaguuaaaau aaggcuaguc 60cg 6215273DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 152tgaatggtcc caaaacggaa gggcctgagt ccgagcagaa
gaagaagttt tagagctatg 60ctgttttgaa tgg 7315399RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 153nnnnnnnnnn nnnnnnnnnn guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu ggcaccgagu cggugcuuu
99154127RNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 154guuuuuguac ucucaagauu uaaguaacug
uacaacguua cuuaaaucuu gcagaagcua 60caaagauaag gcuucaugcc gaaaucaaca
cccugucauu uuauggcagg guguuuucgu 120uauuuaa 12715556DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 155nnnnnnnnnn nnnnnnnnnn gtttttgtac tctcaagatt
taagtaactg tacaac 5615691DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 156gttacttaaa
tcttgcagaa gctacaaaga taaggcttca tgccgaaatc aacaccctgt 60cattttatgg
cagggtgttt tcgttattta a 91157134DNAArtificial SequenceDescription
of Artificial Sequence Synthetic polynucleotide 157nnnnnnnnnn
nnnnnnnnnn gtttttgtac tctcaagatt taaggaaact aaatcttgca 60gaagctacaa
agataaggct tcatgccgaa atcaacaccc tgtcatttta tggcagggtg
120ttttcgttat ttaa 134158131DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 158nnnnnnnnnn
nnnnnnnnnn gtttttgtac tctcaagatt tagaaataaa tcttgcagaa 60gctacaaaga
taaggcttca tgccgaaatc aacaccctgt cattttatgg cagggtgttt
120tcgttattta a 131159125DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 159nnnnnnnnnn
nnnnnnnnnn gtttttgtac tctcaagatg aaaatcttgc agaagctaca 60aagataaggc
ttcatgccga aatcaacacc ctgtcatttt atggcagggt gttttcgtta 120tttaa
125160112DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 160nnnnnnnnnn nnnnnnnnnn gtttttgtac
tctgaaaaga agctacaaag ataaggcttc 60atgccgaaat caacaccctg tcattttatg
gcagggtgtt ttcgttattt aa 112161107DNAArtificial SequenceDescription
of Artificial Sequence Synthetic polynucleotide 161nnnnnnnnnn
nnnnnnnnnn gtttttgtac tgaaaagcta caaagataag gcttcatgcc 60gaaatcaaca
ccctgtcatt ttatggcagg gtgttttcgt tatttaa 107162108DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
162nnnnnnnnnn nnnnnnnnnn gtttttgtac tctcaagatt tagaaataaa
tcttgcagaa 60gctacaaaga taaggcttca tgccgaaatc aacaccctgt cattttat
10816386DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 163nnnnnnnnnn nnnnnnnnnn gtttttgtac
tctcaagatt tagaaataaa tcttgcagaa 60gctacaaaga taaggcttca tgccga
8616479DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 164nnnnnnnnnn nnnnnnnnnn gtttttgtac
tctcaagatt tagaaataaa tcttgcagaa 60gctacaaaga taaggcttc
7916573DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 165nnnnnnnnnn nnnnnnnnnn gtttttgtac
tctcaagatt tagaaataaa tcttgcagaa 60gctacaaaga taa
73166125RNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 166guuuuagucc cuuuuuaaau uucuuuaugg
uaaaauuaua aucucauaag aaauuuaaaa 60agggacuaaa auaaagaguu ugcgggacuc
ugcgggguua caauccccua aaaccgcuuu 120uaaaa 12516791RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 167guuacuuaaa ucuugcagaa gcuacaaaga uaaggcuuca
ugccgaaauc aacacccugu 60cauuuuaugg caggguguuu ucguuauuua a
9116856RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 168gggacucaac caagucauuc guuuuuguac
ucucaagauu uaaguaacug uacaac 56169147RNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
169gggacucaac caagucauuc guuuuuguac ucucaagauu uaaguaacug
uacaacguua 60cuuaaaucuu gcagaagcua caaagauaag gcuucaugcc gaaaucaaca
cccugucauu 120uuauggcagg guguuuucgu uauuuaa 14717070RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 170cuugcagaag cuacaaagau aaggcuucau gccgaaauca
acacccuguc auuuuauggc 60aggguguuuu 7017142RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 171gggacucaac caagucauuc guuuuuguac ucucaagauu ua
42172112RNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 172gggacucaac caagucauuc guuuuuguac
ucucaagauu uacuugcaga agcuacaaag 60auaaggcuuc augccgaaau caacacccug
ucauuuuaug gcaggguguu uu 112173116RNAArtificial SequenceDescription
of Artificial Sequence Synthetic polynucleotide 173gggacucaac
caagucauuc guuuuuguac ucucaagauu uagaaacuug cagaagcuac 60aaagauaagg
cuucaugccg aaaucaacac ccugucauuu uauggcaggg uguuuu
116174116RNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 174gggacucaac caagucauuc guuuuuguac
ucucaagauu uagaaacuug cagaagcuac 60aaagauaagg cuucaugccg aaaucaacac
ccugucauuu uauggcaggg uguuuu 116175102RNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
175gggacucaac caagucauuc guuuuuguag aaauacaaag auaaggcuuc
augccgaaau 60caacacccug ucauuuuaug gcaggguguu uucguuauuu aa
102176102RNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 176gggacucaac caagucauuc guuuuuguag
aaauacaaag auaaggcuuc augccgaaau 60caacacccug ucauuuuaug gcaggguguu
uucguuauuu aa 10217757RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 177gggacucaac
caagucauuc guuuuuguag aaauacaaag auaaggcuuc augccga
5717857RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 178gggacucaac caagucauuc guuuuuguag
aaauacaaag auaaggcuuc augccga 5717923DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 179gtggtgtcac gctcgtcgtt tgg 2318023DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 180tccagtctat taattgttgc cgg 2318164DNAHomo sapiens
181caagaggctt gagtaggaga ggagtgccgc cgaggcgggg cggggcgggg
cgtggagctg 60ggct 6418299RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 182nnnnnnnnnn
nnnnnnnnnn guauuagagc uagaaauagc aaguuaauau aaggcuaguc 60cguuaucaac
uugaaaaagu ggcaccgagu cggugcuuu 99183119RNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
183nnnnnnnnnn nnnnnnnnnn guuuuagagc uaugcuguuu uggaaacaaa
acagcauagc 60aaguuaaaau aaggcuaguc cguuaucaac uugaaaaagu ggcaccgagu
cggugcuuu 119184119RNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 184nnnnnnnnnn nnnnnnnnnn
guauuagagc uaugcuguau uggaaacaau acagcauagc 60aaguuaauau aaggcuaguc
cguuaucaac uugaaaaagu ggcaccgagu cggugcuuu 11918512DNAHomo sapiens
185tagcgggtaa gc 1218612DNAHomo sapiens 186tcggtgacat gt
1218712DNAHomo sapiens 187actccccgta gg 1218812DNAHomo sapiens
188actgcgtgtt aa 1218912DNAHomo sapiens 189acgtcgcctg at
1219012DNAHomo sapiens 190taggtcgacc ag 1219112DNAHomo sapiens
191ggcgttaatg at 1219212DNAHomo sapiens 192tgtcgcatgt ta
1219312DNAHomo sapiens 193atggaaacgc at 1219412DNAHomo sapiens
194gccgaattcc tc 1219512DNAHomo sapiens 195gcatggtacg ga
1219612DNAHomo sapiens 196cggtactctt ac 1219712DNAHomo sapiens
197gcctgtgccg ta 1219812DNAHomo sapiens 198tacggtaagt cg
1219912DNAHomo sapiens 199cacgaaatta cc 1220012DNAHomo sapiens
200aaccaagata cg 1220112DNAHomo sapiens 201gagtcgatac gc
1220212DNAHomo sapiens 202gtctcacgat cg 1220312DNAHomo sapiens
203tcgtcgggtg ca 1220412DNAHomo sapiens 204actccgtagt ga
1220512DNAHomo sapiens 205caggacgtcc gt 1220612DNAHomo sapiens
206tcgtatccct ac 1220712DNAHomo sapiens 207tttcaaggcc gg
1220812DNAHomo sapiens 208cgccggtgga at 1220912DNAHomo sapiens
209gaacccgtcc ta 1221012DNAHomo sapiens 210gattcatcag cg
1221112DNAHomo sapiens 211acaccggtct tc 1221212DNAHomo sapiens
212atcgtgccct aa 1221312DNAHomo sapiens 213gcgtcaatgt tc
1221412DNAHomo sapiens 214ctccgtatct cg 1221512DNAHomo sapiens
215ccgattcctt cg 1221612DNAHomo sapiens 216tgcgcctcca gt
1221712DNAHomo sapiens 217taacgtcgga gc 1221812DNAHomo sapiens
218aaggtcgccc at 1221912DNAHomo sapiens 219gtcggggact at
1222012DNAHomo sapiens 220ttcgagcgat tt 1222112DNAHomo sapiens
221tgagtcgtcg ag 1222212DNAHomo sapiens 222tttacgcaga gg
1222312DNAHomo sapiens 223aggaagtatc gc
1222412DNAHomo sapiens 224actcgatacc at 1222512DNAHomo sapiens
225cgctacatag ca 1222612DNAHomo sapiens 226ttcataaccg gc
1222712DNAHomo sapiens 227ccaaacggtt aa 1222812DNAHomo sapiens
228cgattccttc gt 1222912DNAHomo sapiens 229cgtcatgaat aa
1223012DNAHomo sapiens 230agtggcgatg ac 1223112DNAHomo sapiens
231cccctacggc ac 1223212DNAHomo sapiens 232gccaacccgc ac
1223312DNAHomo sapiens 233tgggacaccg gt 1223412DNAHomo sapiens
234ttgactgcgg cg 1223512DNAHomo sapiens 235actatgcgta gg
1223612DNAHomo sapiens 236tcacccaaag cg 1223712DNAHomo sapiens
237gcaggacgtc cg 1223812DNAHomo sapiens 238acaccgaaaa cg
1223912DNAHomo sapiens 239cggtgtattg ag 1224012DNAHomo sapiens
240cacgaggtat gc 1224112DNAHomo sapiens 241taaagcgacc cg
1224212DNAHomo sapiens 242cttagtcggc ca 1224312DNAHomo sapiens
243cgaaaacgtg gc 1224412DNAHomo sapiens 244cgtgccctga ac
1224512DNAHomo sapiens 245tttaccatcg aa 1224612DNAHomo sapiens
246cgtagccatg tt 1224712DNAHomo sapiens 247cccaaacggt ta
1224812DNAHomo sapiens 248gcgttatcag aa 1224912DNAHomo sapiens
249tcgatggtaa ac 1225012DNAHomo sapiens 250cgactttttg ca
1225112DNAHomo sapiens 251tcgacgactc ac 1225212DNAHomo sapiens
252acgcgtcaga ta 1225312DNAHomo sapiens 253cgtacggcac ag
1225412DNAHomo sapiens 254ctatgccgtg ca 1225512DNAHomo sapiens
255cgcgtcagat at 1225612DNAHomo sapiens 256aagatcggta gc
1225712DNAHomo sapiens 257cttcgcaagg ag 1225812DNAHomo sapiens
258gtcgtggact ac 1225912DNAHomo sapiens 259ggtcgtcatc aa
1226012DNAHomo sapiens 260gttaacagcg tg 1226112DNAHomo sapiens
261tagctaaccg tt 1226212DNAHomo sapiens 262agtaaaggcg ct
1226312DNAHomo sapiens 263ggtaatttcg tg 12264147RNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
264nnnnnnnnnn nnnnnnnnnn guuuuaguac ucuguaauuu uagguaugag
guagacgaaa 60auuguacuua uaccuaaaau uacagaaucu acuaaaacaa ggcaaaaugc
cguguuuauc 120ucgucaacuu guuggcgaga uuuuuuu 14726523DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 265nnnnnnnnnn nnnnnnnnnn ngg 2326615DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 266nnnnnnnnnn nnngg 1526723DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 267nnnnnnnnnn nnnnnnnnnn ngg 2326814DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 268nnnnnnnnnn nngg 1426925DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 269nnnnnnnnnn nnnnnnnnnn nggng 2527017DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 270nnnnnnnnnn nnnggng 1727125DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 271nnnnnnnnnn nnnnnnnnnn nggng 2527216DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 272nnnnnnnnnn nnggng 16
* * * * *
References