U.S. patent application number 16/654613 was filed with the patent office on 2020-05-07 for crispr-based genome modification and regulation.
This patent application is currently assigned to SIGMA-ALDRICH CO. LLC. The applicant listed for this patent is SIGMA-ALDRICH CO. LLC. Invention is credited to Fuqiang CHEN, Gregory D. Davis.
Application Number | 20200140897 16/654613 |
Document ID | / |
Family ID | 50883989 |
Filed Date | 2020-05-07 |
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United States Patent
Application |
20200140897 |
Kind Code |
A1 |
CHEN; Fuqiang ; et
al. |
May 7, 2020 |
CRISPR-BASED GENOME MODIFICATION AND REGULATION
Abstract
The present invention provides RNA-guided endonucleases, which
are engineered for expression in eukaryotic cells or embryos, and
methods of using the RNA-guided endonuclease for targeted genome
modification in eukaryotic cells or embryos. Also provided are
fusion proteins, wherein each fusion protein comprises a
CRISPR/Cas-like protein or fragment thereof and an effector domain.
The effector domain can be a cleavage domain, an epigenetic
modification domain, a transcriptional activation domain, or a
transcriptional repressor domain. Also provided are methods for
using the fusion proteins to modify a chromosomal sequence or
regulate expression of a chromosomal sequence.
Inventors: |
CHEN; Fuqiang; (St. Louis,
MO) ; Davis; Gregory D.; (Webster Groves,
MO) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
SIGMA-ALDRICH CO. LLC |
St. Louis |
MO |
US |
|
|
Assignee: |
SIGMA-ALDRICH CO. LLC
St. Louis
MO
|
Family ID: |
50883989 |
Appl. No.: |
16/654613 |
Filed: |
October 16, 2019 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15188911 |
Jun 21, 2016 |
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16654613 |
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14649777 |
Jun 4, 2015 |
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PCT/US2013/073307 |
Dec 5, 2013 |
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15188911 |
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61734256 |
Dec 6, 2012 |
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61758624 |
Jan 30, 2013 |
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61761046 |
Feb 5, 2013 |
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61794422 |
Mar 15, 2013 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 15/85 20130101;
C12N 15/63 20130101; C12N 2800/22 20130101; C07K 7/06 20130101;
C12N 2310/3513 20130101; Y02A 50/30 20180101; C12N 2310/20
20170501; C12N 9/22 20130101; C12N 15/67 20130101; C12N 7/00
20130101; C12N 15/102 20130101; C12N 2800/80 20130101; C07K 2319/09
20130101; C12Y 301/00 20130101; C12Y 301/21004 20130101; C12N 9/96
20130101; C12N 15/86 20130101; C07K 2319/81 20130101; C12N 15/11
20130101; C12N 15/907 20130101; C07K 14/463 20130101; A61K 38/00
20130101; C12N 2750/14143 20130101; C07K 2319/10 20130101 |
International
Class: |
C12N 15/90 20060101
C12N015/90; C12N 9/22 20060101 C12N009/22; C12N 15/63 20060101
C12N015/63; C12N 15/10 20060101 C12N015/10; C12N 15/85 20060101
C12N015/85; C07K 7/06 20060101 C07K007/06; C12N 15/11 20060101
C12N015/11; C12N 7/00 20060101 C12N007/00; C12N 15/67 20060101
C12N015/67; C12N 15/86 20060101 C12N015/86; C07K 14/46 20060101
C07K014/46; C12N 9/96 20060101 C12N009/96 |
Claims
1. A eukaryotic cell comprising a target chromosomal sequence; and
(i) at least one RNA-guided endonuclease comprising at least one
nuclear localization signal or nucleic acid encoding at least one
RNA-guided endonuclease comprising at least one nuclear
localization signal, wherein the at least one RNA-guided
endonuclease is a clustered regularly interspersed short
palindromic repeats (CRISPR)/CRISPR associated (Cas) (CRISPR-Cas)
type II system protein, wherein the nucleic acid encoding the
CRISPR-Cas9 type II protein is codon optimized for expression in
the eukaryotic cell, and wherein the CRISPR-Cas type II system
protein is a Cas9 protein, and (ii) at least one engineered guide
RNA or DNA encoding at least one engineered guide RNA, each guide
RNA comprising (1) a first region at the 5' end that is capable of
base pairing with a target site in the chromosomal sequence, and
(2) a second region that forms a secondary structure which
interacts with the at least one RNA-guided endonuclease; and
whereby base pairing of the first region to the target site is
capable of targeting the Cas9 protein to the target chromosomal
sequence.
2. The eukaryotic cell of claim 1, wherein the genome of said
eukaryotic cell comprises the target chromosomal sequence.
3. The eukaryotic cell of claim 1, wherein the eukaryotic cell is a
mammalian cell or a human cell.
4. The eukaryotic cell of claim 3, wherein (A) the guide RNA
comprises a single molecule such that the first region and the
second region on present on the same RNA molecule or (B) the guide
RNA comprises a double-molecule such that the first region and the
second region are present on different RNA molecules.
5. The eukaryotic cell of claim 4, comprising two or more first
regions, or one or more nucleic acids comprising two or more
nucleotide sequences encoding different first regions.
6. The eukaryotic cell of claim 1, wherein the system comprises a
nucleic acid molecule comprising a nucleotide sequence encoding the
second region, and wherein said nucleic acid molecule comprising a
nucleotide sequence encoding the second region does not comprise a
nucleotide sequence encoding said Cas9 protein.
7. The eukaryotic cell of claim 1, wherein the system comprises a
double stranded DNA molecule comprising nucleotide sequences
encoding both the first region of the guide RNA and the second
region of the guide RNA, wherein the nucleotide sequences encoding
the first region and the second region are on the same strand.
8. The eukaryotic cell of claim 1, wherein one or more of a) the
nucleic acid comprising the nucleotide sequence encoding said Cas9
protein and b) the one or more nucleic acids comprising one or more
nucleotide sequences encoding said guide RNA, are one or more
vectors, wherein the one or more vectors are selected from the
group consisting of plasmid vectors, phagemids, cosmids,
artificial/mini-chromosomes, transposons, and viral vectors; and
wherein the nucleotide sequence encoding said Cas9 protein and/or
the one or more nucleotide sequences encoding said guide RNA is
operably linked to a control element operable in said eukaryotic
cell.
9. The eukaryotic cell of claim 1, wherein the Cas9 protein
comprises one or more Nuclear Localization Signals (NLSs).
10. The eukaryotic cell of claim 9, wherein the one or more NLSs
comprises an amino acid sequence selected from the group consisting
of SEQ ID NO:1 and SEQ ID NO: 2.
11. The eukaryotic cell of claim 1, wherein the Cas9 protein
comprises one or more mutations in a RuvC domain and/or a HNH
domain.
12. The eukaryotic cell of claim 1, comprising two or more
different guide RNAs, or one or more nucleic acids comprising two
or more nucleotide sequences encoding different guide RNAs.
13. The eukaryotic cell of claim 1, wherein the system comprises a
donor polynucleotide and the system is capable of editing the
target chromosomal sequence by inserting a sequence of the donor
polynucleotide into a cleaved strand of the target chromosomal
sequence.
14. The eukaryotic cell of claim 1, wherein the nucleotide sequence
encoding said Cas9 protein comprises a nucleotide sequence
modification that replaces one or more codons of a wild-type
Cas9-encoding nucleotide sequence with one or more different codons
encoding the same amino acid.
15. The eukaryotic cell of claim 1, wherein said Cas9 protein
comprises one or more mutations in a RuvC domain and/or a HNH
domain and is capable of cleaving only one strand of DNA.
16. The eukaryotic cell of claim 15, wherein the nucleotide
sequence encoding said Cas9 protein comprises a nucleotide sequence
modification that replaces one or more codons of a wild-type
Cas9-encoding nucleotide sequence with one or more different codons
encoding the same amino acid.
17. The eukaryotic cell of claim 15, comprising two or more
different guide RNAs, or one or more nucleic acids comprising two
or more nucleotide sequences encoding different guide RNAs.
18. The eukaryotic cell of claim 15, wherein (A) the guide RNA
comprises a single molecule such that the first region and the
second region on present on the same RNA molecule or (B) the guide
RNA comprises a double-molecule such that the first region and the
second region are present on different RNA molecules.
19. The eukaryotic cell of claim 15, wherein the Cas9 protein
comprises one or more Nuclear Localization Signals (NLSs).
20. The eukaryotic cell of claim 19, wherein the one or more NLSs
comprises an amino acid sequence selected from the group consisting
of SEQ ID NO:1 and SEQ ID NO: 2.
21. A eukaryotic cell comprising a target chromosomal sequence and
an engineered and/or non-naturally occurring Type II Clustered
Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR
associated (Cas) (CRISPR-Cas) system comprising a) a Cas9 protein,
or a nucleic acid comprising a nucleotide sequence encoding said
Cas9 protein; and b) at least one engineered guide RNA or DNA
encoding at least one engineered guide RNA, each guide RNA
comprising i) a first region at the 5' end that is capable of base
pairing with a target site in the chromosomal sequence, and ii) a
second region that forms a secondary structure which interacts with
the at least one RNA-guided endonuclease; and; wherein (I) the
guide RNA comprises a nucleotide sequence that is modified relative
to naturally occurring guide RNAs, and/or (II) the Cas9 protein
comprises an amino acid sequence that is modified relative to
naturally occurring Cas9 proteins, wherein the guide RNA is capable
of forming a complex with the Cas9 protein, thereby targeting the
Cas9 protein to the target chromosomal sequence, whereby said
system is capable of cleaving or editing the target chromosomal
sequence.
22. The eukaryotic cell of claim 21, wherein the Cas9 protein
comprises one or more mutations in a RuvC domain and/or a HNH
domain.
23. The eukaryotic cell of claim 21, wherein one or more of the
nucleic acids of a) and b) are one or more vectors, wherein the one
or more vectors are selected from the group consisting of plasmid
vectors, phagemids, cosmids, artificial/mini-chromosomes,
transposons, and viral vectors; wherein the nucleotide sequence
encoding said Cas9 protein and/or the one or more nucleotide
sequence encoding said DNA-targeting RNA are operably linked to
control elements operable in said eukaryotic cell.
24. The eukaryotic cell of claim 21, wherein the Cas9 protein
comprises one or more Nuclear Localization Signals (NLSs).
25. The eukaryotic cell of claim 24, wherein said Cas9 protein
comprises one or more mutations in a RuvC domain and/or a HNH
domain and is capable of cleaving only one strand of DNA.
26. The eukaryotic cell of claim 25, wherein the one or more NLSs
comprises an amino acid sequence selected from the group consisting
of SEQ ID NO:1 and SEQ ID NO: 2.
27. A non-human plant or animal comprising the eukaryotic cell of
claim 1.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 15/188,911, filed Jun. 21, 2016, which is a
continuation application of U.S. patent application Ser. No.
14/649,777, filed Jun. 4, 2015, which is a U.S. National Stage
Application of PCT International Application No. PCT/US2013/073307,
filed Dec. 5, 2013, which claims priority to U.S. Provisional
Application Ser. No. 61/734,256, filed Dec. 6, 2012; U.S.
Provisional Application Ser. No. 61/758,624, filed Jan. 30, 2013;
U.S. Provisional Application Ser. No. 61/761,046, filed Feb. 5,
2013; and U.S. Provisional Application Ser. No. 61/794,422, filed
Mar. 15, 2013, the disclosure of each is hereby incorporated by
reference in its entirety.
FIELD OF THE INVENTION
[0002] The present disclosure relates targeted genome modification.
In particular, the disclosure relates to RNA-guided endonucleases
or fusion proteins comprising CRISPR/Cas-like protein and methods
of using said proteins to modify or regulate targeted chromosomal
sequences.
BACKGROUND OF THE INVENTION
[0003] Targeted genome modification is a powerful tool for genetic
manipulation of eukaryotic cells, embryos, and animals. For
example, exogenous sequences can be integrated at targeted genomic
locations and/or specific endogenous chromosomal sequences can be
deleted, inactivated, or modified. Current methods rely on the use
of engineered nuclease enzymes, such as, for example, zinc finger
nucleases (ZFNs) or transcription activator-like effector nucleases
(TALENs). These chimeric nucleases contain programmable,
sequence-specific DNA-binding modules linked to a nonspecific DNA
cleavage domain. Each new genomic target, however, requires the
design of a new ZFN or TALEN comprising a novel sequence-specific
DNA-binding module. Thus, these custom designed nucleases tend to
be costly and time-consuming to prepare. Moreover, the
specificities of ZFNs and TALENS are such that they can mediate
off-target cleavages.
[0004] Thus, there is a need for a targeted genome modification
technology that does not require the design of a new nuclease for
each new targeted genomic location. Additionally, there is a need
for a technology with increased specificity with few or no
off-target effects.
SUMMARY OF THE INVENTION
[0005] Among the various aspects of the present disclosure is the
provision of an isolated RNA-guided endonuclease, wherein the
endonuclease comprises at least one nuclear localization signal, at
least one nuclease domain, and at least one domain that interacts
with a guide RNA to target the endonuclease to a specific
nucleotide sequence for cleavage. In one embodiment, the
endonuclease can be derived from a Cas9 protein. In another
embodiment, the endonuclease can be modified to lack at least one
functional nuclease domain. In other embodiments, the endonuclease
can further comprise a cell-penetrating domain, a marker domain, or
both. In a further embodiment, the endonuclease can be part of a
protein-RNA complex comprising the guide RNA. In some instances,
the guide RNA can be a single molecule comprising a 5' region that
is complementary to a target site. Also provided is an isolated
nucleic acid encoding any of the RNA-guided endonucleases disclosed
herein. In some embodiments, the nucleic acid can be codon
optimized for translation in mammalian cells, such as, for example,
human cells. In other embodiments, the nucleic acid sequence
encoding the RNA-guided endonuclease can be operably linked to a
promoter control sequence, and optionally, can be part of a vector.
In other embodiments, a vector comprising sequence encoding the
RNA-guided endonuclease, which can be operably linked to a promoter
control sequence, can also comprise sequence encoding a guide RNA,
which can be operably linked to a promoter control sequence.
[0006] Another aspect of the present invention encompasses a method
for modifying a chromosomal sequence in a eukaryotic cell or
embryo. The method comprises introducing into a eukaryotic cell or
embryo (i) at least one RNA-guided endonuclease comprising at least
one nuclear localization signal or nucleic acid encoding at least
one RNA-guided endonuclease as defined herein, (ii) at least one
guide RNA or DNA encoding at least one guide RNA, and, optionally,
(iii) at least one donor polynucleotide comprising a donor
sequence. The method further comprises culturing the cell or embryo
such that each guide RNA directs a RNA-guided endonuclease to a
targeted site in the chromosomal sequence where the RNA-guided
endonuclease introduces a double-stranded break in the targeted
site, and the double-stranded break is repaired by a DNA repair
process such that the chromosomal sequence is modified. In one
embodiment, the RNA-guided endonuclease can be derived from a Cas9
protein. In another embodiment, the nucleic acid encoding the
RNA-guided endonuclease introduced into the cell or embryo can be
mRNA. In a further embodiment, wherein the nucleic acid encoding
the RNA-guided endonuclease introduced into the cell or embryo can
be DNA. In a further embodiment, the DNA encoding the RNA-guided
endonuclease can be part of a vector that further comprises a
sequence encoding the guide RNA. In certain embodiments, the
eukaryotic cell can be a human cell, a non-human mammalian cell, a
stem cell, a non-mammalian vertebrate cell, an invertebrate cell, a
plant cell, or a single cell eukaryotic organism. In certain other
embodiments, the embryo is a non-human one cell animal embryo.
[0007] A further aspect of the disclosure provides a fusion protein
comprising a CRISPR/Cas-like protein or fragment thereof and an
effector domain. In general, the fusion protein comprises at least
one nuclear localization signal. The effector domain of the fusion
protein can be a cleavage domain, an epigenetic modification
domain, a transcriptional activation domain, or a transcriptional
repressor domain. In one embodiment, the CRISPR/Cas-like protein of
the fusion protein can be derived from a Cas9 protein. In one
iteration, the Cas9 protein can be modified to lack at least one
functional nuclease domain. In an alternate iteration, the Cas9
protein can be modified to lack all nuclease activity. In one
embodiment, the effector domain can be a cleavage domain, such as,
for example, a FokI endonuclease domain or a modified FokI
endonuclease domain. In another embodiment, one fusion protein can
form a dimer with another fusion protein. The dimer can be a
homodimer or a heterodimer. In another embodiment, the fusion
protein can form a heterodimer with a zinc finger nuclease, wherein
the cleavage domain of both the fusion protein and the zinc finger
nucleases is a FokI endonuclease domain or a modified FokI
endonuclease domain. In still another embodiment, the fusion
protein comprises a CRISPR/Cas-like protein derived from a Cas9
protein modified to lack all nuclease activity, and the effector
domain is a FokI endonuclease domain or a modified FokI
endonuclease domain. In still another embodiment, the fusion
protein comprises a CRISPR/Cas-like protein derived from a Cas9
protein modified to lack all nuclease activity, and the effector
domain can be an epigenetic modification domain, a transcriptional
activation domain, or a transcriptional repressor domain. In
additional embodiments, any of the fusion proteins disclosed herein
can comprise at least one additional domain chosen from a nuclear
localization signal, a cell-penetrating domain, and a marker
domain. Also provided are isolated nucleic acids encoding any of
the fusion proteins provided herein.
[0008] Still another aspect of the disclosure encompasses a method
for modifying a chromosomal sequence or regulating expression of a
chromosomal sequence in a cell or embryo. The method comprises
introducing into the cell or embryo (a) at least one fusion protein
or nucleic acid encoding at least one fusion protein, wherein the
fusion protein comprises a CRISPR/Cas-like protein or a fragment
thereof and an effector domain, and (b) at least one guide RNA or
DNA encoding at least one guide RNA, wherein the guide RNA guides
the CRISPR/Cas-like protein of the fusion protein to a targeted
site in the chromosomal sequence and the effector domain of the
fusion protein modifies the chromosomal sequence or regulates
expression of the chromosomal sequence. In one embodiment, the
CRISPR/Cas-like protein of the fusion protein can be derived from a
Cas9 protein. In another embodiment, the CRISPR/Cas-like protein of
the fusion protein can be modified to lack at least one functional
nuclease domain. In still another embodiment, the CRISPR/Cas-like
protein of the fusion protein can be modified to lack all nuclease
activity. In one embodiment in which the fusion protein comprises a
Cas9 protein modified to lack all nuclease activity and a FokI
cleavage domain or a modified FokI cleavage domain, the method can
comprise introducing into the cell or embryo one fusion protein or
nucleic acid encoding one fusion protein and two guide RNAs or DNA
encoding two guide RNAs, and wherein one double-stranded break is
introduced in the chromosomal sequence. In another embodiment in
which the fusion protein comprises a Cas9 protein modified to lack
all nuclease activity and a FokI cleavage domain or a modified FokI
cleavage domain, the method can comprise introducing into the cell
or embryo two fusion proteins or nucleic acid encoding two fusion
proteins and two guide RNAs or DNA encoding two guide RNAs, and
wherein two double-stranded breaks are introduced in the
chromosomal sequence. In still another one embodiment in which the
fusion protein comprises a Cas9 protein modified to lack all
nuclease activity and a FokI cleavage domain or a modified FokI
cleavage domain, the method can comprise introducing into the cell
or embryo one fusion protein or nucleic acid encoding one fusion
protein, one guide RNA or nucleic acid encoding one guide RNA, and
one zinc finger nuclease or nucleic acid encoding one zinc finger
nuclease, wherein the zinc finger nuclease comprises a FokI
cleavage domain or a modified a FokI cleavage domain, and wherein
one double-stranded break is introduced into the chromosomal
sequence. In certain embodiments in which the fusion protein
comprises a cleavage domain, the method can further comprise
introducing into the cell or embryo at least one donor
polynucleotide. In embodiments in which the fusion protein
comprises an effector domain chosen from an epigenetic modification
domain, a transcriptional activation domain, or a transcriptional
repressor domain, the fusion protein can comprise a Cas9 protein
modified to lack all nuclease activity, and the method can comprise
introducing into the cell or embryo one fusion protein or nucleic
acid encoding one fusion protein, and one guide RNA or nucleic acid
encoding one guide RNA, and wherein the structure or expression of
the targeted chromosomal sequence is modified. In certain
embodiments, the eukaryotic cell can be a human cell, a non-human
mammalian cell, a stem cell, a non-mammalian vertebrate cell, an
invertebrate cell, a plant cell, or a single cell eukaryotic
organism. In certain other embodiments, the embryo is a non-human
one cell animal embryo.
[0009] Other aspects and iterations of the disclosure are detailed
below.
BRIEF DESCRIPTION OF THE DRAWINGS
[0010] FIG. 1A diagrams genome modification using protein dimers in
which a double stranded break created by a dimer composed of two
fusion proteins, each of which comprises a Cas-like protein for DNA
binding and a FokI cleavage domain. FIG. 1B depicts a double
stranded break created by a dimer composed of a fusion protein
comprising a Cas-like protein and a FokI cleavage domain and a zinc
finger nuclease comprising a zinc finger (ZF) DNA-binding domain
and a FokI cleavage domain.
[0011] FIG. 2A illustrates regulation of gene expression using
RNA-guided fusion proteins comprising a Cas-like protein used for
DNA binding and an "A/R" domain that activates or represses gene
expression. FIG. 2B diagrams a fusion protein comprising a Cas-like
protein for DNA binding and a epigenetic modification domain
("Epi-mod`) that affects epigenetic states by covalent modification
of proximal DNA or proteins.
[0012] FIG. 3A diagrams a double stranded break created by two
RNA-guided endonuclease that have been converted into nickases.
FIG. 3B depicts two double stranded breaks created by two
RNA-guided endonuclease having endonuclease activity.
[0013] FIG. 4A-F present fluorescence-activated cell sorting (FACS)
of human K562 cells transfected with Cas9 nucleic acid, Cas9
guiding RNA, and AAVS1-GFP DNA donor. The Y axis represents the
auto fluorescence intensity at a red channel, and the X axis
represents the green fluorescence intensity. FIG. 4A presents K562
cells transfected with 10 .mu.g of Cas9 mRNA transcribed with an
Anti-Reverse Cap Analog, 0.3 nmol of pre-annealed crRNA-tracrRNA
duplex, and 10 .mu.g of AAVS1-GFP plasmid DNA; FIG. 4B depicts K562
cells transfected 10 .mu.g of Cas9 mRNA transcribed with an
Anti-Reverse Cap Analog, 0.3 nmol of chimeric RNA, and 10 .mu.g of
AAVS1-GFP plasmid DNA; FIG. 4C shows K562 cells transfected 10
.mu.g of Cas9 mRNA that was capped by post-transcription capping
reaction, 0.3 nmol of chimeric RNA, and 10 .mu.g of AAVS1-GFP
plasmid DNA; FIG. 4D presents K562 cells transfected with 10 .mu.g
of Cas9 plasmid DNA, 5 .mu.g of U6-chimeric RNA plasmid DNA, and 10
.mu.g of AAVS1-GFP plasmid DNA; FIG. 4E shows K562 cells
transfected with 10 .mu.g of AAVS1-GFP plasmid DNA; and FIG. 4F
presents K562 cells transfected with transfection reagents
only.
[0014] FIG. 5 presents a junction PCR analysis documenting the
targeted integration of GFP into the AAVS1 locus in human cells.
Lane M: 1 kb DNA molecular markers; Lane A: K562 cells transfected
with 10 .mu.g of Cas9 mRNA transcribed with an Anti-Reverse Cap
Analog, 0.3 nmol of pre-annealed crRNA-tracrRNA duplex, and 10
.mu.g of AAVS1-GFP plasmid DNA; Lane B: K562 cells transfected 10
.mu.g of Cas9 mRNA transcribed with an Anti-Reverse Cap Analog, 0.3
nmol of chimeric RNA, and 10 .mu.g of AAVS1-GFP plasmid DNA; Lane
C: K562 cells transfected 10 .mu.g of Cas9 mRNA that was capped by
post-transcription capping reaction, 0.3 nmol of chimeric RNA, and
10 .mu.g of AAVS1-GFP plasmid DNA; Lane D: K562 cells transfected
with 10 .mu.g of Cas9 plasmid DNA, 5 .mu.g of U6-chimeric RNA
plasmid DNA, and 10 .mu.g of AAVS1-GFP plasmid DNA; Lane E: K562
cells transfected with 10 .mu.g of AAVS1-GFP plasmid DNA; Lane F:
K562 cells transfected with transfection reagents only.
DETAILED DESCRIPTION OF THE INVENTION
[0015] Provided herein are RNA-guided endonucleases, which comprise
at least one nuclear localization signal, at least one nuclease
domain, and at least one domain that interacts with a guide RNA to
target the endonuclease to a specific nucleotide sequence for
cleavage. Also provided are nucleic acids encoding the RNA-guided
endonucleases, as well as methods of using the RNA-guided
endonucleases to modify chromosomal sequences of eukaryotic cells
or embryos. The RNA-guided endonuclease interacts with specific
guide RNAs, each of which directs the endonuclease to a specific
targeted site, at which site the RNA-guided endonuclease introduces
a double-stranded break that can be repaired by a DNA repair
process such that the chromosomal sequence is modified. Since the
specificity is provided by the guide RNA, the RNA-based
endonuclease is universal and can be used with different guide RNAs
to target different genomic sequences. The methods disclosed herein
can be used to target and modify specific chromosomal sequences
and/or introduce exogenous sequences at targeted locations in the
genome of cells or embryos. Furthermore, the targeting is specific
with limited off target effects.
[0016] The present disclosure provides fusion proteins, wherein a
fusion protein comprises a CRISPR/Cas-like protein or fragment
thereof and an effector domain. Suitable effector domains include,
without limit, cleavage domains, epigenetic modification domains,
transcriptional activation domains, and transcriptional repressor
domains. Each fusion protein is guided to a specific chromosomal
sequence by a specific guide RNA, wherein the effector domain
mediates targeted genome modification or gene regulation. In one
aspect, the fusion proteins can function as dimers thereby
increasing the length of the target site and increasing the
likelihood of its uniqueness in the genome (thus, reducing off
target effects). For example, endogenous CRISPR systems modify
genomic locations based on DNA binding word lengths of
approximately 13-20 bp (Cong et al., Science, 339:819-823). At this
word size, only 5-7% of the target sites are unique within the
genome (Iseli et al, PLos One 2(6):e579). In contrast, DNA binding
word sizes for zinc finger nucleases typically range from 30-36 bp,
resulting in target sites that are approximately 85-87% unique
within the human genome. The smaller sized DNA binding sites
utilized by CRISPR-based systems limits and complicates design of
targeted CRISP-based nucleases near desired locations, such as
disease SNPs, small exons, start codons, and stop codons, as well
as other locations within complex genomes. The present disclosure
not only provides means for expanding the CRISPR DNA binding word
length (i.e., so as to limit off-target activity), but further
provides CRISPR fusion proteins having modified functionality.
According, the disclosed CRISPR fusion proteins have increased
target specificity and unique functionality(ies). Also provided
herein are methods of using the fusion proteins to modify or
regulate expression of targeted chromosomal sequences.
(I) RNA-Guided Endonucleases
[0017] One aspect of the present disclosure provides RNA-guided
endonucleases comprising at least one nuclear localization signal,
which permits entry of the endonuclease into the nuclei of
eukaryotic cells and embryos such as, for example, non-human one
cell embryos. RNA-guided endonucleases also comprise at least one
nuclease domain and at least one domain that interacts with a guide
RNA. An RNA-guided endonuclease is directed to a specific nucleic
acid sequence (or target site) by a guide RNA. The guide RNA
interacts with the RNA-guided endonuclease as well as the target
site such that, once directed to the target site, the RNA-guided
endonuclease is able to introduce a double-stranded break into the
target site nucleic acid sequence. Since the guide RNA provides the
specificity for the targeted cleavage, the endonuclease of the
RNA-guided endonuclease is universal and can be used with different
guide RNAs to cleave different target nucleic acid sequences.
Provided herein are isolated RNA-guided endonucleases, isolated
nucleic acids (i.e., RNA or DNA) encoding the RNA-guided
endonucleases, vectors comprising nucleic acids encoding the
RNA-guided endonucleases, and protein-RNA complexes comprising the
RNA-guided endonuclease plus a guide RNA.
[0018] The RNA-guided endonuclease can be derived from a clustered
regularly interspersed short palindromic repeats
(CRISPR)/CRISPR-associated (Cas) system. The CRISPR/Cas system can
be a type I, a type II, or a type III system. Non-limiting examples
of suitable CRISPR/Cas proteins include Cas3, Cas4, Cas5, Cas5e (or
CasD), Cas6, Cas6e, Cas6f, Cas7, Cas8a1, Cas8a2, Cas8b, Cas8c,
Cas9, Cas10, Cas10d, CasF, CasG, CasH, Csy1, Csy2, Csy3, Cse1 (or
CasA), Cse2 (or CasB), Cse3 (or CasE), Cse4 (or CasC), Csc1, Csc2,
Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5,
Cmr6, Csb1, Csb2, Csb3,Csx17, Csx14, Csx10, Csx16, CsaX, Csx3,
Csz1, Csx15, Csf1, Csf2, Csf3, Csf4, and Cu1966.
[0019] In one embodiment, the RNA-guided endonuclease is derived
from a type II CRISPR/Cas system. In specific embodiments, the
RNA-guided endonuclease is derived from a Cas9 protein. The Cas9
protein can be from Streptococcus pyogenes, Streptococcus
thermophilus, Streptococcus sp., Nocardiopsis dassonvillei,
Streptomyces pristinaespiralis, Streptomyces viridochromogenes,
Streptomyces viridochromogenes, Streptosporangium roseum,
Streptosporangium roseum, Alicyclobacillus acidocaldarius, Bacillus
pseudomycoides, Bacillus selenitireducens, Exiguobacterium
sibiricum, Lactobacillus delbrueckii, Lactobacillus salivarius,
Microscilla marina, Burkholderiales bacterium, Polaromonas
naphthalenivorans, Polaromonas sp., Crocosphaera watsonii,
Cyanothece sp., Microcystis aeruginosa, Synechococcus sp.,
Acetohalobium arabaticum, Ammonifex degensii, Caldicelulosiruptor
becscii, Candidatus Desulforudis, Clostridium botulinum,
Clostridium difficile, Finegoldia magna, Natranaerobius
thermophilus, Pelotomaculum thermopropionicum, Acidithiobacillus
caldus, Acidithiobacillus ferrooxidans, Allochromatium vinosum,
Marinobacter sp., Nitrosococcus halophilus, Nitrosococcus watsoni,
Pseudoalteromonas haloplanktis, Ktedonobacter racemifer,
Methanohalobium evestigatum, Anabaena variabilis, Nodularia
spumigena, Nostoc sp., Arthrospira maxima, Arthrospira platensis,
Arthrospira sp., Lyngbya sp., Microcoleus chthonoplastes,
Oscillatoria sp., Petrotoga mobilis, Thermosipho africanus, or
Acaryochloris marina.
[0020] In general, CRISPR/Cas proteins comprise at least one RNA
recognition and/or RNA binding domain. RNA recognition and/or RNA
binding domains interact with guide RNAs. CRISPR/Cas proteins can
also comprise nuclease domains (i.e., DNase or RNase domains), DNA
binding domains, helicase domains, RNAse domains, protein-protein
interaction domains, dimerization domains, as well as other
domains.
[0021] The CRISPR/Cas-like protein can be a wild type CRISPR/Cas
protein, a modified CRISPR/Cas protein, or a fragment of a wild
type or modified CRISPR/Cas protein. The CRISPR/Cas-like protein
can be modified to increase nucleic acid binding affinity and/or
specificity, alter an enzymatic activity, and/or change another
property of the protein. For example, nuclease (i.e., DNase, RNase)
domains of the CRISPR/Cas-like protein can be modified, deleted, or
inactivated. Alternatively, the CRISPR/Cas-like protein can be
truncated to remove domains that are not essential for the function
of the fusion protein. The CRISPR/Cas-like protein can also be
truncated or modified to optimize the activity of the effector
domain of the fusion protein.
[0022] In some embodiments, the CRISPR/Cas-like protein can be
derived from a wild type Cas9 protein or fragment thereof. In other
embodiments, the CRISPR/Cas-like protein can be derived from
modified Cas9 protein. For example, the amino acid sequence of the
Cas9 protein can be modified to alter one or more properties (e.g.,
nuclease activity, affinity, stability, etc.) of the protein.
Alternatively, domains of the Cas9 protein not involved in
RNA-guided cleavage can be eliminated from the protein such that
the modified Cas9 protein is smaller than the wild type Cas9
protein.
[0023] In general, a Cas9 protein comprises at least two nuclease
(i.e., DNase) domains. For example, a Cas9 protein can comprise a
RuvC-like nuclease domain and a HNH-like nuclease domain. The RuvC
and HNH domains work together to cut single strands to make a
double-stranded break in DNA. (Jinek et al., Science, 337:
816-821). In some embodiments, the Cas9-derived protein can be
modified to contain only one functional nuclease domain (either a
RuvC-like or a HNH-like nuclease domain). For example, the
Cas9-derived protein can be modified such that one of the nuclease
domains is deleted or mutated such that it is no longer functional
(i.e., the nuclease activity is absent). In some embodiments in
which one of the nuclease domains is inactive, the Cas9-derived
protein is able to introduce a nick into a double-stranded nucleic
acid (such protein is termed a "nickase"), but not cleave the
double-stranded DNA. For example, an aspartate to alanine (D10A)
conversion in a RuvC-like domain converts the Cas9-derived protein
into a nickase. Likewise, a histidine to alanine (H840A or H839A)
conversion in a HNH domain converts the Cas9-derived protein into a
nickase. Each nuclease domain can be modified using well-known
methods, such as site-directed mutagenesis, PCR-mediated
mutagenesis, and total gene synthesis, as well as other methods
known in the art.
[0024] The RNA-guided endonuclease disclosed herein comprises at
least one nuclear localization signal. In general, an NLS comprises
a stretch of basic amino acids. Nuclear localization signals are
known in the art (see, e.g., Lange et al., J. Biol. Chem., 2007,
282:5101-5105). For example, in one embodiment, the NLS can be a
monopartite sequence, such as PKKKRKV (SEQ ID NO:1) or PKKKRRV (SEQ
ID NO:2). In another embodiment, the NLS can be a bipartite
sequence. In still another embodiment, the NLS can be
KRPAATKKAGQAKKKK (SEQ ID NO:3). The NLS can be located at the
N-terminus, the C-terminal, or in an internal location of the
RNA-guided endonuclease.
[0025] In some embodiments, the RNA-guided endonuclease can further
comprise at least one cell-penetrating domain. In one embodiment,
the cell-penetrating domain can be a cell-penetrating peptide
sequence derived from the HIV-1 TAT protein. As an example, the TAT
cell-penetrating sequence can be GRKKRRQRRRPPQPKKKRKV (SEQ ID
NO:4). In another embodiment, the cell-penetrating domain can be
TLM (PLSSIFSRIGDPPKKKRKV; SEQ ID NO:5), a cell-penetrating peptide
sequence derived from the human hepatitis B virus. In still another
embodiment, the cell-penetrating domain can be MPG
(GALFLGWLGAAGSTMGAPKKKRKV; SEQ ID NO:6 or
GALFLGFLGAAGSTMGAWSQPKKKRKV; SEQ ID NO:7). In an additional
embodiment, the cell-penetrating domain can be Pep-1
(KETWWETWWVTEWSQPKKKRKV; SEQ ID NO:8), VP22, a cell penetrating
peptide from Herpes simplex virus, or a polyarginine peptide
sequence. The cell-penetrating domain can be located at the
N-terminus, the C-terminus, or in an internal location of the
protein.
[0026] In still other embodiments, the RNA-guided endonuclease can
also comprise at least one marker domain. Non-limiting examples of
marker domains include fluorescent proteins, purification tags, and
epitope tags. In some embodiments, the marker domain can be a
fluorescent protein. Non limiting examples of suitable fluorescent
proteins include green fluorescent proteins (e.g., GFP, GFP-2,
tagGFP, turboGFP, EGFP, Emerald, Azami Green, Monomeric Azami
Green, CopGFP, AceGFP, ZsGreen1), yellow fluorescent proteins (e.g.
YFP, EYFP, Citrine, Venus, YPet, PhiYFP, ZsYellow1,), blue
fluorescent proteins (e.g. EBFP, EBFP2, Azurite, mKalama1, GFPuv,
Sapphire, T-sapphire,), cyan fluorescent proteins (e.g. ECFP,
Cerulean, CyPet, AmCyan1, Midoriishi-Cyan), red fluorescent
proteins (mKate, mKate2, mPlum, DsRed monomer, mCherry, mRFP1,
DsRed-Express, DsRed2, DsRed-Monomer, HcRed-Tandem, HcRed1, AsRed2,
eqFP611, mRasberry, mStrawberry, Jred), and orange fluorescent
proteins (mOrange, mKO, Kusabira-Orange, Monomeric Kusabira-Orange,
mTangerine, tdTomato) or any other suitable fluorescent protein. In
other embodiments, the marker domain can be a purification tag
and/or an epitope tag. Exemplary tags include, but are not limited
to, glutathione-S-transferase (GST), chitin binding protein (CBP),
maltose binding protein, thioredoxin (TRX), poly(NANP), tandem
affinity purification (TAP) tag, myc, AcV5, AU1, AU5, E, ECS, E2,
FLAG, HA, nus, Softag 1, Softag 3, Strep, SBP, Glu-Glu, HSV, KT3,
S, S1, T7, V5, VSV-G, 6.times.His, biotin carboxyl carrier protein
(BCCP), and calmodulin.
[0027] In certain embodiments, the RNA-guided endonuclease may be
part of a protein-RNA complex comprising a guide RNA. The guide RNA
interacts with the RNA-guided endonuclease to direct the
endonuclease to a specific target site, wherein the 5' end of the
guide RNA base pairs with a specific protospacer sequence.
(II) Fusion Proteins
[0028] Another aspect of the present disclosure provides a fusion
protein comprising a CRISPR/Cas-like protein or fragment thereof
and an effector domain. The CRISPR/Cas-like protein is directed to
a target site by a guide RNA, at which site the effector domain can
modify or effect the targeted nucleic acid sequence. The effector
domain can be a cleavage domain, an epigenetic modification domain,
a transcriptional activation domain, or a transcriptional repressor
domain. The fusion protein can further comprise at least one
additional domain chosen from a nuclear localization signal, a
cell-penetrating domain, or a marker domain.
[0029] (a) CRISPR/Cas-Like Protein
[0030] The fusion protein comprises a CRISPR/Cas-like protein or a
fragment thereof. CRISPR/Cas-like proteins are detailed above in
section (I). The CRISPR/Cas-like protein can be located at the
N-terminus, the C-terminus, or in an internal location of the
fusion protein
[0031] In some embodiments, the CRISPR/Cas-like protein of the
fusion protein can be derived from a Cas9 protein. The Cas9-derived
protein can be wild type, modified, or a fragment thereof. In some
embodiments, the Cas9-derived protein can be modified to contain
only one functional nuclease domain (either a RuvC-like or a
HNH-like nuclease domain). For example, the Cas9-derived protein
can be modified such that one of the nuclease domains is deleted or
mutated such that it is no longer functional (i.e., the nuclease
activity is absent). In some embodiments in which one of the
nuclease domains is inactive, the Cas9-derived protein is able to
introduce a nick into a double-stranded nucleic acid (such protein
is termed a "nickase"), but not cleave the double-stranded DNA. For
example, an aspartate to alanine (D10A) conversion in a RuvC-like
domain converts the Cas9-derived protein into a nickase. Likewise,
a histidine to alanine (H840A or H839A) conversion in a HNH domain
converts the Cas9-derived protein into a nickase. In other
embodiments, both of the RuvC-like nuclease domain and the HNH-like
nuclease domain can be modified or eliminated such that the
Cas9-derived protein is unable to nick or cleave double stranded
nucleic acid. In still other embodiments, all nuclease domains of
the Cas9-derived protein can be modified or eliminated such that
the Cas9-derived protein lacks all nuclease activity.
[0032] In any of the above-described embodiments, any or all of the
nuclease domains can be inactivated by one or more deletion
mutations, insertion mutations, and/or substitution mutations using
well-known methods, such as site-directed mutagenesis, PCR-mediated
mutagenesis, and total gene synthesis, as well as other methods
known in the art. In an exemplary embodiment, the CRISPR/Cas-like
protein of the fusion protein is derived from a Cas9 protein in
which all the nuclease domains have been inactivated or
deleted.
[0033] (b) Effector Domain
[0034] The fusion protein also comprises an effector domain. The
effector domain can be a cleavage domain, an epigenetic
modification domain, a transcriptional activation domain, or a
transcriptional repressor domain. The effector domain can be
located at the N-terminus, the C-terminus, or in an internal
location of the fusion protein.
[0035] (i) Cleavage Domain
[0036] In some embodiments, the effector domain is a cleavage
domain. As used herein, a "cleavage domain" refers to a domain that
cleaves DNA. The cleavage domain can be obtained from any
endonuclease or exonuclease. Non-limiting examples of endonucleases
from which a cleavage domain can be derived include, but are not
limited to, restriction endonucleases and homing endonucleases.
See, for example, New England Biolabs Catalog or Belfort et al.
(1997) Nucleic Acids Res. 25:3379-3388. Additional enzymes that
cleave DNA are known (e.g., 51 Nuclease; mung bean nuclease;
pancreatic DNase I; micrococcal nuclease; yeast HO endonuclease).
See also Linn et al. (eds.) Nucleases, Cold Spring Harbor
Laboratory Press, 1993. One or more of these enzymes (or functional
fragments thereof) can be used as a source of cleavage domains.
[0037] In some embodiments, the cleavage domain can be derived from
a type II-S endonuclease. Type II-S endonucleases cleave DNA at
sites that are typically several base pairs away the recognition
site and, as such, have separable recognition and cleavage domains.
These enzymes generally are monomers that transiently associate to
form dimers to cleave each strand of DNA at staggered locations.
Non-limiting examples of suitable type II-S endonucleases include
BfiI, BpmI, BsaI, BsgI, BsmBI, BsmI, BspMI, FokI, MbolI, and SapI.
In exemplary embodiments, the cleavage domain of the fusion protein
is a FokI cleavage domain or a derivative thereof.
[0038] In certain embodiments, the type II-S cleavage can be
modified to facilitate dimerization of two different cleavage
domains (each of which is attached to a CRISPR/Cas-like protein or
fragment thereof). For example, the cleavage domain of FokI can be
modified by mutating certain amino acid residues. By way of
non-limiting example, amino acid residues at positions 446, 447,
479, 483, 484, 486, 487, 490, 491, 496, 498, 499, 500, 531, 534,
537, and 538 of FokI cleavage domains are targets for modification.
For example, modified cleavage domains of FokI that form obligate
heterodimers include a pair in which a first modified cleavage
domain includes mutations at amino acid positions 490 and 538 and a
second modified cleavage domain that includes mutations at amino
acid positions 486 and 499 (Miller et al., 2007, Nat. Biotechnol,
25:778-785; Szczpek et al., 2007, Nat. Biotechnol, 25:786-793). For
example, the Glu (E) at position 490 can be changed to Lys (K) and
the Ile (I) at position 538 can be changed to K in one domain
(E490K, I538K), and the Gln (Q) at position 486 can be changed to E
and the I at position 499 can be changed to Leu (L) in another
cleavage domain (Q486E, I499L). In other embodiments, modified FokI
cleavage domains can include three amino acid changes (Doyon et al.
2011, Nat. Methods, 8:74-81). For example, one modified FokI domain
(which is termed ELD) can comprise Q486E, I499L, N496D mutations
and the other modified FokI domain (which is termed KKR) can
comprise E490K, I538K, H537R mutations.
[0039] In exemplary embodiments, the effector domain of the fusion
protein is a FokI cleavage domain or a modified FokI cleavage
domain.
[0040] In embodiments wherein the effector domain is a cleavage
domain and the CRISPR/Cas-like protein is derived from a Cas9
protein, the Cas9-derived can be modified as discussed herein such
that its endonuclease activity is eliminated. For example, the
Cas9-derived can be modified by mutating the RuvC and HNH domains
such that they no longer possess nuclease activity.
[0041] (ii) Epigenetic Modification Domain
[0042] In other embodiments, the effector domain of the fusion
protein can be an epigenetic modification domain. In general,
epigenetic modification domains alter histone structure and/or
chromosomal structure without altering the DNA sequence. Changes
histone and/or chromatin structure can lead to changes in gene
expression. Examples of epigenetic modification include, without
limit, acetylation or methylation of lysine residues in histone
proteins, and methylation of cytosine residues in DNA. Non-limiting
examples of suitable epigenetic modification domains include
histone acetyltansferase domains, histone deacetylase domains,
histone methyltransferase domains, histone demethylase domains, DNA
methyltransferase domains, and DNA demethylase domains.
[0043] In embodiments in which the effector domain is a histone
acetyltansferase (HAT) domain, the HAT domain can be derived from
EP300 (i.e., E1A binding protein p300), CREBBP (i.e., CREB-binding
protein), CDY1, CDY2, CDYL1, CLOCK, ELP3, ESA1, GCN5 (KAT2A),
HAT1,KAT2B, KAT5, MYST1, MYST2, MYST3, MYST4, NCOA1, NCOA2, NCOA3,
NCOAT, P/CAF, Tip60, TAFII250, or TF3C4. In one such embodiment,
the HAT domain is p300
[0044] In embodiments wherein the effector domain is an epigenetic
modification domain and the CRISPR/Cas-like protein is derived from
a Cas9 protein, the Cas9-derived can be modified as discussed
herein such that its endonuclease activity is eliminated. For
example, the Cas9-derived can be modified by mutating the RuvC and
HNH domains such that they no longer possess nuclease activity.
[0045] (iii) Transcriptional Activation Domain
[0046] In other embodiments, the effector domain of the fusion
protein can be a transcriptional activation domain. In general, a
transcriptional activation domain interacts with transcriptional
control elements and/or transcriptional regulatory proteins (i.e.,
transcription factors, RNA polymerases, etc.) to increase and/or
activate transcription of a gene. In some embodiments, the
transcriptional activation domain can be, without limit, a herpes
simplex virus VP16 activation domain, VP64 (which is a tetrameric
derivative of VP16), a NF.kappa.B p65 activation domain, p53
activation domains 1 and 2, a CREB (cAMP response element binding
protein) activation domain, an E2A activation domain, and an NFAT
(nuclear factor of activated T-cells) activation domain. In other
embodiments, the transcriptional activation domain can be Gal4,
Gcn4, MLL, Rtg3, Gln3, Oaf1, Pip2, Pdr1, Pdr3, Pho4, and Leu3. The
transcriptional activation domain may be wild type, or it may be a
modified version of the original transcriptional activation domain.
In some embodiments, the effector domain of the fusion protein is a
VP16 or VP64 transcriptional activation domain.
[0047] In embodiments wherein the effector domain is a
transcriptional activation domain and the CRISPR/Cas-like protein
is derived from a Cas9 protein, the Cas9-derived protein can be
modified as discussed herein such that its endonuclease activity is
eliminated. For example, the Cas9-derived can be modified by
mutating the RuvC and HNH domains such that they no longer possess
nuclease activity.
[0048] (iv) Transcriptional Repressor Domain
[0049] In still other embodiments, the effector domain of the
fusion protein can be a transcriptional repressor domain. In
general, a transcriptional repressor domain interacts with
transcriptional control elements and/or transcriptional regulatory
proteins (i.e., transcription factors, RNA polymerases, etc.) to
decrease and/or terminate transcription of a gene. Non-limiting
examples of suitable transcriptional repressor domains include
inducible cAMP early repressor (ICER) domains, Kruppel-associated
box A (KRAB-A) repressor domains, YY1 glycine rich repressor
domains, Sp1-like repressors, E(spl) repressors, I.kappa.B
repressor, and MeCP2.
[0050] In embodiments wherein the effector domain is a
transcriptional repressor domain and the CRISPR/Cas-like protein is
derived from a Cas9 protein, the Cas9-derived protein can be
modified as discussed herein such that its endonuclease activity is
eliminated. For example, the cas9 can be modified by mutating the
RuvC and HNH domains such that they no longer possess nuclease
activity.
[0051] (c) Additional Domains
[0052] In some embodiments, the fusion protein further comprises at
least one additional domain. Non-limiting examples of suitable
additional domains include nuclear localization signals,
cell-penetrating or translocation domains, and marker domains.
Non-limiting examples of suitable nuclear localization signals,
cell-penetrating domains, and marker domains are presented above in
section (I).
[0053] (d) Fusion Protein Dimers
[0054] In embodiments in which the effector domain of the fusion
protein is a cleavage domain, a dimer comprising at least one
fusion protein can form. The dimer can be a homodimer or a
heterodimer. In some embodiments, the heterodimer comprises two
different fusion proteins. In other embodiments, the heterodimer
comprises one fusion protein and an additional protein.
[0055] In some embodiments, the dimer is a homodimer in which the
two fusion protein monomers are identical with respect to the
primary amino acid sequence. In one embodiment where the dimer is a
homodimer, the Cas9-derived proteins are modified such that their
endonuclease activity is eliminated, i.e., such that they have no
functional nuclease domains. In certain embodiments wherein the
Cas9-derived proteins are modified such that their endonuclease
activity is eliminated, each fusion protein monomer comprises an
identical Cas9 like protein and an identical cleavage domain. The
cleavage domain can be any cleavage domain, such as any of the
exemplary cleavage domains provided herein. In one specific
embodiment, the cleavage domain is a FokI cleavage domain or a
modified FokI cleavage domain. In such embodiments, specific guide
RNAs would direct the fusion protein monomers to different but
closely adjacent sites such that, upon dimer formation, the
nuclease domains of the two monomers would create a double stranded
break in the target DNA.
[0056] In other embodiments, the dimer is a heterodimer of two
different fusion proteins. For example, the CRISPR/Cas-like protein
of each fusion protein can be derived from a different CRISPR/Cas
protein or from an orthologous CRISPR/Cas protein from a different
bacterial species. For example, each fusion protein can comprise a
Cas9-like protein, which Cas9-like protein is derived from a
different bacterial species. In these embodiments, each fusion
protein would recognize a different target site (i.e., specified by
the protospacer and/or PAM sequence). For example, the guide RNAs
could position the heterodimer to different but closely adjacent
sites such that their nuclease domains results in an effective
double stranded break in the target DNA. The heterodimer can also
have modified Cas9 proteins with nicking activity such that the
nicking locations are different.
[0057] Alternatively, two fusion proteins of a heterodimer can have
different effector domains. In embodiments in which the effector
domain is a cleavage domain, each fusion protein can contain a
different modified cleavage domain. For example, each fusion
protein can contain a different modified FokI cleavage domain, as
detailed above in section (II)(b)(i). In these embodiments, the
Cas-9 proteins can be modified such that their endonuclease
activities are eliminated.
[0058] As will be appreciated by those skilled in the art, the two
fusion proteins forming a heterodimer can differ in both the
CRISPR/Cas-like protein domain and the effector domain.
[0059] In any of the above-described embodiments, the homodimer or
heterodimer can comprise at least one additional domain chosen from
nuclear localization signals (NLSs), cell-penetrating,
translocation domains and marker domains, as detailed above.
[0060] In any of the above-described embodiments, one or both of
the Cas9-derived proteins can be modified such that its
endonuclease activity is eliminated or modified.
[0061] In still alternate embodiments, the heterodimer comprises
one fusion protein and an additional protein. For example, the
additional protein can be a nuclease. In one embodiment, the
nuclease is a zinc finger nuclease. A zinc finger nuclease
comprises a zinc finger DNA binding domain and a cleavage domain. A
zinc finger recognizes and binds three (3) nucleotides. A zinc
finger DNA binding domain can comprise from about three zinc
fingers to about seven zinc fingers. The zinc finger DNA binding
domain can be derived from a naturally occurring protein or it can
be engineered. See, for example, Beerli et al. (2002) Nat.
Biotechnol. 20:135-141; Pabo et al. (2001) Ann. Rev. Biochem.
70:313-340; Isalan et al. (2001) Nat. Biotechnol. 19:656-660; Segal
et al. (2001) Curr. Opin. Biotechnol. 12:632-637; Choo et al.
(2000) Curr. Opin. Struct. Biol. 10:411-416; Zhang et al. (2000) J.
Biol. Chem. 275(43):33850-33860; Doyon et al. (2008) Nat.
Biotechnol. 26:702-708; and Santiago et al. (2008) Proc. Natl.
Acad. Sci. USA 105:5809-5814. The cleavage domain of the zinc
finger nuclease can be any cleavage domain detailed above in
section (II)(b)(i). In exemplary embodiments, the cleavage domain
of the zinc finger nuclease is a FokI cleavage domain or a modified
FokI cleavage domain. Such a zinc finger nuclease will dimerize
with a fusion protein comprising a FokI cleavage domain or a
modified FokI cleavage domain.
[0062] In some embodiments, the zinc finger nuclease can comprise
at least one additional domain chosen from nuclear localization
signals, cell-penetrating or translocation domains, which are
detailed above.
[0063] In certain embodiments, any of the fusion protein detailed
above or a dimer comprising at least one fusion protein may be part
of a protein-RNA complex comprising at least one guide RNA. A guide
RNA interacts with the CRISPR-Cas0like protein of the fusion
protein to direct the fusion protein to a specific target site,
wherein the 5' end of the guide RNA base pairs with a specific
protospacer sequence.
(III) Nucleic Acids Encoding RNA-Guided Endonucleases or Fusion
Proteins
[0064] Another aspect of the present disclosure provides nucleic
acids encoding any of the RNA-guided endonucleases or fusion
proteins described above in sections (I) and (II), respectively.
The nucleic acid can be RNA or DNA. In one embodiment, the nucleic
acid encoding the RNA-guided endonuclease or fusion protein is
mRNA. The mRNA can be 5' capped and/or 3' polyadenylated. In
another embodiment, the nucleic acid encoding the RNA-guided
endonuclease or fusion protein is DNA. The DNA can be present in a
vector (see below).
[0065] The nucleic acid encoding the RNA-guided endonuclease or
fusion protein can be codon optimized for efficient translation
into protein in the eukaryotic cell or animal of interest. For
example, codons can be optimized for expression in humans, mice,
rats, hamsters, cows, pigs, cats, dogs, fish, amphibians, plants,
yeast, insects, and so forth. Programs for codon optimization are
available as freeware. Commercial codon optimization programs are
also available.
[0066] In some embodiments, DNA encoding the RNA-guided
endonuclease or fusion protein can be operably linked to at least
one promoter control sequence. In some iterations, the DNA coding
sequence can be operably linked to a promoter control sequence for
expression in the eukaryotic cell or animal of interest. The
promoter control sequence can be constitutive, regulated, or
tissue-specific. Suitable constitutive promoter control sequences
include, but are not limited to, cytomegalovirus immediate early
promoter (CMV), simian virus (SV40) promoter, adenovirus major late
promoter, Rous sarcoma virus (RSV) promoter, mouse mammary tumor
virus (MMTV) promoter, phosphoglycerate kinase (PGK) promoter,
elongation factor (ED1)-alpha promoter, ubiquitin promoters, actin
promoters, tubulin promoters, immunoglobulin promoters, fragments
thereof, or combinations of any of the foregoing. Examples of
suitable regulated promoter control sequences include without limit
those regulated by heat shock, metals, steroids, antibiotics, or
alcohol. Non-limiting examples of tissue-specific promoters include
B29 promoter, CD14 promoter, CD43 promoter, CD45 promoter, CD68
promoter, desmin promoter, elastase-1 promoter, endoglin promoter,
fibronectin promoter, Flt-1 promoter, GFAP promoter, GPIIb
promoter, ICAM-2 promoter, INF-.beta. promoter, Mb promoter, NphsI
promoter, OG-2 promoter, SP-B promoter, SYN1 promoter, and WASP
promoter. The promoter sequence can be wild type or it can be
modified for more efficient or efficacious expression. In one
exemplary embodiment, the encoding DNA can be operably linked to a
CMV promoter for constitutive expression in mammalian cells.
[0067] In certain embodiments, the sequence encoding the RNA-guided
endonuclease or fusion protein can be operably linked to a promoter
sequence that is recognized by a phage RNA polymerase for in vitro
mRNA synthesis. In such embodiments, the in vitro-transcribed RNA
can be purified for use in the methods detailed below in sections
(IV) and (V). For example, the promoter sequence can be a T7, T3,
or SP6 promoter sequence or a variation of a T7, T3, or SP6
promoter sequence. In an exemplary embodiment, the DNA encoding the
fusion protein is operably linked to a T7 promoter for in vitro
mRNA synthesis using T7 RNA polymerase.
[0068] In alternate embodiments, the sequence encoding the
RNA-guided endonuclease or fusion protein can be operably linked to
a promoter sequence for in vitro expression of the RNA-guided
endonuclease or fusion protein in bacterial or eukaryotic cells. In
such embodiments, the expressed protein can be purified for use in
the methods detailed below in sections (IV) and (V). Suitable
bacterial promoters include, without limit, T7 promoters, lac
operon promoters, trp promoters, variations thereof, and
combinations thereof. An exemplary bacterial promoter is tac which
is a hybrid of trp and lac promoters. Non-limiting examples of
suitable eukaryotic promoters are listed above.
[0069] In additional aspects, the DNA encoding the RNA-guided
endonuclease or fusion protein also can be linked to a
polyadenylation signal (e.g., SV40 polyA signal, bovine growth
hormone (BGH) polyA signal, etc.) and/or at least one
transcriptional termination sequence. Additionally, the sequence
encoding the RNA-guided endonuclease or fusion protein also can be
linked to sequence encoding at least one nuclear localization
signal, at least one cell-penetrating domain, and/or at least one
marker domain, which are detailed above in section (I).
[0070] In various embodiments, the DNA encoding the RNA-guided
endonuclease or fusion protein can be present in a vector. Suitable
vectors include plasmid vectors, phagemids, cosmids,
artificial/mini-chromosomes, transposons, and viral vectors (e.g.,
lentiviral vectors, adeno-associated viral vectors, etc.). In one
embodiment, the DNA encoding the RNA-guided endonuclease or fusion
protein is present in a plasmid vector. Non-limiting examples of
suitable plasmid vectors include pUC, pBR322, pET, pBluescript, and
variants thereof. The vector can comprise additional expression
control sequences (e.g., enhancer sequences, Kozak sequences,
polyadenylation sequences, transcriptional termination sequences,
etc.), selectable marker sequences (e.g., antibiotic resistance
genes), origins of replication, and the like. Additional
information can be found in "Current Protocols in Molecular
Biology" Ausubel et al., John Wiley & Sons, New York, 2003 or
"Molecular Cloning: A Laboratory Manual" Sambrook & Russell,
Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 3rd edition,
2001.
[0071] In some embodiments, the expression vector comprising the
sequence encoding the RNA-guided endonuclease or fusion protein can
further comprise sequence encoding a guide RNA. The sequence
encoding the guide RNA generally is operably linked to at least one
transcriptional control sequence for expression of the guide RNA in
the cell or embryo of interest. For example, DNA encoding the guide
RNA can be operably linked to a promoter sequence that is
recognized by RNA polymerase III (Pol III). Examples of suitable
Pol III promoters include, but are not limited to, mammalian U6,
U3, H1, and 7SL RNA promoters.
(IV) Method for Modifying a Chromosomal Sequence Using an
RNA-Guided Endonuclease
[0072] Another aspect of the present disclosure encompasses a
method for modifying a chromosomal sequence in a eukaryotic cell or
embryo. The method comprises introducing into a eukaryotic cell or
embryo (i) at least one RNA-guided endonuclease comprising at least
one nuclear localization signal or nucleic acid encoding at least
one RNA-guided endonuclease comprising at least one nuclear
localization signal, (ii) at least one guide RNA or DNA encoding at
least one guide RNA, and, optionally, (iii) at least one donor
polynucleotide comprising a donor sequence. The method further
comprises culturing the cell or embryo such that each guide RNA
directs an RNA-guided endonuclease to a targeted site in the
chromosomal sequence where the RNA-guided endonuclease introduces a
double-stranded break in the targeted site, and the double-stranded
break is repaired by a DNA repair process such that the chromosomal
sequence is modified.
[0073] In some embodiments, the method can comprise introducing one
RNA-guided endonuclease (or encoding nucleic acid) and one guide
RNA (or encoding DNA) into a cell or embryo, wherein the RNA-guided
endonuclease introduces one double-stranded break in the targeted
chromosomal sequence. In embodiments in which the optional donor
polynucleotide is not present, the double-stranded break in the
chromosomal sequence can be repaired by a non-homologous
end-joining (NHEJ) repair process. Because NHEJ is error-prone,
deletions of at least one nucleotide, insertions of at least one
nucleotide, substitutions of at least one nucleotide, or
combinations thereof can occur during the repair of the break.
Accordingly, the targeted chromosomal sequence can be modified or
inactivated. For example, a single nucleotide change (SNP) can give
rise to an altered protein product, or a shift in the reading frame
of a coding sequence can inactivate or "knock out" the sequence
such that no protein product is made. In embodiments in which the
optional donor polynucleotide is present, the donor sequence in the
donor polynucleotide can be exchanged with or integrated into the
chromosomal sequence at the targeted site during repair of the
double-stranded break. For example, in embodiments in which the
donor sequence is flanked by upstream and downstream sequences
having substantial sequence identity with upstream and downstream
sequences, respectively, of the targeted site in the chromosomal
sequence, the donor sequence can be exchanged with or integrated
into the chromosomal sequence at the targeted site during repair
mediated by homology-directed repair process. Alternatively, in
embodiments in which the donor sequence is flanked by compatible
overhangs (or the compatible overhangs are generated in situ by the
RNA-guided endonuclease) the donor sequence can be ligated directly
with the cleaved chromosomal sequence by a non-homologous repair
process during repair of the double-stranded break. Exchange or
integration of the donor sequence into the chromosomal sequence
modifies the targeted chromosomal sequence or introduces an
exogenous sequence into the chromosomal sequence of the cell or
embryo.
[0074] In other embodiments, the method can comprise introducing
two RNA-guided endonucleases (or encoding nucleic acid) and two
guide RNAs (or encoding DNA) into a cell or embryo, wherein the
RNA-guided endonucleases introduce two double-stranded breaks in
the chromosomal sequence. See FIG. 3B. The two breaks can be within
several base pairs, within tens of base pairs, or can be separated
by many thousands of base pairs. In embodiments in which the
optional donor polynucleotide is not present, the resultant
double-stranded breaks can be repaired by a non-homologous repair
process such that the sequence between the two cleavage sites is
lost and/or deletions of at least one nucleotide, insertions of at
least one nucleotide, substitutions of at least one nucleotide, or
combinations thereof can occur during the repair of the break(s).
In embodiments in which the optional donor polynucleotide is
present, the donor sequence in the donor polynucleotide can be
exchanged with or integrated into the chromosomal sequence during
repair of the double-stranded breaks by either a homology-based
repair process (e.g., in embodiments in which the donor sequence is
flanked by upstream and downstream sequences having substantial
sequence identity with upstream and downstream sequences,
respectively, of the targeted sites in the chromosomal sequence) or
a non-homologous repair process (e.g., in embodiments in which the
donor sequence is flanked by compatible overhangs).
[0075] In still other embodiments, the method can comprise
introducing one RNA-guided endonuclease modified to cleave one
strand of a double-stranded sequence (or encoding nucleic acid) and
two guide RNAs (or encoding DNA) into a cell or embryo, wherein
each guide RNA directs the RNA-guided endonuclease to a specific
target site, at which site the modified endonuclease cleaves one
strand (i.e., nicks) of the double-stranded chromosomal sequence,
and wherein the two nicks are in opposite stands and in close
enough proximity to constitute a double-stranded break. See FIG.
3A. In embodiments in which the optional donor polynucleotide is
not present, the resultant double-stranded break can be repaired by
a non-homologous repair process such that deletions of at least one
nucleotide, insertions of at least one nucleotide, substitutions of
at least one nucleotide, or combinations thereof can occur during
the repair of the break. In embodiments in which the optional donor
polynucleotide is present, the donor sequence in the donor
polynucleotide can be exchanged with or integrated into the
chromosomal sequence during repair of the double-stranded break by
either a homology-based repair process (e.g., in embodiments in
which the donor sequence is flanked by upstream and downstream
sequences having substantial sequence identity with upstream and
downstream sequences, respectively, of the targeted sites in the
chromosomal sequence) or a non-homologous repair process (e.g., in
embodiments in which the donor sequence is flanked by compatible
overhangs).
[0076] (a) RNA-Guided Endonuclease
[0077] The method comprises introducing into a cell or embryo at
least one RNA-guided endonuclease comprising at least one nuclear
localization signal or nucleic acid encoding at least one
RNA-guided endonuclease comprising at least one nuclear
localization signal. Such RNA-guided endonucleases and nucleic
acids encoding RNA-guided endonucleases are described above in
sections (I) and (III), respectively.
[0078] In some embodiments, the RNA-guided endonuclease can be
introduced into the cell or embryo as an isolated protein. In such
embodiments, the RNA-guided endonuclease can further comprise at
least one cell-penetrating domain, which facilitates cellular
uptake of the protein. In other embodiments, the RNA-guided
endonuclease can be introduced into the cell or embryo as an mRNA
molecule. In still other embodiments, the RNA-guided endonuclease
can be introduced into the cell or embryo as a DNA molecule. In
general, DNA sequence encoding the fusion protein is operably
linked to a promoter sequence that will function in the cell or
embryo of interest. The DNA sequence can be linear, or the DNA
sequence can be part of a vector. In still other embodiments, the
fusion protein can be introduced into the cell or embryo as an
RNA-protein complex comprising the fusion protein and the guide
RNA.
[0079] In alternate embodiments, DNA encoding the RNA-guided
endonuclease can further comprise sequence encoding a guide RNA. In
general, each of the sequences encoding the RNA-guided endonuclease
and the guide RNA is operably linked to appropriate promoter
control sequence that allows expression of the RNA-guided
endonuclease and the guide RNA, respectively, in the cell or
embryo. The DNA sequence encoding the RNA-guided endonuclease and
the guide RNA can further comprise additional expression control,
regulatory, and/or processing sequence(s). The DNA sequence
encoding the RNA-guided endonuclease and the guide RNA can be
linear or can be part of a vector
[0080] (b) Guide RNA
[0081] The method also comprises introducing into a cell or embryo
at least one guide RNA or DNA encoding at least one guide RNA. A
guide RNA interacts with the RNA-guided endonuclease to direct the
endonuclease to a specific target site, at which site the 5' end of
the guide RNA base pairs with a specific protospacer sequence in
the chromosomal sequence.
[0082] Each guide RNA comprises three regions: a first region at
the 5' end that is complementary to the target site in the
chromosomal sequence, a second internal region that forms a stem
loop structure, and a third 3' region that remains essentially
single-stranded. The first region of each guide RNA is different
such that each guide RNA guides a fusion protein to a specific
target site. The second and third regions of each guide RNA can be
the same in all guide RNAs.
[0083] The first region of the guide RNA is complementary to
sequence (i.e., protospacer sequence) at the target site in the
chromosomal sequence such that the first region of the guide RNA
can base pair with the target site. In various embodiments, the
first region of the guide RNA can comprise from about 10
nucleotides to more than about 25 nucleotides. For example, the
region of base pairing between the first region of the guide RNA
and the target site in the chromosomal sequence can be about 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, or more
than 25 nucleotides in length. In an exemplary embodiment, the
first region of the guide RNA is about 19, 20, or 21 nucleotides in
length.
[0084] The guide RNA also comprises a second region that forms a
secondary structure. In some embodiments, the secondary structure
comprises a stem (or hairpin) and a loop. The length of the loop
and the stem can vary. For example, the loop can range from about 3
to about 10 nucleotides in length, and the stem can range from
about 6 to about 20 base pairs in length. The stem can comprise one
or more bulges of 1 to about 10 nucleotides. Thus, the overall
length of the second region can range from about 16 to about 60
nucleotides in length. In an exemplary embodiment, the loop is
about 4 nucleotides in length and the stem comprises about 12 base
pairs.
[0085] The guide RNA also comprises a third region at the 3' end
that remains essentially single-stranded. Thus, the third region
has no complementarity to any chromosomal sequence in the cell of
interest and has no complementarity to the rest of the guide RNA.
The length of the third region can vary. In general, the third
region is more than about 4 nucleotides in length. For example, the
length of the third region can range from about 5 to about 60
nucleotides in length.
[0086] The combined length of the second and third regions (also
called the universal or scaffold region) of the guide RNA can range
from about 30 to about 120 nucleotides in length. In one aspect,
the combined length of the second and third regions of the guide
RNA range from about 70 to about 100 nucleotides in length.
[0087] In some embodiments, the guide RNA comprises a single
molecule comprising all three regions. In other embodiments, the
guide RNA can comprise two separate molecules. The first RNA
molecule can comprise the first region of the guide RNA and one
half of the "stem" of the second region of the guide RNA. The
second RNA molecule can comprise the other half of the "stem" of
the second region of the guide RNA and the third region of the
guide RNA. Thus, in this embodiment, the first and second RNA
molecules each contain a sequence of nucleotides that are
complementary to one another. For example, in one embodiment, the
first and second RNA molecules each comprise a sequence (of about 6
to about 20 nucleotides) that base pairs to the other sequence to
form a functional guide RNA.
[0088] In some embodiments, the guide RNA can be introduced into
the cell or embryo as a RNA molecule. The RNA molecule can be
transcribed in vitro. Alternatively, the RNA molecule can be
chemically synthesized.
[0089] In other embodiments, the guide RNA can be introduced into
the cell or embryo as a DNA molecule. In such cases, the DNA
encoding the guide RNA can be operably linked to promoter control
sequence for expression of the guide RNA in the cell or embryo of
interest. For example, the RNA coding sequence can be operably
linked to a promoter sequence that is recognized by RNA polymerase
III (Pol III). Examples of suitable Pol III promoters include, but
are not limited to, mammalian U6 or H1 promoters. In exemplary
embodiments, the RNA coding sequence is linked to a mouse or human
U6 promoter. In other exemplary embodiments, the RNA coding
sequence is linked to a mouse or human H1 promoter.
[0090] The DNA molecule encoding the guide RNA can be linear or
circular. In some embodiments, the DNA sequence encoding the guide
RNA can be part of a vector. Suitable vectors include plasmid
vectors, phagemids, cosmids, artificial/mini-chromosomes,
transposons, and viral vectors. In an exemplary embodiment, the DNA
encoding the RNA-guided endonuclease is present in a plasmid
vector. Non-limiting examples of suitable plasmid vectors include
pUC, pBR322, pET, pBluescript, and variants thereof. The vector can
comprise additional expression control sequences (e.g., enhancer
sequences, Kozak sequences, polyadenylation sequences,
transcriptional termination sequences, etc.), selectable marker
sequences (e.g., antibiotic resistance genes), origins of
replication, and the like.
[0091] In embodiments in which both the RNA-guided endonuclease and
the guide RNA are introduced into the cell as DNA molecules, each
can be part of a separate molecule (e.g., one vector containing
fusion protein coding sequence and a second vector containing guide
RNA coding sequence) or both can be part of the same molecule
(e.g., one vector containing coding (and regulatory) sequence for
both the fusion protein and the guide RNA).
[0092] (c) Target Site
[0093] An RNA-guided endonuclease in conjunction with a guide RNA
is directed to a target site in the chromosomal sequence, wherein
the RNA-guided endonuclease introduces a double-stranded break in
the chromosomal sequence. The target site has no sequence
limitation except that the sequence is immediately followed
(downstream) by a consensus sequence. This consensus sequence is
also known as a protospacer adjacent motif (PAM). Examples of PAM
include, but are not limited to, NGG, NGGNG, and NNAGAAW (wherein N
is defined as any nucleotide and W is defined as either A or T). As
detailed above in section (IV)(b), the first region (at the 5' end)
of the guide RNA is complementary to the protospacer of the target
sequence. Typically, the first region of the guide RNA is about 19
to 21 nucleotides in length. Thus, in certain aspects, the sequence
of the target site in the chromosomal sequence is
5'-N.sub.19-21-NGG-3'. The PAM is in italics.
[0094] The target site can be in the coding region of a gene, in an
intron of a gene, in a control region of a gene, in a non-coding
region between genes, etc. The gene can be a protein coding gene or
an RNA coding gene. The gene can be any gene of interest.
[0095] (d) Optional Donor Polynucleotide
[0096] In some embodiments, the method further comprises
introducing at least one donor polynucleotide into the embryo. A
donor polynucleotide comprises at least one donor sequence. In some
aspects, a donor sequence of the donor polynucleotide corresponds
to an endogenous or native chromosomal sequence. For example, the
donor sequence can be essentially identical to a portion of the
chromosomal sequence at or near the targeted site, but which
comprises at least one nucleotide change. Thus, the donor sequence
can comprise a modified version of the wild type sequence at the
targeted site such that, upon integration or exchange with the
native sequence, the sequence at the targeted chromosomal location
comprises at least one nucleotide change. For example, the change
can be an insertion of one or more nucleotides, a deletion of one
or more nucleotides, a substitution of one or more nucleotides, or
combinations thereof. As a consequence of the integration of the
modified sequence, the cell or embryo/animal can produce a modified
gene product from the targeted chromosomal sequence.
[0097] In other aspects, the donor sequence of the donor
polynucleotide corresponds to an exogenous sequence. As used
herein, an "exogenous" sequence refers to a sequence that is not
native to the cell or embryo, or a sequence whose native location
in the genome of the cell or embryo is in a different location. For
example, the exogenous sequence can comprise protein coding
sequence, which can be operably linked to an exogenous promoter
control sequence such that, upon integration into the genome, the
cell or embryo/animal is able to express the protein coded by the
integrated sequence. Alternatively, the exogenous sequence can be
integrated into the chromosomal sequence such that its expression
is regulated by an endogenous promoter control sequence. In other
iterations, the exogenous sequence can be a transcriptional control
sequence, another expression control sequence, an RNA coding
sequence, and so forth. Integration of an exogenous sequence into a
chromosomal sequence is termed a "knock in."
[0098] As can be appreciated by those skilled in the art, the
length of the donor sequence can and will vary. For example, the
donor sequence can vary in length from several nucleotides to
hundreds of nucleotides to hundreds of thousands of
nucleotides.
[0099] Donor Polynucleotide Comprising Upstream and Downstream
Sequences.
[0100] In some embodiments, the donor sequence in the donor
polynucleotide is flanked by an upstream sequence and a downstream
sequence, which have substantial sequence identity to sequences
located upstream and downstream, respectively, of the targeted site
in the chromosomal sequence. Because of these sequence
similarities, the upstream and downstream sequences of the donor
polynucleotide permit homologous recombination between the donor
polynucleotide and the targeted chromosomal sequence such that the
donor sequence can be integrated into (or exchanged with) the
chromosomal sequence.
[0101] The upstream sequence, as used herein, refers to a nucleic
acid sequence that shares substantial sequence identity with a
chromosomal sequence upstream of the targeted site. Similarly, the
downstream sequence refers to a nucleic acid sequence that shares
substantial sequence identity with a chromosomal sequence
downstream of the targeted site. As used herein, the phrase
"substantial sequence identity" refers to sequences having at least
about 75% sequence identity. Thus, the upstream and downstream
sequences in the donor polynucleotide can have about 75%, 76%, 77%,
78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% A sequence identity
with sequence upstream or downstream to the targeted site. In an
exemplary embodiment, the upstream and downstream sequences in the
donor polynucleotide can have about 95% or 100% sequence identity
with chromosomal sequences upstream or downstream to the targeted
site. In one embodiment, the upstream sequence shares substantial
sequence identity with a chromosomal sequence located immediately
upstream of the targeted site (i.e., adjacent to the targeted
site). In other embodiments, the upstream sequence shares
substantial sequence identity with a chromosomal sequence that is
located within about one hundred (100) nucleotides upstream from
the targeted site. Thus, for example, the upstream sequence can
share substantial sequence identity with a chromosomal sequence
that is located about 1 to about 20, about 21 to about 40, about 41
to about 60, about 61 to about 80, or about 81 to about 100
nucleotides upstream from the targeted site. In one embodiment, the
downstream sequence shares substantial sequence identity with a
chromosomal sequence located immediately downstream of the targeted
site (i.e., adjacent to the targeted site). In other embodiments,
the downstream sequence shares substantial sequence identity with a
chromosomal sequence that is located within about one hundred (100)
nucleotides downstream from the targeted site. Thus, for example,
the downstream sequence can share substantial sequence identity
with a chromosomal sequence that is located about 1 to about 20,
about 21 to about 40, about 41 to about 60, about 61 to about 80,
or about 81 to about 100 nucleotides downstream from the targeted
site.
[0102] Each upstream or downstream sequence can range in length
from about 20 nucleotides to about 5000 nucleotides. In some
embodiments, upstream and downstream sequences can comprise about
50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200,
1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300,
2400, 2500, 2600, 2800, 3000, 3200, 3400, 3600, 3800, 4000, 4200,
4400, 4600, 4800, or 5000 nucleotides. In exemplary embodiments,
upstream and downstream sequences can range in length from about 50
to about 1500 nucleotides.
[0103] Donor polynucleotides comprising the upstream and downstream
sequences with sequence similarity to the targeted chromosomal
sequence can be linear or circular. In embodiments in which the
donor polynucleotide is circular, it can be part of a vector. For
example, the vector can be a plasmid vector.
[0104] Donor Polynucleotide Comprising Targeted Cleavage
Site(s).
[0105] In other embodiments, the donor polynucleotide can
additionally comprise at least one targeted cleavage site that is
recognized by the RNA-guided endonuclease. The targeted cleavage
site added to the donor polynucleotide can be placed upstream or
downstream or both upstream and downstream of the donor sequence.
For example, the donor sequence can be flanked by targeted cleavage
sites such that, upon cleavage by the RNA-guided endonuclease, the
donor sequence is flanked by overhangs that are compatible with
those in the chromosomal sequence generated upon cleavage by the
RNA-guided endonuclease. Accordingly, the donor sequence can be
ligated with the cleaved chromosomal sequence during repair of the
double stranded break by a non-homologous repair process.
Generally, donor polynucleotides comprising the targeted cleavage
site(s) will be circular (e.g., can be part of a plasmid
vector).
[0106] Donor Polynucleotide Comprising a Short Donor Sequence with
Optional Overhangs.
[0107] In still alternate embodiments, the donor polynucleotide can
be a linear molecule comprising a short donor sequence with
optional short overhangs that are compatible with the overhangs
generated by the RNA-guided endonuclease. In such embodiments, the
donor sequence can be ligated directly with the cleaved chromosomal
sequence during repair of the double-stranded break. In some
instances, the donor sequence can be less than about 1,000, less
than about 500, less than about 250, or less than about 100
nucleotides. In certain cases, the donor polynucleotide can be a
linear molecule comprising a short donor sequence with blunt ends.
In other iterations, the donor polynucleotide can be a linear
molecule comprising a short donor sequence with 5' and/or 3'
overhangs. The overhangs can comprise 1, 2, 3, 4, or 5
nucleotides.
[0108] Typically, the donor polynucleotide will be DNA. The DNA may
be single-stranded or double-stranded and/or linear or circular.
The donor polynucleotide may be a DNA plasmid, a bacterial
artificial chromosome (BAC), a yeast artificial chromosome (YAC), a
viral vector, a linear piece of DNA, a PCR fragment, a naked
nucleic acid, or a nucleic acid complexed with a delivery vehicle
such as a liposome or poloxamer. In certain embodiments, the donor
polynucleotide comprising the donor sequence can be part of a
plasmid vector. In any of these situations, the donor
polynucleotide comprising the donor sequence can further comprise
at least one additional sequence.
[0109] (e) Introducing into the Cell or Embryo
[0110] The RNA-targeted endonuclease(s) (or encoding nucleic acid),
the guide RNA(s) (or encoding DNA), and the optional donor
polynucleotide(s) can be introduced into a cell or embryo by a
variety of means. In some embodiments, the cell or embryo is
transfected. Suitable transfection methods include calcium
phosphate-mediated transfection, nucleofection (or
electroporation), cationic polymer transfection (e.g., DEAE-dextran
or polyethylenimine), viral transduction, virosome transfection,
virion transfection, liposome transfection, cationic liposome
transfection, immunoliposome transfection, nonliposomal lipid
transfection, dendrimer transfection, heat shock transfection,
magnetofection, lipofection, gene gun delivery, impalefection,
sonoporation, optical transfection, and proprietary agent-enhanced
uptake of nucleic acids. Transfection methods are well known in the
art (see, e.g., "Current Protocols in Molecular Biology" Ausubel et
al., John Wiley & Sons, New York, 2003 or "Molecular Cloning: A
Laboratory Manual" Sambrook & Russell, Cold Spring Harbor
Press, Cold Spring Harbor, N.Y., 3.sup.rd edition, 2001). In other
embodiments, the molecules are introduced into the cell or embryo
by microinjection. Typically, the embryo is a fertilized one-cell
stage embryo of the species of interest. For example, the molecules
can be injected into the pronuclei of one cell embryos.
[0111] The RNA-targeted endonuclease(s) (or encoding nucleic acid),
the guide RNA(s) (or DNAs encoding the guide RNA), and the optional
donor polynucleotide(s) can be introduced into the cell or embryo
simultaneously or sequentially. The ratio of the RNA-targeted
endonuclease(s) (or encoding nucleic acid) to the guide RNA(s) (or
encoding DNA) generally will be about stoichiometric such that they
can form an RNA-protein complex. In one embodiment, DNA encoding an
RNA-targeted endonuclease and DNA encoding a guide RNA are
delivered together within the plasmid vector.
[0112] (f) Culturing the cell or embryo
[0113] The method further comprises maintaining the cell or embryo
under appropriate conditions such that the guide RNA(s) directs the
RNA-guided endonuclease(s) to the targeted site(s) in the
chromosomal sequence, and the RNA-guided endonuclease(s) introduce
at least one double-stranded break in the chromosomal sequence. A
double-stranded break can be repaired by a DNA repair process such
that the chromosomal sequence is modified by a deletion of at least
one nucleotide, an insertion of at least one nucleotide, a
substitution of at least one nucleotide, or a combination
thereof.
[0114] In embodiments in which no donor polynucleotide is
introduced into the cell or embryo, the double-stranded break can
be repaired via a non-homologous end-joining (NHEJ) repair process.
Because NHEJ is error-prone, deletions of at least one nucleotide,
insertions of at least one nucleotide, substitutions of at least
one nucleotide, or combinations thereof can occur during the repair
of the break. Accordingly, the sequence at the chromosomal sequence
can be modified such that the reading frame of a coding region can
be shifted and that the chromosomal sequence is inactivated or
"knocked out." An inactivated protein-coding chromosomal sequence
does not give rise to the protein coded by the wild type
chromosomal sequence.
[0115] In embodiments in which a donor polynucleotide comprising
upstream and downstream sequences is introduced into the cell or
embryo, the double-stranded break can be repaired by a
homology-directed repair (HDR) process such that the donor sequence
is integrated into the chromosomal sequence. Accordingly, an
exogenous sequence can be integrated into the genome of the cell or
embryo, or the targeted chromosomal sequence can be modified by
exchange of a modified sequence for the wild type chromosomal
sequence.
[0116] In embodiments in which a donor polynucleotide comprising
the targeted cleave site is introduced into the cell or embryo, the
RNA-guided endonuclease can cleave both the targeted chromosomal
sequence and the donor polynucleotide. The linearized donor
polynucleotide can be integrated into the chromosomal sequence at
the site of the double-stranded break by ligation between the donor
polynucleotide and the cleaved chromosomal sequence via a NHEJ
process.
[0117] In embodiments in which a linear donor polynucleotide
comprising a short donor sequence is introduced into the cell or
embryo, the short donor sequence can be integrated into the
chromosomal sequence at the site of the double-stranded break via a
NHEJ process. The integration can proceed via the ligation of blunt
ends between the short donor sequence and the chromosomal sequence
at the site of the double stranded break. Alternatively, the
integration can proceed via the ligation of sticky ends (i.e.,
having 5' or 3' overhangs) between a short donor sequence that is
flanked by overhangs that are compatible with those generated by
the RNA-targeting endonuclease in the cleaved chromosomal
sequence.
[0118] In general, the cell is maintained under conditions
appropriate for cell growth and/or maintenance. Suitable cell
culture conditions are well known in the art and are described, for
example, in Santiago et al. (2008) PNAS 105:5809-5814; Moehle et
al. (2007) PNAS 104:3055-3060; Urnov et al. (2005) Nature
435:646-651; and Lombardo et al (2007) Nat. Biotechnology
25:1298-1306. Those of skill in the art appreciate that methods for
culturing cells are known in the art and can and will vary
depending on the cell type. Routine optimization may be used, in
all cases, to determine the best techniques for a particular cell
type.
[0119] An embryo can be cultured in vitro (e.g., in cell culture).
Typically, the embryo is cultured at an appropriate temperature and
in appropriate media with the necessary O.sub.2/CO.sub.2 ratio to
allow the expression of the RNA endonuclease and guide RNA, if
necessary. Suitable non-limiting examples of media include M2, M16,
KSOM, BMOC, and HTF media. A skilled artisan will appreciate that
culture conditions can and will vary depending on the species of
embryo. Routine optimization may be used, in all cases, to
determine the best culture conditions for a particular species of
embryo. In some cases, a cell line may be derived from an in
vitro-cultured embryo (e.g., an embryonic stem cell line).
[0120] Alternatively, an embryo may be cultured in vivo by
transferring the embryo into the uterus of a female host. Generally
speaking the female host is from the same or similar species as the
embryo. Preferably, the female host is pseudo-pregnant. Methods of
preparing pseudo-pregnant female hosts are known in the art.
Additionally, methods of transferring an embryo into a female host
are known. Culturing an embryo in vivo permits the embryo to
develop and can result in a live birth of an animal derived from
the embryo. Such an animal would comprise the modified chromosomal
sequence in every cell of the body.
[0121] (g) Cell and Embryo Types
[0122] A variety of eukaryotic cells and embryos are suitable for
use in the method. For example, the cell can be a human cell, a
non-human mammalian cell, a non-mammalian vertebrate cell, an
invertebrate cell, an insect cell, a plant cell, a yeast cell, or a
single cell eukaryotic organism. In general, the embryo is
non-human mammalian embryo. In specific embodiments, the embryos
can be a one cell non-human mammalian embryo. Exemplary mammalian
embryos, including one cell embryos, include without limit mouse,
rat, hamster, rodent, rabbit, feline, canine, ovine, porcine,
bovine, equine, and primate embryos. In still other embodiments,
the cell can be a stem cell. Suitable stem cells include without
limit embryonic stem cells, ES-like stem cells, fetal stem cells,
adult stem cells, pluripotent stem cells, induced pluripotent stem
cells, multipotent stem cells, oligopotent stem cells, unipotent
stem cells and others. In exemplary embodiments, the cell is a
mammalian cell.
[0123] Non-limiting examples of suitable mammalian cells include
Chinese hamster ovary (CHO) cells, baby hamster kidney (BHK) cells;
mouse myeloma NS0 cells, mouse embryonic fibroblast 3T3 cells
(NIH3T3), mouse B lymphoma A20 cells; mouse melanoma B16 cells;
mouse myoblast C2C12 cells; mouse myeloma SP2/0 cells; mouse
embryonic mesenchymal C3H-10T1/2 cells; mouse carcinoma CT26 cells,
mouse prostate DuCuP cells; mouse breast EMT6 cells; mouse hepatoma
Hepa1c1c7 cells; mouse myeloma J5582 cells; mouse epithelial MTD-1A
cells; mouse myocardial MyEnd cells; mouse renal RenCa cells; mouse
pancreatic RIN-5F cells; mouse melanoma X64 cells; mouse lymphoma
YAC-1 cells; rat glioblastoma 9L cells; rat B lymphoma RBL cells;
rat neuroblastoma B35 cells; rat hepatoma cells (HTC); buffalo rat
liver BRL 3A cells; canine kidney cells (MDCK); canine mammary
(CMT) cells; rat osteosarcoma D17 cells; rat monocyte/macrophage
DH82 cells; monkey kidney SV-40 transformed fibroblast (COS7)
cells; monkey kidney CVI-76 cells; African green monkey kidney
(VERO-76) cells; human embryonic kidney cells (HEK293, HEK293T);
human cervical carcinoma cells (HELA); human lung cells (W138);
human liver cells (Hep G2); human U2-OS osteosarcoma cells, human
A549 cells, human A-431 cells, and human K562 cells. An extensive
list of mammalian cell lines may be found in the American Type
Culture Collection catalog (ATCC, Mamassas, Va.).
(V) Method for Using a Fusion Protein to Modify a Chromosomal
Sequence or Regulate Expression of a Chromosomal Sequence
[0124] Another aspect of the present disclosure encompasses a
method for modifying a chromosomal sequence or regulating
expression of a chromosomal sequence in a cell or embryo. The
method comprises introducing into the cell or embryo (a) at least
one fusion protein or nucleic acid encoding at least one fusion
protein, wherein the fusion protein comprises a CRISPR/Cas-like
protein or a fragment thereof and an effector domain, and (b) at
least one guide RNA or DNA encoding the guide RNA, wherein the
guide RNA guides the CRISPR/Cas-like protein of the fusion protein
to a targeted site in the chromosomal sequence and the effector
domain of the fusion protein modifies the chromosomal sequence or
regulates expression of the chromosomal sequence.
[0125] Fusion proteins comprising a CRISPR/Cas-like protein or a
fragment thereof and an effector domain are detailed above in
section (II). In general, the fusion proteins disclosed herein
further comprise at least one nuclear localization signal. Nucleic
acids encoding fusion proteins are described above in section
(III). In some embodiments, the fusion protein can be introduced
into the cell or embryo as an isolated protein (which can further
comprise a cell-penetrating domain). Furthermore, the isolated
fusion protein can be part of a protein-RNA complex comprising the
guide RNA. In other embodiments, the fusion protein can be
introduced into the cell or embryo as a RNA molecule (which can be
capped and/or polyadenylated). In still other embodiments, the
fusion protein can be introduced into the cell or embryo as a DNA
molecule. For example, the fusion protein and the guide RNA can be
introduced into the cell or embryo as discrete DNA molecules or as
part of the same DNA molecule. Such DNA molecules can be plasmid
vectors.
[0126] In some embodiments, the method further comprises
introducing into the cell or embryo at least one zinc finger
nuclease. Zinc finger nucleases are described above in section
(II)(d). In still other embodiments, the method further comprises
introducing into the cell or embryo at least one donor
polynucleotide. Donor polynucleotides are detailed above in section
(IV)(d). Means for introducing molecules into cells or embryos, as
well as means for culturing cell or embryos are described above in
sections (IV)(e) and (IV)(f), respectively. Suitable cells and
embryos are described above in section (IV)(g).
[0127] In certain embodiments in which the effector domain of the
fusion protein is a cleavage domain (e.g., a FokI cleavage domain
or a modified FokI cleavage domain), the method can comprise
introducing into the cell or embryo one fusion protein (or nucleic
acid encoding one fusion protein) and two guide RNAs (or DNA
encoding two guide RNAs). The two guide RNAs direct the fusion
protein to two different target sites in the chromosomal sequence,
wherein the fusion protein dimerizes (e.g., form a homodimer) such
that the two cleavage domains can introduce a double stranded break
into the chromosomal sequence. See FIG. 1A. In embodiments in which
the optional donor polynucleotide is not present, the
double-stranded break in the chromosomal sequence can be repaired
by a non-homologous end-joining (NHEJ) repair process. Because NHEJ
is error-prone, deletions of at least one nucleotide, insertions of
at least one nucleotide, substitutions of at least one nucleotide,
or combinations thereof can occur during the repair of the break.
Accordingly, the targeted chromosomal sequence can be modified or
inactivated. For example, a single nucleotide change (SNP) can give
rise to an altered protein product, or a shift in the reading frame
of a coding sequence can inactivate or "knock out" the sequence
such that no protein product is made. In embodiments in which the
optional donor polynucleotide is present, the donor sequence in the
donor polynucleotide can be exchanged with or integrated into the
chromosomal sequence at the targeted site during repair of the
double-stranded break. For example, in embodiments in which the
donor sequence is flanked by upstream and downstream sequences
having substantial sequence identity with upstream and downstream
sequences, respectively, of the targeted site in the chromosomal
sequence, the donor sequence can be exchanged with or integrated
into the chromosomal sequence at the targeted site during repair
mediated by homology-directed repair process. Alternatively, in
embodiments in which the donor sequence is flanked by compatible
overhangs (or the compatible overhangs are generated in situ by the
RNA-guided endonuclease) the donor sequence can be ligated directly
with the cleaved chromosomal sequence by a non-homologous repair
process during repair of the double-stranded break. Exchange or
integration of the donor sequence into the chromosomal sequence
modifies the targeted chromosomal sequence or introduces an
exogenous sequence into the chromosomal sequence of the cell or
embryo.
[0128] In other embodiments in which the effector domain of the
fusion protein is a cleavage domain (e.g., a FokI cleavage domain
or a modified FokI cleavage domain), the method can comprise
introducing into the cell or embryo two different fusion proteins
(or nucleic acid encoding two different fusion proteins) and two
guide RNAs (or DNA encoding two guide RNAs). The fusion proteins
can differ as detailed above in section (II). Each guide RNA
directs a fusion protein to a specific target site in the
chromosomal sequence, wherein the fusion proteins dimerize (e.g.,
form a heterodimer) such that the two cleavage domains can
introduce a double stranded break into the chromosomal sequence. In
embodiments in which the optional donor polynucleotide is not
present, the resultant double-stranded breaks can be repaired by a
non-homologous repair process such that deletions of at least one
nucleotide, insertions of at least one nucleotide, substitutions of
at least one nucleotide, or combinations thereof can occur during
the repair of the break. In embodiments in which the optional donor
polynucleotide is present, the donor sequence in the donor
polynucleotide can be exchanged with or integrated into the
chromosomal sequence during repair of the double-stranded break by
either a homology-based repair process (e.g., in embodiments in
which the donor sequence is flanked by upstream and downstream
sequences having substantial sequence identity with upstream and
downstream sequences, respectively, of the targeted sites in the
chromosomal sequence) or a non-homologous repair process (e.g., in
embodiments in which the donor sequence is flanked by compatible
overhangs).
[0129] In still other embodiments in which the effector domain of
the fusion protein is a cleavage domain (e.g., a FokI cleavage
domain or a modified FokI cleavage domain), the method can comprise
introducing into the cell or embryo one fusion protein (or nucleic
acid encoding one fusion protein), one guide RNA (or DNA encoding
one guide RNA), and one zinc finger nuclease (or nucleic acid
encoding the zinc finger nuclease), wherein the zinc finger
nuclease comprises a FokI cleavage domain or a modified FokI
cleavage domain. The guide RNA directs the fusion protein to a
specific chromosomal sequence, and the zinc finger nuclease is
directed to another chromosomal sequence, wherein the fusion
protein and the zinc finger nuclease dimerize such that the
cleavage domain of the fusion protein and the cleavage domain of
the zinc finger nuclease can introduce a double stranded break into
the chromosomal sequence. See FIG. 1B. In embodiments in which the
optional donor polynucleotide is not present, the resultant
double-stranded breaks can be repaired by a non-homologous repair
process such that deletions of at least one nucleotide, insertions
of at least one nucleotide, substitutions of at least one
nucleotide, or combinations thereof can occur during the repair of
the break. In embodiments in which the optional donor
polynucleotide is present, the donor sequence in the donor
polynucleotide can be exchanged with or integrated into the
chromosomal sequence during repair of the double-stranded break by
either a homology-based repair process (e.g., in embodiments in
which the donor sequence is flanked by upstream and downstream
sequences having substantial sequence identity with upstream and
downstream sequences, respectively, of the targeted sites in the
chromosomal sequence) or a non-homologous repair process (e.g., in
embodiments in which the donor sequence is flanked by compatible
overhangs).
[0130] In still other embodiments in which the effector domain of
the fusion protein is a transcriptional activation domain or a
transcriptional repressor domain, the method can comprise
introducing into the cell or embryo one fusion protein (or nucleic
acid encoding one fusion protein) and one guide RNA (or DNA
encoding one guide RNA). The guide RNA directs the fusion protein
to a specific chromosomal sequence, wherein the transcriptional
activation domain or a transcriptional repressor domain activates
or represses expression, respectively, of the targeted chromosomal
sequence. See FIG. 2A.
[0131] In alternate embodiments in which the effector domain of the
fusion protein is an epigenetic modification domain, the method can
comprise introducing into the cell or embryo one fusion protein (or
nucleic acid encoding one fusion protein) and one guide RNA (or DNA
encoding one guide RNA). The guide RNA directs the fusion protein
to a specific chromosomal sequence, wherein the epigenetic
modification domain modifies the structure of the targeted the
chromosomal sequence. See FIG. 2B. Epigenetic modifications include
acetylation, methylation of histone proteins and/or nucleotide
methylation. In some instances, structural modification of the
chromosomal sequence leads to changes in expression of the
chromosomal sequence.
(VI) Genetically Modified Cells and Animals
[0132] The present disclosure encompasses genetically modified
cells, non-human embryos, and non-human animals comprising at least
one chromosomal sequence that has been modified using an RNA-guided
endonuclease-mediated or fusion protein-mediated process, for
example, using the methods described herein. The disclosure
provides cells comprising at least one DNA or RNA molecule encoding
an RNA-guided endonuclease or fusion protein targeted to a
chromosomal sequence of interest or a fusion protein, at least one
guide RNA, and optionally one or more donor polynucleotide(s). The
disclosure also provides non-human embryos comprising at least one
DNA or RNA molecule encoding an RNA-guided endonuclease or fusion
protein targeted to a chromosomal sequence of interest, at least
one guide RNA, and optionally one or more donor
polynucleotide(s).
[0133] The present disclosure provides genetically modified
non-human animals, non-human embryos, or animal cells comprising at
least one modified chromosomal sequence. The modified chromosomal
sequence may be modified such that it is (1) inactivated, (2) has
an altered expression or produces an altered protein product, or
(3) comprises an integrated sequence. The chromosomal sequence is
modified with an RNA guided endonuclease-mediated or fusion
protein-mediated process, using the methods described herein.
[0134] As discussed, one aspect of the present disclosure provides
a genetically modified animal in which at least one chromosomal
sequence has been modified. In one embodiment, the genetically
modified animal comprises at least one inactivated chromosomal
sequence. The modified chromosomal sequence may be inactivated such
that the sequence is not transcribed and/or a functional protein
product is not produced. Thus, a genetically modified animal
comprising an inactivated chromosomal sequence may be termed a
"knock out" or a "conditional knock out." The inactivated
chromosomal sequence can include a deletion mutation (i.e.,
deletion of one or more nucleotides), an insertion mutation (i.e.,
insertion of one or more nucleotides), or a nonsense mutation
(i.e., substitution of a single nucleotide for another nucleotide
such that a stop codon is introduced). As a consequence of the
mutation, the targeted chromosomal sequence is inactivated and a
functional protein is not produced. The inactivated chromosomal
sequence comprises no exogenously introduced sequence. Also
included herein are genetically modified animals in which two,
three, four, five, six, seven, eight, nine, or ten or more
chromosomal sequences are inactivated.
[0135] In another embodiment, the modified chromosomal sequence can
be altered such that it codes for a variant protein product. For
example, a genetically modified animal comprising a modified
chromosomal sequence can comprise a targeted point mutation(s) or
other modification such that an altered protein product is
produced. In one embodiment, the chromosomal sequence can be
modified such that at least one nucleotide is changed and the
expressed protein comprises one changed amino acid residue
(missense mutation). In another embodiment, the chromosomal
sequence can be modified to comprise more than one missense
mutation such that more than one amino acid is changed.
Additionally, the chromosomal sequence can be modified to have a
three nucleotide deletion or insertion such that the expressed
protein comprises a single amino acid deletion or insertion. The
altered or variant protein can have altered properties or
activities compared to the wild type protein, such as altered
substrate specificity, altered enzyme activity, altered kinetic
rates, etc.
[0136] In another embodiment, the genetically modified animal can
comprise at least one chromosomally integrated sequence. A
genetically modified animal comprising an integrated sequence may
be termed a "knock in" or a "conditional knock in." The
chromosomally integrated sequence can, for example, encode an
orthologous protein, an endogenous protein, or combinations of
both. In one embodiment, a sequence encoding an orthologous protein
or an endogenous protein can be integrated into a chromosomal
sequence encoding a protein such that the chromosomal sequence is
inactivated, but the exogenous sequence is expressed. In such a
case, the sequence encoding the orthologous protein or endogenous
protein may be operably linked to a promoter control sequence.
Alternatively, a sequence encoding an orthologous protein or an
endogenous protein may be integrated into a chromosomal sequence
without affecting expression of a chromosomal sequence. For
example, a sequence encoding a protein can be integrated into a
"safe harbor" locus, such as the Rosa26 locus, HPRT locus, or AAV
locus. The present disclosure also encompasses genetically modified
animals in which two, three, four, five, six, seven, eight, nine,
or ten or more sequences, including sequences encoding protein(s),
are integrated into the genome.
[0137] The chromosomally integrated sequence encoding a protein can
encode the wild type form of a protein of interest or can encode a
protein comprising at least one modification such that an altered
version of the protein is produced. For example, a chromosomally
integrated sequence encoding a protein related to a disease or
disorder can comprise at least one modification such that the
altered version of the protein produced causes or potentiates the
associated disorder. Alternatively, the chromosomally integrated
sequence encoding a protein related to a disease or disorder can
comprise at least one modification such that the altered version of
the protein protects against the development of the associated
disorder.
[0138] In an additional embodiment, the genetically modified animal
can be a "humanized" animal comprising at least one chromosomally
integrated sequence encoding a functional human protein. The
functional human protein can have no corresponding ortholog in the
genetically modified animal. Alternatively, the wild type animal
from which the genetically modified animal is derived may comprise
an ortholog corresponding to the functional human protein. In this
case, the orthologous sequence in the "humanized" animal is
inactivated such that no functional protein is made and the
"humanized" animal comprises at least one chromosomally integrated
sequence encoding the human protein.
[0139] In yet another embodiment, the genetically modified animal
can comprise at least one modified chromosomal sequence encoding a
protein such that the expression pattern of the protein is altered.
For example, regulatory regions controlling the expression of the
protein, such as a promoter or a transcription factor binding site,
can be altered such that the protein is over-produced, or the
tissue-specific or temporal expression of the protein is altered,
or a combination thereof. Alternatively, the expression pattern of
the protein can be altered using a conditional knockout system. A
non-limiting example of a conditional knockout system includes a
Cre-lox recombination system. A Cre-lox recombination system
comprises a Cre recombinase enzyme, a site-specific DNA recombinase
that can catalyze the recombination of a nucleic acid sequence
between specific sites (lox sites) in a nucleic acid molecule.
Methods of using this system to produce temporal and tissue
specific expression are known in the art. In general, a genetically
modified animal is generated with lox sites flanking a chromosomal
sequence. The genetically modified animal comprising the
lox-flanked chromosomal sequence can then be crossed with another
genetically modified animal expressing Cre recombinase. Progeny
animals comprising the lox-flanked chromosomal sequence and the Cre
recombinase are then produced, and the lox-flanked chromosomal
sequence is recombined, leading to deletion or inversion of the
chromosomal sequence encoding the protein. Expression of Cre
recombinase can be temporally and conditionally regulated to effect
temporally and conditionally regulated recombination of the
chromosomal sequence.
[0140] In any of these embodiments, the genetically modified animal
disclosed herein can be heterozygous for the modified chromosomal
sequence. Alternatively, the genetically modified animal can be
homozygous for the modified chromosomal sequence.
[0141] The genetically modified animals disclosed herein can be
crossbred to create animals comprising more than one modified
chromosomal sequence or to create animals that are homozygous for
one or more modified chromosomal sequences. For example, two
animals comprising the same modified chromosomal sequence can be
crossbred to create an animal homozygous for the modified
chromosomal sequence. Alternatively, animals with different
modified chromosomal sequences can be crossbred to create an animal
comprising both modified chromosomal sequences.
[0142] For example, a first animal comprising an inactivated
chromosomal sequence gene "x" can be crossed with a second animal
comprising a chromosomally integrated sequence encoding a human
gene "X" protein to give rise to "humanized" gene "X" offspring
comprising both the inactivated gene "x" chromosomal sequence and
the chromosomally integrated human gene "X" sequence. Also, a
humanized gene "X" animal can be crossed with a humanized gene "Y"
animal to create humanized gene X/gene Y offspring. Those of skill
in the art will appreciate that many combinations are possible.
[0143] In other embodiments, an animal comprising a modified
chromosomal sequence can be crossbred to combine the modified
chromosomal sequence with other genetic backgrounds. By way of
non-limiting example, other genetic backgrounds may include
wild-type genetic backgrounds, genetic backgrounds with deletion
mutations, genetic backgrounds with another targeted integration,
and genetic backgrounds with non-targeted integrations.
[0144] The term "animal," as used herein, refers to a non-human
animal. The animal may be an embryo, a juvenile, or an adult.
Suitable animals include vertebrates such as mammals, birds,
reptiles, amphibians, shellfish, and fish. Examples of suitable
mammals include without limit rodents, companion animals,
livestock, and primates. Non-limiting examples of rodents include
mice, rats, hamsters, gerbils, and guinea pigs. Suitable companion
animals include but are not limited to cats, dogs, rabbits,
hedgehogs, and ferrets. Non-limiting examples of livestock include
horses, goats, sheep, swine, cattle, llamas, and alpacas. Suitable
primates include but are not limited to capuchin monkeys,
chimpanzees, lemurs, macaques, marmosets, tamarins, spider monkeys,
squirrel monkeys, and vervet monkeys. Non-limiting examples of
birds include chickens, turkeys, ducks, and geese. Alternatively,
the animal may be an invertebrate such as an insect, a nematode,
and the like. Non-limiting examples of insects include Drosophila
and mosquitoes. An exemplary animal is a rat. Non-limiting examples
of suitable rat strains include Dahl Salt-Sensitive, Fischer 344,
Lewis, Long Evans Hooded, Sprague-Dawley, and Wistar. In one
embodiment, the animal is not a genetically modified mouse. In each
of the foregoing iterations of suitable animals for the invention,
the animal does not include exogenously introduced, randomly
integrated transposon sequences.
[0145] A further aspect of the present disclosure provides
genetically modified cells or cell lines comprising at least one
modified chromosomal sequence. The genetically modified cell or
cell line can be derived from any of the genetically modified
animals disclosed herein. Alternatively, the chromosomal sequence
can be modified in a cell as described herein above (in the
paragraphs describing chromosomal sequence modifications in
animals) using the methods descried herein. The disclosure also
encompasses a lysate of said cells or cell lines.
[0146] In general, the cells are eukaryotic cells. Suitable host
cells include fungi or yeast, such as Pichia, Saccharomyces, or
Schizosaccharomyces; insect cells, such as SF9 cells from
Spodoptera frugiperda or S2 cells from Drosophila melanogaster; and
animal cells, such as mouse, rat, hamster, non-human primate, or
human cells. Exemplary cells are mammalian. The mammalian cells can
be primary cells. In general, any primary cell that is sensitive to
double strand breaks may be used. The cells may be of a variety of
cell types, e.g., fibroblast, myoblast, T or B cell, macrophage,
epithelial cell, and so forth.
[0147] When mammalian cell lines are used, the cell line can be any
established cell line or a primary cell line that is not yet
described. The cell line can be adherent or non-adherent, or the
cell line can be grown under conditions that encourage adherent,
non-adherent or organotypic growth using standard techniques known
to individuals skilled in the art. Non-limiting examples of
suitable mammalian cells and cell lines are provided herein in
section (IV)(g). In still other embodiments, the cell can be a stem
cell. Non-limiting examples of suitable stem cells are provided in
section (IV)(g).
[0148] The present disclosure also provides a genetically modified
non-human embryo comprising at least one modified chromosomal
sequence. The chromosomal sequence can be modified in an embryo as
described herein above (in the paragraphs describing chromosomal
sequence modifications in animals) using the methods descried
herein. In one embodiment, the embryo is a non-human fertilized
one-cell stage embryo of the animal species of interest. Exemplary
mammalian embryos, including one cell embryos, include without
limit, mouse, rat, hamster, rodent, rabbit, feline, canine, ovine,
porcine, bovine, equine, and primate embryos.
Definitions
[0149] Unless defined otherwise, all technical and scientific terms
used herein have the meaning commonly understood by a person
skilled in the art to which this invention belongs. The following
references provide one of skill with a general definition of many
of the terms used in this invention: Singleton et al., Dictionary
of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge
Dictionary of Science and Technology (Walker ed., 1988); The
Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer
Verlag (1991); and Hale & Marham, The Harper Collins Dictionary
of Biology (1991). As used herein, the following terms have the
meanings ascribed to them unless specified otherwise.
[0150] When introducing elements of the present disclosure or the
preferred embodiments(s) thereof, the articles "a", "an", "the" and
"said" are intended to mean that there are one or more of the
elements. The terms "comprising", "including" and "having" are
intended to be inclusive and mean that there may be additional
elements other than the listed elements.
[0151] As used herein, the term "endogenous sequence" refers to a
chromosomal sequence that is native to the cell.
[0152] The term "exogenous," as used herein, refers to a sequence
that is not native to the cell, or a chromosomal sequence whose
native location in the genome of the cell is in a different
chromosomal location.
[0153] A "gene," as used herein, refers to a DNA region (including
exons and introns) encoding a gene product, as well as all DNA
regions which regulate the production of the gene product, whether
or not such regulatory sequences are adjacent to coding and/or
transcribed sequences. Accordingly, a gene includes, but is not
necessarily limited to, promoter sequences, terminators,
translational regulatory sequences such as ribosome binding sites
and internal ribosome entry sites, enhancers, silencers,
insulators, boundary elements, replication origins, matrix
attachment sites, and locus control regions.
[0154] The term "heterologous" refers to an entity that is not
endogenous or native to the cell of interest. For example, a
heterologous protein refers to a protein that is derived from or
was originally derived from an exogenous source, such as an
exogenously introduced nucleic acid sequence. In some instances,
the heterologous protein is not normally produced by the cell of
interest.
[0155] The terms "nucleic acid" and "polynucleotide" refer to a
deoxyribonucleotide or ribonucleotide polymer, in linear or
circular conformation, and in either single- or double-stranded
form. For the purposes of the present disclosure, these terms are
not to be construed as limiting with respect to the length of a
polymer. The terms can encompass known analogs of natural
nucleotides, as well as nucleotides that are modified in the base,
sugar and/or phosphate moieties (e.g., phosphorothioate backbones).
In general, an analog of a particular nucleotide has the same
base-pairing specificity; i.e., an analog of A will base-pair with
T.
[0156] The term "nucleotide" refers to deoxyribonucleotides or
ribonucleotides. The nucleotides may be standard nucleotides (i.e.,
adenosine, guanosine, cytidine, thymidine, and uridine) or
nucleotide analogs. A nucleotide analog refers to a nucleotide
having a modified purine or pyrimidine base or a modified ribose
moiety. A nucleotide analog may be a naturally occurring nucleotide
(e.g., inosine) or a non-naturally occurring nucleotide.
Non-limiting examples of modifications on the sugar or base
moieties of a nucleotide include the addition (or removal) of
acetyl groups, amino groups, carboxyl groups, carboxymethyl groups,
hydroxyl groups, methyl groups, phosphoryl groups, and thiol
groups, as well as the substitution of the carbon and nitrogen
atoms of the bases with other atoms (e.g., 7-deaza purines).
Nucleotide analogs also include dideoxy nucleotides, 2'-O-methyl
nucleotides, locked nucleic acids (LNA), peptide nucleic acids
(PNA), and morpholinos.
[0157] The terms "polypeptide" and "protein" are used
interchangeably to refer to a polymer of amino acid residues.
[0158] Techniques for determining nucleic acid and amino acid
sequence identity are known in the art. Typically, such techniques
include determining the nucleotide sequence of the mRNA for a gene
and/or determining the amino acid sequence encoded thereby, and
comparing these sequences to a second nucleotide or amino acid
sequence. Genomic sequences can also be determined and compared in
this fashion. In general, identity refers to an exact
nucleotide-to-nucleotide or amino acid-to-amino acid correspondence
of two polynucleotides or polypeptide sequences, respectively. Two
or more sequences (polynucleotide or amino acid) can be compared by
determining their percent identity. The percent identity of two
sequences, whether nucleic acid or amino acid sequences, is the
number of exact matches between two aligned sequences divided by
the length of the shorter sequences and multiplied by 100. An
approximate alignment for nucleic acid sequences is provided by the
local homology algorithm of Smith and Waterman, Advances in Applied
Mathematics 2:482-489 (1981). This algorithm can be applied to
amino acid sequences by using the scoring matrix developed by
Dayhoff, Atlas of Protein Sequences and Structure, M. O. Dayhoff
ed., 5 suppl. 3:353-358, National Biomedical Research Foundation,
Washington, D.C., USA, and normalized by Gribskov, Nucl. Acids Res.
14(6):6745-6763 (1986). An exemplary implementation of this
algorithm to determine percent identity of a sequence is provided
by the Genetics Computer Group (Madison, Wis.) in the "BestFit"
utility application. Other suitable programs for calculating the
percent identity or similarity between sequences are generally
known in the art, for example, another alignment program is BLAST,
used with default parameters. For example, BLASTN and BLASTP can be
used using the following default parameters: genetic code=standard;
filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62;
Descriptions=50 sequences; sort by=HIGH SCORE;
Databases=non-redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDS
translations+Swiss protein+Spupdate+PIR. Details of these programs
can be found on the GenBank website.
[0159] As various changes could be made in the above-described
cells and methods without departing from the scope of the
invention, it is intended that all matter contained in the above
description and in the examples given below, shall be interpreted
as illustrative and not in a limiting sense.
EXAMPLES
[0160] The following examples illustrate certain aspects of the
invention.
Example 1: Modification of Cas9 Gene for Mammalian Expression
[0161] A Cas9 gene from Streptococcus pyogenes strain MGAS15252
(Accession number YP_005388840.1) was optimized with Homo sapiens
codon preference to enhance its translation in mammalian cells. The
Cas9 gene also was modified by adding a nuclear localization signal
PKKKRKV (SEQ ID NO:1) at the C terminus for targeting the protein
into the nuclei of mammalian cells. Table 1 presents the modified
Cas9 amino acid sequence, with the nuclear localization sequence
underlined. Table 2 presents the codon optimized, modified Cas9 DNA
sequence.
TABLE-US-00001 TABLE 1 Modified Cas9 Amino Acid Sequence
MDKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTDRHSIKKNLIGA
LLFGSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHR
LEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLADSTDKAD
LRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQIYNQLFEENP
INASRVDAKAILSARLSKSRRLENLIAQLPGEKRNGLFGNLIALSLGLTP
NFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI
LLSDILRVNSEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEI
FFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLR
KQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPY
YVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDK
NLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVD
LLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGAYHDLLKI
IKDKDFLDNEENEDILEDIVLTLTLFEDRGMIEERLKTYAHLFDDKVMKQ
LKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDD
SLTFKEDIQKAQVSGQGHSLHEQIANLAGSPAIKKGILQTVKIVDELVKV
MGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPV
ENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFIKDDS
IDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLT
KAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIR
EVKVITLKSKLVSDFRKDFQFYKVREINNYHHANDAYLNAVVGTALIKKY
PKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEIT
LANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQ
TGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEK
GKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKY
SLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPED
NEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKP
IREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQS
ITGLYETRIDLSQLGGDPKKKRKV (SEQ ID NO: 9)
TABLE-US-00002 TABLE 2 Optimized Cas9 DNA Sequence (5'-3')
ATGGACAAGAAGTACAGCATCGGCCTGGACATCGGCACCAACTCTGTGGG
CTGGGCCGTGATCACCGACGACTACAAGGTGCCCAGCAAGAAATTCAAGG
TGCTGGGCAACACCGACCGGCACAGCATCAAGAAGAACCTGATCGGCGCC
CTGCTGTTCGGCTCTGGCGAAACAGCCGAGGCCACCCGGCTGAAGAGAAC
CGCCAGAAGAAGATACACCAGACGGAAGAACCGGATCTGCTATCTGCAAG
AGATCTTCAGCAACGAGATGGCCAAGGTGGACGACAGCTTCTTCCACAGA
CTGGAAGAGTCCTTCCTGGTGGAAGAGGATAAGAAGCACGAGCGGCACCC
CATCTTCGGCAACATCGTGGACGAGGTGGCCTACCACGAGAAGTACCCCA
CCATCTACCACCTGAGAAAGAAGCTGGCCGACAGCACCGACAAGGCCGAC
CTGAGACTGATCTACCTGGCCCTGGCCCACATGATCAAGTTCCGGGGCCA
CTTCCTGATCGAGGGCGACCTGAACCCCGACAACAGCGACGTGGACAAGC
TGTTCATCCAGCTGGTGCAGATCTACAATCAGCTGTTCGAGGAAAACCCC
ATCAACGCCAGCAGAGTGGACGCCAAGGCCATCCTGAGCGCCAGACTGAG
CAAGAGCAGACGGCTGGAAAATCTGATCGCCCAGCTGCCCGGCGAGAAGC
GGAATGGCCTGTTCGGCAACCTGATTGCCCTGAGCCTGGGCCTGACCCCC
AACTTCAAGAGCAACTTCGACCTGGCCGAGGATGCCAAACTGCAGCTGAG
CAAGGACACCTACGACGACGACCTGGACAACCTGCTGGCCCAGATCGGCG
ACCAGTACGCCGACCTGTTTCTGGCCGCCAAGAACCTGTCCGACGCCATC
CTGCTGAGCGACATCCTGAGAGTGAACAGCGAGATCACCAAGGCCCCCCT
GTCCGCCTCTATGATCAAGAGATACGACGAGCACCACCAGGACCTGACCC
TGCTGAAAGCTCTCGTGCGGCAGCAGCTGCCTGAGAAGTACAAAGAGATT
TTCTTCGACCAGAGCAAGAACGGCTACGCCGGCTACATCGATGGCGGAGC
CAGCCAGGAAGAGTTCTACAAGTTCATCAAGCCCATCCTGGAAAAGATGG
ACGGCACCGAGGAACTGCTCGTGAAGCTGAACAGAGAGGACCTGCTGCGG
AAGCAGCGGACCTTCGACAACGGCAGCATCCCCCACCAGATCCACCTGGG
AGAGCTGCACGCCATTCTGCGGCGGCAGGAAGATTTTTACCCATTCCTGA
AGGACAACCGGGAAAAGATCGAGAAGATCCTGACCTTCAGAATCCCCTAC
TACGTGGGCCCTCTGGCCAGGGGAAACAGCAGATTCGCCTGGATGACCAG
AAAGAGCGAGGAAACCATCACCCCCTGGAACTTCGAGGAAGTGGTGGACA
AGGGCGCCAGCGCCCAGAGCTTCATCGAGCGGATGACCAACTTCGATAAG
AACCTGCCCAACGAGAAGGTGCTGCCCAAGCACAGCCTGCTGTACGAGTA
CTTCACCGTGTACAACGAGCTGACCAAAGTGAAATACGTGACCGAGGGAA
TGCGGAAGCCCGCCTTTCTGAGCGGCGAGCAGAAAAAGGCCATCGTGGAC
CTGCTGTTCAAGACCAACCGGAAAGTGACCGTGAAGCAGCTGAAAGAGGA
CTACTTCAAGAAAATCGAGTGCTTCGACAGCGTGGAAATCAGCGGCGTGG
AAGATCGGTTCAACGCCTCCCTGGGCGCCTATCACGATCTGCTGAAAATT
ATCAAGGACAAGGACTTCCTGGACAATGAGGAAAACGAGGACATTCTGGA
AGATATCGTGCTGACCCTGACACTGTTTGAGGACCGGGGCATGATCGAGG
AACGGCTGAAAACCTATGCCCACCTGTTCGACGACAAAGTGATGAAGCAG
CTGAAGCGGCGGAGATACACCGGCTGGGGCAGGCTGAGCCGGAAGCTGAT
CAACGGCATCCGGGACAAGCAGTCCGGCAAGACAATCCTGGATTTCCTGA
AGTCCGACGGCTTCGCCAACAGAAACTTCATGCAGCTGATCCACGACGAC
AGCCTGACCTTTAAAGAGGACATCCAGAAAGCCCAGGTGTCCGGCCAGGG
ACACTCTCTGCACGAGCAGATCGCCAATCTGGCCGGATCCCCCGCCATTA
AGAAGGGCATCCTGCAGACAGTGAAGATTGTGGACGAGCTCGTGAAAGTG
ATGGGCCACAAGCCCGAGAACATCGTGATCGAAATGGCCAGAGAGAACCA
GACCACCCAGAAGGGACAGAAGAACAGCCGCGAGAGAATGAAGCGGATCG
AAGAGGGCATCAAAGAGCTGGGCAGCCAGATCCTGAAAGAACACCCCGTG
GAAAACACCCAGCTGCAGAACGAGAAGCTGTACCTGTACTACCTGCAGAA
TGGGCGGGATATGTACGTGGACCAGGAACTGGACATCAACCGGCTGTCCG
ACTACGATGTGGACCACATTGTGCCCCAGTCCTTCATCAAGGACGACTCC
ATCGATAACAAAGTGCTGACTCGGAGCGACAAGAACCGGGGCAAGAGCGA
CAACGTGCCCTCCGAAGAGGTCGTGAAGAAGATGAAGAACTACTGGCGCC
AGCTGCTGAATGCCAAGCTGATTACCCAGAGGAAGTTCGACAATCTGACC
AAGGCCGAGAGAGGCGGCCTGAGCGAACTGGATAAGGCCGGCTTCATTAA
GCGGCAGCTGGTGGAAACCCGGCAGATCACAAAGCACGTGGCACAGATCC
TGGACTCCCGGATGAACACTAAGTACGACGAGAACGACAAACTGATCCGG
GAAGTGAAAGTGATCACCCTGAAGTCCAAGCTGGTGTCCGACTTCAGAAA
GGATTTCCAGTTTTACAAAGTGCGCGAGATCAACAACTACCACCACGCCC
ACGACGCCTACCTGAACGCCGTCGTGGGAACCGCCCTGATCAAAAAGTAC
CCTAAGCTGGAAAGCGAGTTCGTGTACGGCGATTACAAGGTGTACGACGT
GCGGAAGATGATCGCCAAGAGCGAGCAGGAAATCGGCAAGGCTACCGCCA
AGTACTTCTTCTACAGCAACATCATGAACTTTTTCAAGACCGAGATCACA
CTGGCCAACGGCGAGATCAGAAAGCGGCCTCTGATCGAGACAAACGGCGA
AACCGGGGAGATCGTGTGGGATAAGGGCCGGGATTTTGCCACAGTGCGGA
AAGTGCTGTCCATGCCCCAAGTGAATATCGTGAAAAAGACCGAGGTGCAG
ACCGGCGGCTTCAGCAAAGAGTCTATCCTGCCCAAGAGGAACTCCGACAA
GCTGATCGCCAGAAAGAAGGATTGGGACCCTAAGAAGTACGGCGGCTTTG
ACAGCCCCACCGTGGCCTACTCTGTGCTGGTGGTGGCCAAAGTGGAAAAG
GGCAAGTCCAAGAAACTGAAGAGTGTGAAAGAGCTGCTGGGGATCACCAT
CATGGAAAGAAGCAGCTTCGAGAAGAATCCCATCGACTTTCTGGAAGCCA
AGGGCTACAAAGAAGTGAAAAAGGACCTGATCATCAAGCTGCCTAAGTAC
TCCCTGTTCGAGCTGGAAAACGGCCGGAAGCGGATGCTGGCTTCTGCCGG
CGAACTGCAGAAGGGAAACGAGCTGGCCCTGCCCTCCAAATATGTGAACT
TCCTGTACCTGGCCAGCCACTATGAGAAGCTGAAGGGCTCCCCCGAGGAT
AATGAGCAGAAACAGCTGTTTGTGGAACAGCACAAGCACTACCTGGACGA
GATCATCGAGCAGATTAGCGAGTTCTCCAAGCGCGTGATCCTGGCCGATG
CCAACCTGGACAAGGTGCTGAGCGCCTACAACAAGCACCGGGATAAGCCC
ATCAGAGAGCAGGCCGAGAATATCATCCACCTGTTTACCCTGACCAACCT
GGGAGCCCCTGCCGCCTTCAAGTACTTTGACACCACCATCGACCGGAAGA
GGTACACCAGCACCAAAGAGGTGCTGGACGCCACCCTGATCCACCAGAGC
ATCACCGGCCTGTACGAGACACGGATCGACCTGTCTCAGCTGGGAGGCGA
CCCCAAGAAAAAGCGCAAAGTG (SEQ ID NO: 10)
[0162] The modified Cas9 DNA sequence was placed under the control
of cytomegalovirus (CMV) promoter for constituent expression in
mammalian cells. The modified Cas9 DNA sequence was also placed
under the control T7 promoter for in vitro mRNA synthesis with T7
RNA polymerase. In vitro RNA transcription was performed by using
MessageMAX T7 ARCA-Capped Message Transcription Kit and T7 mScript
Standard mRNA Production System (Cellscript).
Example 2: Targeting Cas9
[0163] The adeno-associated virus integration site 1 (AAVS1) locus
was used as a target for Cas9-mediated human genome modification.
The human AAVS1 locus is located in intron 1 (4427 bp) of protein
phosphatase 1, regulatory subunit 12C (PPP1R12C). Table 3 presents
the first exon (shaded gray) and the first intron of PPP1R12C. The
underlined sequence within the intron is the targeted modification
site (i.e., AAVS1 locus).
TABLE-US-00003 TABLE 3 First Exon and Intron of PPP1R12C (5'-3')
##STR00001## ACCCTCTGCTGCGCCACCTGGGGCATCCTCCTTCCCCGTTGCCAGTC
TCGATCCGCCCCGTCGTTCCTGGCCCTGGGCTTTGCCACCCTATGCT
GACACCCCGTCCCAGTCCCCCTTACCATTCCCCTTCGACCACCCCAC
TTCCGAATTGGAGCCGCTTCAACTGGCCCTGGGCTTAGCCACTCTGT
GCTGACCACTCTGCCCCAGGCCTCCTTACCATTCCCCTTCGACCTAC
TCTCTTCCGCATTGGAGTCGCTTTAACTGGCCCTGGCTTTGGCAGCC
TGTGCTGACCCATGCAGTCCTCCTTACCATCCCTCCCTCGACTTCCC
CTCTTCCGATGTTGAGCCCCTCCAGCCGGTCCTGGACTTTGTCTCCT
TCCCTGCCCTGCCCTCTCCTGAACCTGAGCCAGCTCCCATAGCTCAG
TCTGGTCTATCTGCCTGGCCCTGGCCATTGTCACTTTGCGCTGCCCT
CCTCTCGCCCCCGAGTGCCCTTGCTGTGCCGCCGGAACTCTGCCCTC
TAACGCTGCCGTCTCTCTCCTGAGTCCGGACCACTTTGAGCTCTACT
GGCTTCTGCGCCGCCTCTGGCCCACTGTTTCCCCTTCCCAGGCAGGT
CCTGCTTTCTCTGACCTGCATTCTCTCCCCTGGGCCTGTGCCGCTTT
CTGTCTGCAGCTTGTGGCCTGGGTCACCTCTACGGCTGGCCCAGATC
CTTCCCTGCCGCCTCCTTCAGGTTCCGTCTTCCTCCACTCCCTCTTC
CCCTTGCTCTCTGCTGTGTTGCTGCCCAAGGATGCTCTTTCCGGAGC
ACTTCCTTCTCGGCGCTGCACCACGTGATGTCCTCTGAGCGGATCCT
CCCCGTGTCTGGGTCCTCTCCGGGCATCTCTCCTCCCTCACCCAACC
CCATGCCGTCTTCACTCGCTGGGTTCCCTTTTCCTTCTCCTTCTGGG
GCCTGTGCCATCTCTCGTTTCTTAGGATGGCCTTCTCCGACGGATGT
CTCCCTTGCGTCCCGCCTCCCCTTCTTGTAGGCCTGCATCATCACCG
TTTTTCTGGACAACCCCAAAGTACCCCGTCTCCCTGGCTTTAGCCAC
CTCTCCATCCTCTTGCTTTCTTTGCCTGGACACCCCGTTCTCCTGTG
GATTCGGGTCACCTCTCACTCCTTTCATTTGGGCAGCTCCCCTACCC
CCCTTACCTCTCTAGTCTGTGCTAGCTCTTCCAGCCCCCTGTCATGG
CATCTTCCAGGGGTCCGAGAGCTCAGCTAGTCTTCTTCCTCCAACCC
GGGCCCCTATGTCCACTTCAGGACAGCATGTTTGCTGCCTCCAGGGA
TCCTGTGTCCCCGAGCTGGGACCACCTTATATTCCCAGGGCCGGTTA
ATGTGGCTCTGGTTCTGGGTACTTTTATCTGTCCCCTCCACCCCACA
GTGGGGCCACTAGGGACAGGATTGGTGACAGAAAAGCCCCATCCTTA
GGCCTCCTCCTTCCTAGTCTCCTGATATTGGGTCTAACCCCCACCTC
CTGTTAGGCAGATTCCTTATCTGGTGACACACCCCCATTTCCTGGAG
CCATCTCTCTCCTTGCCAGAACCTCTAAGGTTTGCTTACGATGGAGC
CAGAGAGGATCCTGGGAGGGAGAGCTTGGCAGGGGGTGGGAGGGAAG
GGGGGGATGCGTGACCTGCCCGGTTCTCAGTGGCCACCCTGCGCTAC
CCTCTCCCAGAACCTGAGCTGCTCTGACGCGGCCGTCTGGTGCGTTT
CACTGATCCTGGTGCTGCAGCTTCCTTACACTTCCCAAGAGGAGAAG
CAGTTTGGAAAAACAAAATCAGAATAAGTTGGTCCTGAGTTCTAACT
TTGGCTCTTCACCTTTCTAGTCCCCAATTTATATTGTTCCTCCGTGC
GTCAGTTTTACCTGTGAGATAAGGCCAGTAGCCAGCCCCGTCCTGGC
AGGGCTGTGGTGAGGAGGGGGGTGTCCGTGTGGAAAACTCCCTTTGT
GAGAATGGTGCGTCCTAGGTGTTCACCAGGTCGTGGCCGCCTCTACT
CCCTTTCTCTTTCTCCATCCTTCTTTCCTTAAAGAGTCCCCAGTGCT
ATCTGGGACATATTCCTCCGCCCAGAGCAGGGTCCCGCTTCCCTAAG
GCCCTGCTCTGGGCTTCTGGGTTTGAGTCCTTGGCAAGCCCAGGAGA
GGCGCTCAGGCTTCCCTGTCCCCCTTCCTCGTCCACCATCTCATGCC
CCTGGCTCTCCTGCCCCTTCCCTACAGGGGTTCCTGGCTCTGCTCTT
CAGACTGAGCCCCGTTCCCCTGCATCCCCGTTCCCCTGCATCCCCCT
TCCCCTGCATCCCCCAGAGGCCCCAGGCCACCTACTTGGCCTGGACC
CCACGAGAGGCCACCCCAGCCCTGTCTACCAGGCTGCCTTTTGGGTG
GATTCTCCTCCAACTGTGGGGTGACTGCTTGGCAAACTCACTCTTCG
GGGTATCCCAGGAGGCCTGGAGCATTGGGGTGGGCTGGGGTTCAGAG
AGGAGGGATTCCCTTCTCAGGTTACGTGGCCAAGAAGCAGGGGAGCT
GGGTTTGGGTCAGGTCTGGGTGTGGGGTGACCAGCTTATGCTGTTTG
CCCAGGACAGCCTAGTTTTAGCACTGAAACCCTCAGTCCTAGGAAAA
CAGGGATGGTTGGTCACTGTCTCTGGGTGACTCTTGATTCCCGGCCA
GTTTCTCCACCTGGGGCTGTGTTTCTCGTCCTGCATCCTTCTCCAGG
CAGGTCCCCAAGCATCGCCCCCCTGCTGTGGCTGTTCCCAAGTTCTT
AGGGTACCCCACGTGGGTTTATCAACCACTTGGTGAGGCTGGTACCC
TGCCCCCATTCCTGCACCCCAATTGCCTTAGTGGCTAGGGGGTTGGG
GGCTAGAGTAGGAGGGGCTGGAGCCAGGATTCTTAGGGCTGAACAGA
GAAGAGCTGGGGGCCTGGGCTCCTGGGTTTGAGAGAGGAGGGGCTGG
GGCCTGGACTCCTGGGTCCGAGGGAGGAGGGGCTGGGGCCTGGACTC
CTGGGTCTGAGGGTGGAGGGACTGGGGGCCTGGACTCCTGGGTCCGA
GGGAGGAGGGGCTGGGGCCTGGACTCGTGGGTCTGAGGGAGGAGGGG
CTGGGGGCCTGGACTTCTGGGTCTTAGGGAGGCGGGGCTGGGCCTGG
ACCCCTGGGTCTGAATGGGGAGAGGCTGGGGGCCTGGACTCCTTCAT
CTGAGGGCGGAAGGGCTGGGGCCTGGCCTCCTGGGTTGAATGGGGAG
GGGTTGGGCCTGGACTCTGGAGTCCCTGGTGCCCAGGCCTCAGGCAT
CTTTCACAGGGATGCCTGTACTGGGCAGGTCCTTGAAAGGGAAAGGC
CCATTGCTCTCCTTGCCCCCCTCCCCTATCGCCATGACAACTGGGTG
GAAATAAACGAGCCGAGTTCATCCCGTTCCCAGGGCACGTGCGGCCC
CTTCACAGCCCGAGTTTCCATGACCTCATGCTCTTGGCCCTCGTAGC
TCCCTCCCGCCTCCTCCAGATGGGCAGCTTTGGAGAGGTGAGGGACT
TGGGGGGTAATTTATCCCGTGGATCTAGGAGTTTAGCTTCACTCCTT
CCTCAGCTCCAGTTCAGGTCCCGGAGCCCACCCAGTGTCCACAAGGC
CTGGGGCAAGTCCCTCCTCCGACCCCCTGGACTTCGGCTTTTGTCCC
CCCAAGTTTTGGACCCCTAAGGGAAGAATGAGAAACGGTGGCCCGTG
TCAGCCCCTGGCTGCAGGGCCCCGTGCAGAGGGGGCCTCAGTGAACT
GGAGTGTGACAGCCTGGGGCCCAGGCACACAGGTGTGCAGCTGTCTC
ACCCCTCTGGGAGTCCCGCCCAGGCCCCTGAGTCTGTCCCAGCACAG
GGTGGCCTTCCTCCACCCTGCATAGCCCTGGGCCCACGGCTTCGTTC
CTGCAGAGTATCTGCTGGGGTGGTTTCCGAGCTTGACCCTTGGAAGG
ACCTGGCTGGGTTTAAGGCAGGAGGGGCTGGGGGCCAGGACTCCTGG
CTCTGAAGGAGGAGGGGCTGGAACCTCTTCCCTAGTCTGAGCACTGG
AAGCGCCACCTGTGGGTGGTGACGGGGGTTTTGCCGTGTCTAACAGG
TACCATGTGGGGTTCCCGCACCCAGATGAGAAGCCCCCTCCCTTCCC
CGTTCACTTCCTGTTTGCAGATAGCCAGGAGTCCTTTCGTGGTTTCC
ACTGAGCACTGAAGGCCTGGCCGGCCTGACCACTGGGCAACCAGGCG
TATCTTAAACAGCCAGTGGCCAGAGGCTGTTGGGTCATTTTCCCCAC
TGTCCTAGCACCGTGTCCCTGGATCTGTTTTCGTGGCTCCCTCTGGA
GTCCCGACTTGCTGGGACACCGTGGCTGGGGTAGGTGCGGCTGACGG CTGTTTCCCACCCCCAG
(SEQ ID NO: 11)
[0164] Cas9 guide RNAs were designed for targeting the human AAVS1
locus. A 42 nucleotide RNA (referred to herein as a "crRNA"
sequence) comprising (5' to 3') a target recognition sequence
(i.e., sequence complementary to the non-coding strand of the
target sequence) and protospacer sequence; a 85 nucleotide RNA
(referred to herein as a "tracrRNA" sequence) comprising 5'
sequence with complementarity to the 3' sequence of the crRNA and
additional hairpin sequence; and a chimeric RNA comprising
nucleotides 1-32 of the crRNA, a GAAA loop, and nucleotides 19-45
of the tracrRNA were prepared. The crRNA was chemically synthesized
by Sigma-Aldrich. The tracrRNA and chimeric RNA were synthesized by
in vitro transcription with T7 RNA polymerase using T7-Scribe
Standard RNA IVT Kit (Cellscript). The chimeric RNA coding sequence
was also placed under the control of human U6 promoter for in vivo
transcription in human cells. Table 4 presents the sequences of the
guide RNAs.
TABLE-US-00004 TABLE 4 Guide RNAs SEQ ID RNA 5'-3' Sequence NO:
AAVS1- ACCCCACAGUGGGGCCACUAGUUUUAGAGCUAUG 12 crRNA CUGUUUUG
tracrRNA GGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUA 13
AGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCAC CGAGUCGGUGCUUUUUUU chimeric
ACCCCACAGUGGGGCCACUAGUUUUAGAGCUAGA 14 RNA
AAUAGCAAGUUAAAAUAAGGCUAGUCCG
Example 3: Preparation of Donor Polynucleotide to Monitor Genome
Modification
[0165] Targeted integration of a GFP protein into the N terminus of
PPP1R12C was used to monitor Cas9-mediated genome modification. To
mediate integration by homologous recombination a donor
polynucleotide was prepared. The AAVS1-GFP DNA donor contained a 5'
(1185 bp) AAVS1 locus homologous arm, an RNA splicing receptor, a
turbo GFP coding sequence, a 3' transcription terminator, and a 3'
(1217 bp) AAVS1 locus homologous arm. Table 5 presents the
sequences of the RNA splicing receptor and the GFP coding sequence
followed by the 3' transcription terminator. Plasmid DNA was
prepared by using GenElute Endotoxin-Free Plasmid Maxiprep Kit
(Sigma).
TABLE-US-00005 TABLE 5 Sequences in the AAVS1-GFP DNA donor
sequence SEQ ID 5'-3' Sequence NO: RNA splicing
CTGACCTCTTCTCTTCCTCCCACAG 15 receptor GFP coding
GCCACCATGGACTACAAAGACGATGACGACAAGGTCGACT 16 sequence and
CTAGAGCTGCAGAGAGCGACGAGAGCGGCCTGCCCGCCA transcription
TGGAGATCGAGTGCCGCATCACCGGCACCCTGAACGGCG terminator
TGGAGTTCGAGCTGGTGGGCGGCGGAGAGGGCACCCCCG
AGCAGGGCCGCATGACCAACAAGATGAAGAGCACCAAAGG
CGCCCTGACCTTCAGCCCCTACCTGCTGAGCCACGTGATG
GGCTACGGCTTCTACCACTTCGGCACCTACCCCAGCGGCT
ACGAGAACCCCTTCCTGCACGCCATCAACAACGGCGGCTA
CACCAACACCCGCATCGAGAAGTACGAGGACGGCGGCGT
GCTGCACGTGAGCTTCAGCTACCGCTACGAGGCCGGCCG
CGTGATCGGCGACTTCAAGGTGATGGGCACCGGCTTCCCC
GAGGACAGCGTGATCTTCACCGACAAGATCGTCCGCAGCA
ACGCCACCGTGGAGCACCTGCACCCCATGGGCGATAACG
ATCTGGATGGCAGCTTCACCCGCACCTTCAGCCTGCGCGA
CGGCGGCTACTACAGCTCCGTGGTGGACAGCCACATGCAC
TTCAAGAGCGCCATCCACCCCAGCATCCTGCAGAACGGGG
GCCCCATGTTCGCCTTCCGCCGCGTGGAGGAGGATCACA
GCAACACCGAGCTGGGCATCGTGGAGTACCAGCACGCCTT
CAAGACCCCGGATGCAGATGCCGGTGAAGAATGAAGATCT
CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCC
CCCGTGCCTTCCTTGACCCTGGAAGGTGCCACTCCCACTG
TCCTTTCCTAATAAAATGAGGAAATTGCATCGCATTGTCTGA
GTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGG
ACAGCAAGGGGGAGGATTGGGAAGACAATAGCAGGCATG
CTGGGGATGCGGTGGGCTCTATGGACTCGAGGTTTAAACG TCGACGCGGCCGCGT
[0166] Targeted gene integration will result in a fusion protein
between the first 107 amino acids of the PPP1R12C and the turbo
GFP. The expected fusion protein contains the first 107 amino acid
residues of PPP1R12C (highlighted in grey) from RNA splicing
between the first exon of PPP1R12C and the engineered splice
receptor (see Table 6).
TABLE-US-00006 TABLE 6 Predicted amino acid sequence of the
PPP1R12C-GFP fusion protein. ##STR00002##
TLNGVEFELVGGGEGTPEQGRMTNKMKSTKGALTFSPYLLSHVMGYG
FYHFGTYPSGYENPFLHAINNGGYTNTRIEKYEDGGVLHVSFSYRYE
AGRVIGDFKVMGTGFPEDSVIFTDKIVRSNATVEHLHPMGDNDLDGS
FTRTFSLRDGGYYSSVVDSHMHFKSAIHPSILQNGGPMFAFRRVEED
HSNTELGIVEYQHAFKTPDADAGEE (SEQ ID NO: 17)
Example 4: Cas9-Mediated Targeted Integration
[0167] Transfection was performed on human K562 cells. The K562
cell line was obtained from American Type Culture Collection (ATCC)
and grown in Iscove's Modified Dulbecco's Medium, supplemented with
10% FBS and 2 mM L-glutamine. All media and supplements were
obtained from Sigma-Aldrich. Cultures were split one day before
transfection (at approximately 0.5 million cells per mL before
transfection). Cells were transfected with Nucleofector Solution V
(Lonza) on a Nucleofector (Lonza) with the T-016 program. Each
nucleofection contained approximately 0.6 million cells.
Transfection treatments are detailed in Table 7. Cells were grown
at 37.degree. C. and 5% CO.sub.2 immediately after
nucleofection.
TABLE-US-00007 TABLE 7 Transfection Treatments. Treatment Modified
Cas9 Guide RNA Donor sequence A Cas9 mRNA transcribed pre-annealed
AAVS1-GFP with an Anti-Reverse Cap crRNA-tracrRNA plasmid DNA
Analog (10 .mu.g) duplex (0.3 nmol) (10 .mu.g) B Cas9 mRNA
transcribed chimeric RNA AAVS1-GFP with an Anti-Reverse (0.3 nmol)
plasmid DNA Cap Analog (10 .mu.g) (10 .mu.g) C Cas9 mRNA capped via
chimeric RNA AAVS1-GFP post-transcription (0.3 nmol) plasmid DNA
capping (10 .mu.g) reaction (10 .mu.g) D Cas9 plasmid U6-chimeric
RNA AAVS1-GFP DNA (10 .mu.g) plasmid plasmid DNA DNA (5 .mu.g) (10
.mu.g) E None None AAVS1-GFP plasmid DNA (10 .mu.g) F None None
None
[0168] Fluorescence-activated cell sorting (FACS) was performed 4
days after transfection. FACS data are presented in FIGS. 4A-F. The
percent GFP detected in each of the four experimental treatments
(FIGS. 4A-D) was greater than in the control treatments (FIGS. 4E
and 4F), confirming integration of the donor sequence and
expression of the fusion protein.
Example 5: PCR Confirmation of Targeted Integration
[0169] Genomic DNA was extracted from transfected cells with
GenElute Mammalian Genomic DNA Miniprep Kit (Sigma) 12 days after
transfection. Genomic DNA was then PCR amplified with a forward
primer located outside the 5' homologous arm of the AAVS1-GFP
plasmid donor and a reverse primer located at the 5' region of the
GFP. The forward primer was 5'-CCACTCTGTGCTGACCACTCT-3' (SEQ ID
NO:18) and reverse primer was 5'-GCGGCACTCGATCTCCA-3' (SEQ ID
NO:19). The expected fragment size from the junction PCR was 1388
bp. The amplification was carried out with JumpStart Taq ReadyMix
(Sigma), using the following cycling conditions: 98.degree. C. for
2 minutes for initial denaturation; 35 cycles of 98.degree. C. for
15 seconds, 62.degree. C. for 30 seconds, and 72.degree. C. for 1
minutes and 30 seconds; and a final extension at 72.degree. C. for
5 minutes. PCR products were resolved on 1% agarose gel.
[0170] Cells transfected with 10 .mu.g of Cas9 mRNA transcribed
with an Anti-Reverse Cap Analog, 0.3 nmol of pre-annealed
crRNA-tracrRNA duplex, and 10 .mu.g of AAVS1-GFP plasmid DNA
displayed a PCR product of the expected size (see lane A in FIG.
5).
Example 6: Cas9-Based Genome Editing in Mouse Embryos
[0171] The mouse Rosa26 locus can be targeted for genome
modifications. Table 8 presents a portion of the mouse Rosa26
sequence in which potential target sites are shown in bold. Each
target site comprises a protospacer.
TABLE-US-00008 TABLE 8 Mouse Rosa26 Sequence
GAGCGGCTGCGGGGCGGGTGCAAGCACGTTTCCGACTTGAGTTGCCTCAA
GAGGGGCGTGCTGAGCCAGACCTCCATCGCGCACTCCGGGGAGTGGAGGG
AAGGAGCGAGGGCTCAGTTGGGCTGTTTTGGAGGCAGGAAGCACTTGCTC
TCCCAAAGTCGCTCTGAGTTGTTATCAGTAAGGGAGCTGCAGTGGAGTAG
GCGGGGAGAAGGCCGCACCCTTCTCCGGAGGGGGGAGGGGAGTGTTGCAA
TACCTTTCTGGGAGTTCTCTGCTGCCTCCTGGCTTCTGAGGACCGCCCTG
GGCCTGGGAGAATCCCTTCCCCCTCTTCCCTCGTGATCTGCAACTCCAGT
CTTTCTAGAAGATGGGCGGGAGTCTTCTGGGCAGGCTTAAAGGCTAACCT
GGTGTGTGGGCGTTGTCCTGCAGGGGAATTGAACAGGTGTAAAATTGGAG
GGACAAGACTTCCCACAGATTTTCGGTTTTGTCGGGAAGTTTTTTAATAG
GGGCAAATAAGGAAAATGGGAGGATAGGTAGTCATCTGGGGTTTTATGCA
GCAAAACTACAGGTTATTATTGCTTGTGATCCGCCTCGGAGTATTTTCCA
TCGAGGTAGATTAAAGACATGCTCACCCGAGTTTTATACTCTCCTGCTTG
AGATCCTTACTACAGTATGAAATTACAGTGTCGCGAGTTAGACTATGTAA GCAGAATTTTA (SEQ
ID NO: 20)
[0172] Guide RNAs were designed to target each of the target sites
in the mouse Rosa26 locus. The sequences are shown in Table 9, each
is 42 nucleotides in length and the 5' region is complementary to
the strand that is not presented in Table 8 (i.e., the strand that
is complementary to the strand shown in Table 8).
TABLE-US-00009 TABLE 9 Mouse Rosa26 Guide RNAs SEQ ID RNA 5'-3'
Sequence NO: mRosa26- CUCCAGUCUUUCUAGAAGAUGUUUUAGAGCUAU 21 crRNA-1
GCUGUUUUG mRosa26- UGAACAGGUGUAAAAUUGGAGUUUUAGAGCUAU 22 crRNA-2
GCUGUUUUG mRosa26- UGUCGGGAAGUUUUUUAAUAGUUUUAGAGCUAU 23 crRNA-3
GCUGUUUUG
[0173] The crRNAs were chemically synthesized and pre-annealed to
the tracrRNA (SEQ ID NO:13; see Example 2). Pre-annealed
crRNA/tracrRNA and in vitro transcribed mRNA encoding modified Cas9
protein (SEQ ID NO. 9; see Example 1) can be microinjected into the
pronuclei of fertilized mouse embryos. Upon guidance to the target
set by the crRNA, the Cas9 protein cleaves the target site, and the
resultant double-stranded break can be repaired via a
non-homologous end-joining (NHEJ) repair process. The injected
embryos can be either incubated at 37.degree. C., 5% CO.sub.2
overnight or for up to 4 days, followed by genotyping analysis, or
the injected embryos can be implanted into recipient female mice
such that live born animals can be genotyped. The in
vitro-incubated embryos or tissues from live born animals can be
screened for the presence of Cas9-induced mutation at the Rosa
locus using standard methods. For example, the embryos or tissues
from fetus or live-born animals can be harvested for DNA extraction
and analysis. DNA can be isolated using standard procedures. The
targeted region of the Rosa26 locus can be PCR amplified using
appropriate primers. Because NHEJ is error-prone, deletions of at
least one nucleotide, insertions of at least one nucleotide,
substitutions of at least one nucleotide, or combinations thereof
can occur during the repair of the break. Mutations can be detected
using PCR-based genotyping methods, such as Cel-I mismatch assays
and DNA sequencing.
Example 7: Cas9-Based Genome Modification in Mouse Embryos
[0174] The Rosa26 locus can be modified in mouse embryos by
co-injecting a donor polynucleotide, as detailed above in section
(IV)(d), along with the pre-annealed crRNA/tracrRNA and mRNA
encoding modified Cas9 as described above in Example 6. In
vitro-incubated embryos or tissues from live born animals (as
described in Example 6) can be screened for a modified Rosa26 locus
using PCR-based genotyping methods, such as RFLP assays, junction
PCR, and DNA sequencing.
Example 8: Cas9-Based Genome Editing in Rat Embryos
[0175] The rat Rosa26 locus can be targeted for genome
modifications. Table 10 presents a portion of the rat sequence in
which potential target sites are shown in bold. Each target site
comprises a protospacer.
TABLE-US-00010 TABLE 10 Rat Rosa26 Sequence
GGGATTCCTCCTTGAGTTGTGGCACTGAGGAACGTGCTGAACAAGACCTA
CATTGCACTCCAGGGAGTGGATGAAGGAGTTGGGGCTCAGTCGGGTTGTA
TTGGAGACAAGAAGCACTTGCTCTCCAAAAGTCGGTTTGAGTTATCATTA
AGGGAGCTGCAGTGGAGTAGGCGGAGAAAAGGCCGCACCCTTCTCAGGAC
GGGGGAGGGGAGTGTTGCAATACCTTTCTGGGAGTTCTCTGCTGCCTCCT
GTCTTCTGAGGACCGCCCTGGGCCTGGAAGATTCCCTTCCCCCTTCTTCC
CTCGTGATCTGCAACTGGAGTCTTTCTGGAAGATAGGCGGGAGTCTTCTG
GGCAGGCTTAAAGGCTAACCTGGTGCGTGGGGCGTTGTCCTGCAGAGGAA
TTGAACAGGTGTAAAATTGGAGGGGCAAGACTTCCCACAGATTTTCGATT
GTGTTGTTAAGTATTGTAATAGGGGCAAATAAGGGAAATAGACTAGGCAC
TCACCTGGGGTTTTATGCAGCAAAACTACAGGTTATTATTGCTTGTGATC
CGCCCTGGAGAATTTTTCACCGAGGTAGATTGAAGACATGCCCACCCAAA
TTTTAATATTCTTCCACTTGCGATCCTTGCTACAGTATGAAA (SEQ ID NO: 24)
[0176] Guide RNAs were designed to target each of the target sites
in the rat Rosa26 locus. The sequences are shown in Table 11, each
is 42 nucleotides in length and the 5' region is complementary to
the strand that is not presented in Table 10 (i.e., the strand that
is complementary to the strand shown in Table 10).
TABLE-US-00011 TABLE 11 Rat Rosa26 Guide RNAs SEQ ID RNA 5'-3'
Sequence NO: rRosa26- AGGGGGAAGGGAAUCUUCCAGUUUUAGAGCUA 25 crRNA-1
UGCUGUUUUG rRosa26- UCUGCAACUGGAGUCUUUCUGUUUUAGAGCUA 26 crRNA-2
UGCUGUUUUG rRosa26- AGGCGGGAGUCUUCUGGGCAGUUUUAGAGCUA 27 crRNA-3
UGCUGUUUUG
[0177] The crRNAs were chemically synthesized and pre-annealed to
the tracrRNA (SEQ ID NO:13; see Example 2). Pre-annealed
crRNA/tracrRNA and in vitro transcribed mRNA encoding modified Cas9
protein (SEQ ID NO. 9; see Example 1) can be microinjected into the
pronuclei of fertilized rat embryos. Upon guidance to the target
site by the crRNA, the Cas9 protein cleaves the target site, and
the resultant double-stranded break can be repaired via a
non-homologous end-joining (NHEJ) repair process. The injected
embryos can be either incubated at 37.degree. C., 5% CO.sub.2
overnight or for up to 4 days, followed by genotyping analysis, or
the injected embryos can be implanted into recipient female mice
such that live born animals can be genotyped. The in
vitro-incubated embryos or tissues from live born animals can be
screened for the presence of Cas9-induced mutation at the Rosa
locus using standard methods. For example, the embryos or tissues
from fetus or live-born animals can be harvested for DNA extraction
and analysis. DNA can be isolated using standard procedures. The
targeted region of the Rosa26 locus can be PCR amplified using
appropriate primers. Because NHEJ is error-prone, deletions of at
least one nucleotide, insertions of at least one nucleotide,
substitutions of at least one nucleotide, or combinations thereof
can occur during the repair of the break. Mutations can be detected
using PCR-based genotyping methods, such as Cel-I mismatch assays
and DNA sequencing.
Example 9: Cas9-Based Genome Modification in Rat Embryos
[0178] The Rosa26 locus can be modified in rat embryos by
co-injecting a donor polynucleotide, as detailed above in section
(IV)(d), along with the pre-annealed crRNA/tracrRNA and mRNA
encoding modified Cas9 as described above in Example 8. In
vitro-incubated embryos or tissues from live born rats (as
described in Example 8) can be screened for a modified Rosa26 locus
using PCR-based genotyping methods, such as RFLP assays, junction
PCR, and DNA sequencing.
Sequence CWU 1
1
2717PRTArtificial SequenceSYNTHESIZED 1Pro Lys Lys Lys Arg Lys Val1
527PRTArtificial SequenceSYNTHESIZED 2Pro Lys Lys Lys Arg Arg Val1
5316PRTArtificial SequenceSYNTHESIZED 3Lys Arg Pro Ala Ala Thr Lys
Lys Ala Gly Gln Ala Lys Lys Lys Lys1 5 10 15420PRTArtificial
SequenceSYNTHESIZED 4Gly Arg Lys Lys Arg Arg Gln Arg Arg Arg Pro
Pro Gln Pro Lys Lys1 5 10 15Lys Arg Lys Val 20519PRTArtificial
SequenceSYNTHESIZED 5Pro Leu Ser Ser Ile Phe Ser Arg Ile Gly Asp
Pro Pro Lys Lys Lys1 5 10 15Arg Lys Val624PRTArtificial
SequenceSYNTHESIZED 6Gly Ala Leu Phe Leu Gly Trp Leu Gly Ala Ala
Gly Ser Thr Met Gly1 5 10 15Ala Pro Lys Lys Lys Arg Lys Val
20727PRTArtificial SequenceSYNTHESIZED 7Gly Ala Leu Phe Leu Gly Phe
Leu Gly Ala Ala Gly Ser Thr Met Gly1 5 10 15Ala Trp Ser Gln Pro Lys
Lys Lys Arg Lys Val 20 25821PRTArtificial SequenceSYNTHESIZED 8Lys
Glu Thr Trp Trp Glu Thr Trp Trp Thr Glu Trp Ser Gln Pro Lys1 5 10
15Lys Lys Arg Lys Val 2091374PRTArtificial SequenceSYNTHESIZED 9Met
Asp Lys Lys Tyr Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val1 5 10
15Gly Trp Ala Val Ile Thr Asp Asp Tyr Lys Val Pro Ser Lys Lys Phe
20 25 30Lys Val Leu Gly Asn Thr Asp Arg His Ser Ile Lys Lys Asn Leu
Ile 35 40 45Gly Ala Leu Leu Phe Gly Ser Gly Glu Thr Ala Glu Ala Thr
Arg Leu 50 55 60Lys Arg Thr Ala Arg Arg Arg Tyr Thr Arg Arg Lys Asn
Arg Ile Cys65 70 75 80Tyr Leu Gln Glu Ile Phe Ser Asn Glu Met Ala
Lys Val Asp Asp Ser 85 90 95Phe Phe His Arg Leu Glu Glu Ser Phe Leu
Val Glu Glu Asp Lys Lys 100 105 110His Glu Arg His Pro Ile Phe Gly
Asn Ile Val Asp Glu Val Ala Tyr 115 120 125His Glu Lys Tyr Pro Thr
Ile Tyr His Leu Arg Lys Lys Leu Ala Asp 130 135 140Ser Thr Asp Lys
Ala Asp Leu Arg Leu Ile Tyr Leu Ala Leu Ala His145 150 155 160Met
Ile Lys Phe Arg Gly His Phe Leu Ile Glu Gly Asp Leu Asn Pro 165 170
175Asp Asn Ser Asp Val Asp Lys Leu Phe Ile Gln Leu Val Gln Ile Tyr
180 185 190Asn Gln Leu Phe Glu Glu Asn Pro Ile Asn Ala Ser Arg Val
Asp Ala 195 200 205Lys Ala Ile Leu Ser Ala Arg Leu Ser Lys Ser Arg
Arg Leu Glu Asn 210 215 220Leu Ile Ala Gln Leu Pro Gly Glu Lys Arg
Asn Gly Leu Phe Gly Asn225 230 235 240Leu Ile Ala Leu Ser Leu Gly
Leu Thr Pro Asn Phe Lys Ser Asn Phe 245 250 255Asp Leu Ala Glu Asp
Ala Lys Leu Gln Leu Ser Lys Asp Thr Tyr Asp 260 265 270Asp Asp Leu
Asp Asn Leu Leu Ala Gln Ile Gly Asp Gln Tyr Ala Asp 275 280 285Leu
Phe Leu Ala Ala Lys Asn Leu Ser Asp Ala Ile Leu Leu Ser Asp 290 295
300Ile Leu Arg Val Asn Ser Glu Ile Thr Lys Ala Pro Leu Ser Ala
Ser305 310 315 320Met Ile Lys Arg Tyr Asp Glu His His Gln Asp Leu
Thr Leu Leu Lys 325 330 335Ala Leu Val Arg Gln Gln Leu Pro Glu Lys
Tyr Lys Glu Ile Phe Phe 340 345 350Asp Gln Ser Lys Asn Gly Tyr Ala
Gly Tyr Ile Asp Gly Gly Ala Ser 355 360 365Gln Glu Glu Phe Tyr Lys
Phe Ile Lys Pro Ile Leu Glu Lys Met Asp 370 375 380Gly Thr Glu Glu
Leu Leu Val Lys Leu Asn Arg Glu Asp Leu Leu Arg385 390 395 400Lys
Gln Arg Thr Phe Asp Asn Gly Ser Ile Pro His Gln Ile His Leu 405 410
415Gly Glu Leu His Ala Ile Leu Arg Arg Gln Glu Asp Phe Tyr Pro Phe
420 425 430Leu Lys Asp Asn Arg Glu Lys Ile Glu Lys Ile Leu Thr Phe
Arg Ile 435 440 445Pro Tyr Tyr Val Gly Pro Leu Ala Arg Gly Asn Ser
Arg Phe Ala Trp 450 455 460Met Thr Arg Lys Ser Glu Glu Thr Ile Thr
Pro Trp Asn Phe Glu Glu465 470 475 480Val Val Asp Lys Gly Ala Ser
Ala Gln Ser Phe Ile Glu Arg Met Thr 485 490 495Asn Phe Asp Lys Asn
Leu Pro Asn Glu Lys Val Leu Pro Lys His Ser 500 505 510Leu Leu Tyr
Glu Tyr Phe Thr Val Tyr Asn Glu Leu Thr Lys Val Lys 515 520 525Tyr
Val Thr Glu Gly Met Arg Lys Pro Ala Phe Leu Ser Gly Glu Gln 530 535
540Lys Lys Ala Ile Val Asp Leu Leu Phe Lys Thr Asn Arg Lys Val
Thr545 550 555 560Val Lys Gln Leu Lys Glu Asp Tyr Phe Lys Lys Ile
Glu Cys Phe Asp 565 570 575Ser Val Glu Ile Ser Gly Val Glu Asp Arg
Phe Asn Ala Ser Leu Gly 580 585 590Ala Tyr His Asp Leu Leu Lys Ile
Ile Lys Asp Lys Asp Phe Leu Asp 595 600 605Asn Glu Glu Asn Glu Asp
Ile Leu Glu Asp Ile Val Leu Thr Leu Thr 610 615 620Leu Phe Glu Asp
Arg Gly Met Ile Glu Glu Arg Leu Lys Thr Tyr Ala625 630 635 640His
Leu Phe Asp Asp Lys Val Met Lys Gln Leu Lys Arg Arg Arg Tyr 645 650
655Thr Gly Trp Gly Arg Leu Ser Arg Lys Leu Ile Asn Gly Ile Arg Asp
660 665 670Lys Gln Ser Gly Lys Thr Ile Leu Asp Phe Leu Lys Ser Asp
Gly Phe 675 680 685Ala Asn Arg Asn Phe Met Gln Leu Ile His Asp Asp
Ser Leu Thr Phe 690 695 700Lys Glu Asp Ile Gln Lys Ala Gln Val Ser
Gly Gln Gly His Ser Leu705 710 715 720His Glu Gln Ile Ala Asn Leu
Ala Gly Ser Pro Ala Ile Lys Lys Gly 725 730 735Ile Leu Gln Thr Val
Lys Ile Val Asp Glu Leu Val Lys Val Met Gly 740 745 750His Lys Pro
Glu Asn Ile Val Ile Glu Met Ala Arg Glu Asn Gln Thr 755 760 765Thr
Gln Lys Gly Gln Lys Asn Ser Arg Glu Arg Met Lys Arg Ile Glu 770 775
780Glu Gly Ile Lys Glu Leu Gly Ser Gln Ile Leu Lys Glu His Pro
Val785 790 795 800Glu Asn Thr Gln Leu Gln Asn Glu Lys Leu Tyr Leu
Tyr Tyr Leu Gln 805 810 815Asn Gly Arg Asp Met Tyr Val Asp Gln Glu
Leu Asp Ile Asn Arg Leu 820 825 830Ser Asp Tyr Asp Val Asp His Ile
Val Pro Gln Ser Phe Ile Lys Asp 835 840 845Asp Ser Ile Asp Asn Lys
Val Leu Thr Arg Ser Asp Lys Asn Arg Gly 850 855 860Lys Ser Asp Asn
Val Pro Ser Glu Glu Val Val Lys Lys Met Lys Asn865 870 875 880Tyr
Trp Arg Gln Leu Leu Asn Ala Lys Leu Ile Thr Gln Arg Lys Phe 885 890
895Asp Asn Leu Thr Lys Ala Glu Arg Gly Gly Leu Ser Glu Leu Asp Lys
900 905 910Ala Gly Phe Ile Lys Arg Gln Leu Val Glu Thr Arg Gln Ile
Thr Lys 915 920 925His Val Ala Gln Ile Leu Asp Ser Arg Met Asn Thr
Lys Tyr Asp Glu 930 935 940Asn Asp Lys Leu Ile Arg Glu Val Lys Val
Ile Thr Leu Lys Ser Lys945 950 955 960Leu Val Ser Asp Phe Arg Lys
Asp Phe Gln Phe Tyr Lys Val Arg Glu 965 970 975Ile Asn Asn Tyr His
His Ala His Asp Ala Tyr Leu Asn Ala Val Val 980 985 990Gly Thr Ala
Leu Ile Lys Lys Tyr Pro Lys Leu Glu Ser Glu Phe Val 995 1000
1005Tyr Gly Asp Tyr Lys Val Tyr Asp Val Arg Lys Met Ile Ala Lys
1010 1015 1020Ser Glu Gln Glu Ile Gly Lys Ala Thr Ala Lys Tyr Phe
Phe Tyr 1025 1030 1035Ser Asn Ile Met Asn Phe Phe Lys Thr Glu Ile
Thr Leu Ala Asn 1040 1045 1050Gly Glu Ile Arg Lys Arg Pro Leu Ile
Glu Thr Asn Gly Glu Thr 1055 1060 1065Gly Glu Ile Val Trp Asp Lys
Gly Arg Asp Phe Ala Thr Val Arg 1070 1075 1080Lys Val Leu Ser Met
Pro Gln Val Asn Ile Val Lys Lys Thr Glu 1085 1090 1095Val Gln Thr
Gly Gly Phe Ser Lys Glu Ser Ile Leu Pro Lys Arg 1100 1105 1110Asn
Ser Asp Lys Leu Ile Ala Arg Lys Lys Asp Trp Asp Pro Lys 1115 1120
1125Lys Tyr Gly Gly Phe Asp Ser Pro Thr Val Ala Tyr Ser Val Leu
1130 1135 1140Val Val Ala Lys Val Glu Lys Gly Lys Ser Lys Lys Leu
Lys Ser 1145 1150 1155Val Lys Glu Leu Leu Gly Ile Thr Ile Met Glu
Arg Ser Ser Phe 1160 1165 1170Glu Lys Asn Pro Ile Asp Phe Leu Glu
Ala Lys Gly Tyr Lys Glu 1175 1180 1185Val Lys Lys Asp Leu Ile Ile
Lys Leu Pro Lys Tyr Ser Leu Phe 1190 1195 1200Glu Leu Glu Asn Gly
Arg Lys Arg Met Leu Ala Ser Ala Gly Glu 1205 1210 1215Leu Gln Lys
Gly Asn Glu Leu Ala Leu Pro Ser Lys Tyr Val Asn 1220 1225 1230Phe
Leu Tyr Leu Ala Ser His Tyr Glu Lys Leu Lys Gly Ser Pro 1235 1240
1245Glu Asp Asn Glu Gln Lys Gln Leu Phe Val Glu Gln His Lys His
1250 1255 1260Tyr Leu Asp Glu Ile Ile Glu Gln Ile Ser Glu Phe Ser
Lys Arg 1265 1270 1275Val Ile Leu Ala Asp Ala Asn Leu Asp Lys Val
Leu Ser Ala Tyr 1280 1285 1290Asn Lys His Arg Asp Lys Pro Ile Arg
Glu Gln Ala Glu Asn Ile 1295 1300 1305Ile His Leu Phe Thr Leu Thr
Asn Leu Gly Ala Pro Ala Ala Phe 1310 1315 1320Lys Tyr Phe Asp Thr
Thr Ile Asp Arg Lys Arg Tyr Thr Ser Thr 1325 1330 1335Lys Glu Val
Leu Asp Ala Thr Leu Ile His Gln Ser Ile Thr Gly 1340 1345 1350Leu
Tyr Glu Thr Arg Ile Asp Leu Ser Gln Leu Gly Gly Asp Pro 1355 1360
1365Lys Lys Lys Arg Lys Val 1370104122DNAArtificial
SequenceSYNTHESIZED 10atggacaaga agtacagcat cggcctggac atcggcacca
actctgtggg ctgggccgtg 60atcaccgacg actacaaggt gcccagcaag aaattcaagg
tgctgggcaa caccgaccgg 120cacagcatca agaagaacct gatcggcgcc
ctgctgttcg gctctggcga aacagccgag 180gccacccggc tgaagagaac
cgccagaaga agatacacca gacggaagaa ccggatctgc 240tatctgcaag
agatcttcag caacgagatg gccaaggtgg acgacagctt cttccacaga
300ctggaagagt ccttcctggt ggaagaggat aagaagcacg agcggcaccc
catcttcggc 360aacatcgtgg acgaggtggc ctaccacgag aagtacccca
ccatctacca cctgagaaag 420aagctggccg acagcaccga caaggccgac
ctgagactga tctacctggc cctggcccac 480atgatcaagt tccggggcca
cttcctgatc gagggcgacc tgaaccccga caacagcgac 540gtggacaagc
tgttcatcca gctggtgcag atctacaatc agctgttcga ggaaaacccc
600atcaacgcca gcagagtgga cgccaaggcc atcctgagcg ccagactgag
caagagcaga 660cggctggaaa atctgatcgc ccagctgccc ggcgagaagc
ggaatggcct gttcggcaac 720ctgattgccc tgagcctggg cctgaccccc
aacttcaaga gcaacttcga cctggccgag 780gatgccaaac tgcagctgag
caaggacacc tacgacgacg acctggacaa cctgctggcc 840cagatcggcg
accagtacgc cgacctgttt ctggccgcca agaacctgtc cgacgccatc
900ctgctgagcg acatcctgag agtgaacagc gagatcacca aggcccccct
gtccgcctct 960atgatcaaga gatacgacga gcaccaccag gacctgaccc
tgctgaaagc tctcgtgcgg 1020cagcagctgc ctgagaagta caaagagatt
ttcttcgacc agagcaagaa cggctacgcc 1080ggctacatcg atggcggagc
cagccaggaa gagttctaca agttcatcaa gcccatcctg 1140gaaaagatgg
acggcaccga ggaactgctc gtgaagctga acagagagga cctgctgcgg
1200aagcagcgga ccttcgacaa cggcagcatc ccccaccaga tccacctggg
agagctgcac 1260gccattctgc ggcggcagga agatttttac ccattcctga
aggacaaccg ggaaaagatc 1320gagaagatcc tgaccttcag aatcccctac
tacgtgggcc ctctggccag gggaaacagc 1380agattcgcct ggatgaccag
aaagagcgag gaaaccatca ccccctggaa cttcgaggaa 1440gtggtggaca
agggcgccag cgcccagagc ttcatcgagc ggatgaccaa cttcgataag
1500aacctgccca acgagaaggt gctgcccaag cacagcctgc tgtacgagta
cttcaccgtg 1560tacaacgagc tgaccaaagt gaaatacgtg accgagggaa
tgcggaagcc cgcctttctg 1620agcggcgagc agaaaaaggc catcgtggac
ctgctgttca agaccaaccg gaaagtgacc 1680gtgaagcagc tgaaagagga
ctacttcaag aaaatcgagt gcttcgacag cgtggaaatc 1740agcggcgtgg
aagatcggtt caacgcctcc ctgggcgcct atcacgatct gctgaaaatt
1800atcaaggaca aggacttcct ggacaatgag gaaaacgagg acattctgga
agatatcgtg 1860ctgaccctga cactgtttga ggaccggggc atgatcgagg
aacggctgaa aacctatgcc 1920cacctgttcg acgacaaagt gatgaagcag
ctgaagcggc ggagatacac cggctggggc 1980aggctgagcc ggaagctgat
caacggcatc cgggacaagc agtccggcaa gacaatcctg 2040gatttcctga
agtccgacgg cttcgccaac agaaacttca tgcagctgat ccacgacgac
2100agcctgacct ttaaagagga catccagaaa gcccaggtgt ccggccaggg
acactctctg 2160cacgagcaga tcgccaatct ggccggatcc cccgccatta
agaagggcat cctgcagaca 2220gtgaagattg tggacgagct cgtgaaagtg
atgggccaca agcccgagaa catcgtgatc 2280gaaatggcca gagagaacca
gaccacccag aagggacaga agaacagccg cgagagaatg 2340aagcggatcg
aagagggcat caaagagctg ggcagccaga tcctgaaaga acaccccgtg
2400gaaaacaccc agctgcagaa cgagaagctg tacctgtact acctgcagaa
tgggcgggat 2460atgtacgtgg accaggaact ggacatcaac cggctgtccg
actacgatgt ggaccacatt 2520gtgccccagt ccttcatcaa ggacgactcc
atcgataaca aagtgctgac tcggagcgac 2580aagaaccggg gcaagagcga
caacgtgccc tccgaagagg tcgtgaagaa gatgaagaac 2640tactggcgcc
agctgctgaa tgccaagctg attacccaga ggaagttcga caatctgacc
2700aaggccgaga gaggcggcct gagcgaactg gataaggccg gcttcattaa
gcggcagctg 2760gtggaaaccc ggcagatcac aaagcacgtg gcacagatcc
tggactcccg gatgaacact 2820aagtacgacg agaacgacaa actgatccgg
gaagtgaaag tgatcaccct gaagtccaag 2880ctggtgtccg acttcagaaa
ggatttccag ttttacaaag tgcgcgagat caacaactac 2940caccacgccc
acgacgccta cctgaacgcc gtcgtgggaa ccgccctgat caaaaagtac
3000cctaagctgg aaagcgagtt cgtgtacggc gattacaagg tgtacgacgt
gcggaagatg 3060atcgccaaga gcgagcagga aatcggcaag gctaccgcca
agtacttctt ctacagcaac 3120atcatgaact ttttcaagac cgagatcaca
ctggccaacg gcgagatcag aaagcggcct 3180ctgatcgaga caaacggcga
aaccggggag atcgtgtggg ataagggccg ggattttgcc 3240acagtgcgga
aagtgctgtc catgccccaa gtgaatatcg tgaaaaagac cgaggtgcag
3300accggcggct tcagcaaaga gtctatcctg cccaagagga actccgacaa
gctgatcgcc 3360agaaagaagg attgggaccc taagaagtac ggcggctttg
acagccccac cgtggcctac 3420tctgtgctgg tggtggccaa agtggaaaag
ggcaagtcca agaaactgaa gagtgtgaaa 3480gagctgctgg ggatcaccat
catggaaaga agcagcttcg agaagaatcc catcgacttt 3540ctggaagcca
agggctacaa agaagtgaaa aaggacctga tcatcaagct gcctaagtac
3600tccctgttcg agctggaaaa cggccggaag cggatgctgg cttctgccgg
cgaactgcag 3660aagggaaacg agctggccct gccctccaaa tatgtgaact
tcctgtacct ggccagccac 3720tatgagaagc tgaagggctc ccccgaggat
aatgagcaga aacagctgtt tgtggaacag 3780cacaagcact acctggacga
gatcatcgag cagattagcg agttctccaa gcgcgtgatc 3840ctggccgatg
ccaacctgga caaggtgctg agcgcctaca acaagcaccg ggataagccc
3900atcagagagc aggccgagaa tatcatccac ctgtttaccc tgaccaacct
gggagcccct 3960gccgccttca agtactttga caccaccatc gaccggaaga
ggtacaccag caccaaagag 4020gtgctggacg ccaccctgat ccaccagagc
atcaccggcc tgtacgagac acggatcgac 4080ctgtctcagc tgggaggcga
ccccaagaaa aagcgcaaag tg 4122114764DNAHomo sapiens 11gcgggcgggc
ggtgcgatgt ccggagagga tggcccggcg gctggcccgg gggcggcggc 60ggcggctgcc
cgggagcggc gacgggagca gctgcggcag tggggggcgc gggcgggcgc
120cgagcctggc cccggagagc gccgcgcccg caccgtccgc ttcgagcgcg
ccgccgagtt 180cctggcggcc tgtgcgggcg gcgacctgga cgaggcgcgt
ctgatgctgc gcgccgccga 240ccctggcccc ggcgccgagc tcgaccccgc
cgcgccgccg cccgcccgcg ccgtgctgga 300ctccaccaac gccgacggta
tcagcgccct gcaccaggtc agcgcccccc gcccggcgtc 360tcccggggcc
aggtccaccc tctgctgcgc cacctggggc atcctccttc cccgttgcca
420gtctcgatcc gccccgtcgt tcctggccct gggctttgcc accctatgct
gacaccccgt 480cccagtcccc cttaccattc cccttcgacc accccacttc
cgaattggag ccgcttcaac 540tggccctggg cttagccact ctgtgctgac
cactctgccc caggcctcct taccattccc 600cttcgaccta ctctcttccg
cattggagtc gctttaactg gccctggctt tggcagcctg 660tgctgaccca
tgcagtcctc cttaccatcc ctccctcgac ttcccctctt ccgatgttga
720gcccctccag ccggtcctgg actttgtctc cttccctgcc ctgccctctc
ctgaacctga 780gccagctccc atagctcagt ctggtctatc tgcctggccc
tggccattgt cactttgcgc 840tgccctcctc tcgcccccga gtgcccttgc
tgtgccgccg gaactctgcc ctctaacgct 900gccgtctctc tcctgagtcc
ggaccacttt gagctctact ggcttctgcg ccgcctctgg 960cccactgttt
ccccttccca ggcaggtcct gctttctctg acctgcattc tctcccctgg
1020gcctgtgccg ctttctgtct gcagcttgtg gcctgggtca cctctacggc
tggcccagat 1080ccttccctgc cgcctccttc aggttccgtc ttcctccact
ccctcttccc cttgctctct 1140gctgtgttgc tgcccaagga tgctctttcc
ggagcacttc cttctcggcg ctgcaccacg 1200tgatgtcctc tgagcggatc
ctccccgtgt ctgggtcctc tccgggcatc tctcctccct 1260cacccaaccc
catgccgtct tcactcgctg ggttcccttt tccttctcct tctggggcct
1320gtgccatctc tcgtttctta ggatggcctt ctccgacgga
tgtctccctt gcgtcccgcc 1380tccccttctt gtaggcctgc atcatcaccg
tttttctgga caaccccaaa gtaccccgtc 1440tccctggctt tagccacctc
tccatcctct tgctttcttt gcctggacac cccgttctcc 1500tgtggattcg
ggtcacctct cactcctttc atttgggcag ctcccctacc ccccttacct
1560ctctagtctg tgctagctct tccagccccc tgtcatggca tcttccaggg
gtccgagagc 1620tcagctagtc ttcttcctcc aacccgggcc cctatgtcca
cttcaggaca gcatgtttgc 1680tgcctccagg gatcctgtgt ccccgagctg
ggaccacctt atattcccag ggccggttaa 1740tgtggctctg gttctgggta
cttttatctg tcccctccac cccacagtgg ggccactagg 1800gacaggattg
gtgacagaaa agccccatcc ttaggcctcc tccttcctag tctcctgata
1860ttgggtctaa cccccacctc ctgttaggca gattccttat ctggtgacac
acccccattt 1920cctggagcca tctctctcct tgccagaacc tctaaggttt
gcttacgatg gagccagaga 1980ggatcctggg agggagagct tggcaggggg
tgggagggaa gggggggatg cgtgacctgc 2040ccggttctca gtggccaccc
tgcgctaccc tctcccagaa cctgagctgc tctgacgcgg 2100ccgtctggtg
cgtttcactg atcctggtgc tgcagcttcc ttacacttcc caagaggaga
2160agcagtttgg aaaaacaaaa tcagaataag ttggtcctga gttctaactt
tggctcttca 2220cctttctagt ccccaattta tattgttcct ccgtgcgtca
gttttacctg tgagataagg 2280ccagtagcca gccccgtcct ggcagggctg
tggtgaggag gggggtgtcc gtgtggaaaa 2340ctccctttgt gagaatggtg
cgtcctaggt gttcaccagg tcgtggccgc ctctactccc 2400tttctctttc
tccatccttc tttccttaaa gagtccccag tgctatctgg gacatattcc
2460tccgcccaga gcagggtccc gcttccctaa ggccctgctc tgggcttctg
ggtttgagtc 2520cttggcaagc ccaggagagg cgctcaggct tccctgtccc
ccttcctcgt ccaccatctc 2580atgcccctgg ctctcctgcc ccttccctac
aggggttcct ggctctgctc ttcagactga 2640gccccgttcc cctgcatccc
cgttcccctg catccccctt cccctgcatc ccccagaggc 2700cccaggccac
ctacttggcc tggaccccac gagaggccac cccagccctg tctaccaggc
2760tgccttttgg gtggattctc ctccaactgt ggggtgactg cttggcaaac
tcactcttcg 2820gggtatccca ggaggcctgg agcattgggg tgggctgggg
ttcagagagg agggattccc 2880ttctcaggtt acgtggccaa gaagcagggg
agctgggttt gggtcaggtc tgggtgtggg 2940gtgaccagct tatgctgttt
gcccaggaca gcctagtttt agcactgaaa ccctcagtcc 3000taggaaaaca
gggatggttg gtcactgtct ctgggtgact cttgattccc ggccagtttc
3060tccacctggg gctgtgtttc tcgtcctgca tccttctcca ggcaggtccc
caagcatcgc 3120ccccctgctg tggctgttcc caagttctta gggtacccca
cgtgggttta tcaaccactt 3180ggtgaggctg gtaccctgcc cccattcctg
caccccaatt gccttagtgg ctagggggtt 3240gggggctaga gtaggagggg
ctggagccag gattcttagg gctgaacaga gaagagctgg 3300gggcctgggc
tcctgggttt gagagaggag gggctggggc ctggactcct gggtccgagg
3360gaggaggggc tggggcctgg actcctgggt ctgagggtgg agggactggg
ggcctggact 3420cctgggtccg agggaggagg ggctggggcc tggactcgtg
ggtctgaggg aggaggggct 3480gggggcctgg acttctgggt cttagggagg
cggggctggg cctggacccc tgggtctgaa 3540tggggagagg ctgggggcct
ggactccttc atctgagggc ggaagggctg gggcctggcc 3600tcctgggttg
aatggggagg ggttgggcct ggactctgga gtccctggtg cccaggcctc
3660aggcatcttt cacagggatg cctgtactgg gcaggtcctt gaaagggaaa
ggcccattgc 3720tctccttgcc cccctcccct atcgccatga caactgggtg
gaaataaacg agccgagttc 3780atcccgttcc cagggcacgt gcggcccctt
cacagcccga gtttccatga cctcatgctc 3840ttggccctcg tagctccctc
ccgcctcctc cagatgggca gctttggaga ggtgagggac 3900ttggggggta
atttatcccg tggatctagg agtttagctt cactccttcc tcagctccag
3960ttcaggtccc ggagcccacc cagtgtccac aaggcctggg gcaagtccct
cctccgaccc 4020cctggacttc ggcttttgtc cccccaagtt ttggacccct
aagggaagaa tgagaaacgg 4080tggcccgtgt cagcccctgg ctgcagggcc
ccgtgcagag ggggcctcag tgaactggag 4140tgtgacagcc tggggcccag
gcacacaggt gtgcagctgt ctcacccctc tgggagtccc 4200gcccaggccc
ctgagtctgt cccagcacag ggtggccttc ctccaccctg catagccctg
4260ggcccacggc ttcgttcctg cagagtatct gctggggtgg tttccgagct
tgacccttgg 4320aaggacctgg ctgggtttaa ggcaggaggg gctgggggcc
aggactcctg gctctgaagg 4380aggaggggct ggaacctctt ccctagtctg
agcactggaa gcgccacctg tgggtggtga 4440cgggggtttt gccgtgtcta
acaggtacca tgtggggttc ccgcacccag atgagaagcc 4500ccctcccttc
cccgttcact tcctgtttgc agatagccag gagtcctttc gtggtttcca
4560ctgagcactg aaggcctggc cggcctgacc actgggcaac caggcgtatc
ttaaacagcc 4620agtggccaga ggctgttggg tcattttccc cactgtccta
gcaccgtgtc cctggatctg 4680ttttcgtggc tccctctgga gtcccgactt
gctgggacac cgtggctggg gtaggtgcgg 4740ctgacggctg tttcccaccc ccag
47641242RNAArtificial SequenceSYNTHESIZED 12accccacagu ggggccacua
guuuuagagc uaugcuguuu ug 421386RNAArtificial SequenceSYNTHESIZED
13ggaaccauuc aaaacagcau agcaaguuaa aauaaggcua guccguuauc aacuugaaaa
60aguggcaccg agucggugcu uuuuuu 861462RNAArtificial
SequenceSYNTHESIZED 14accccacagu ggggccacua guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cg 621525DNAArtificial SequenceSYNTHESIZED
15ctgacctctt ctcttcctcc cacag 25161009DNAArtificial
SequenceSYNTHESIZED 16gccaccatgg actacaaaga cgatgacgac aaggtcgact
ctagagctgc agagagcgac 60gagagcggcc tgcccgccat ggagatcgag tgccgcatca
ccggcaccct gaacggcgtg 120gagttcgagc tggtgggcgg cggagagggc
acccccgagc agggccgcat gaccaacaag 180atgaagagca ccaaaggcgc
cctgaccttc agcccctacc tgctgagcca cgtgatgggc 240tacggcttct
accacttcgg cacctacccc agcggctacg agaacccctt cctgcacgcc
300atcaacaacg gcggctacac caacacccgc atcgagaagt acgaggacgg
cggcgtgctg 360cacgtgagct tcagctaccg ctacgaggcc ggccgcgtga
tcggcgactt caaggtgatg 420ggcaccggct tccccgagga cagcgtgatc
ttcaccgaca agatcgtccg cagcaacgcc 480accgtggagc acctgcaccc
catgggcgat aacgatctgg atggcagctt cacccgcacc 540ttcagcctgc
gcgacggcgg ctactacagc tccgtggtgg acagccacat gcacttcaag
600agcgccatcc accccagcat cctgcagaac gggggcccca tgttcgcctt
ccgccgcgtg 660gaggaggatc acagcaacac cgagctgggc atcgtggagt
accagcacgc cttcaagacc 720ccggatgcag atgccggtga agaatgaaga
tctctgtgcc ttctagttgc cagccatctg 780ttgtttgccc ctcccccgtg
ccttccttga ccctggaagg tgccactccc actgtccttt 840cctaataaaa
tgaggaaatt gcatcgcatt gtctgagtag gtgtcattct attctggggg
900gtggggtggg gcaggacagc aagggggagg attgggaaga caatagcagg
catgctgggg 960atgcggtggg ctctatggac tcgaggttta aacgtcgacg cggccgcgt
100917355PRTArtificial SequenceSYNTHESIZED 17Met Ser Gly Glu Asp
Gly Pro Ala Ala Gly Pro Gly Ala Ala Ala Ala1 5 10 15Ala Ala Arg Glu
Arg Arg Arg Glu Gln Leu Arg Gln Trp Gly Ala Arg 20 25 30Ala Gly Ala
Glu Pro Gly Pro Gly Glu Arg Arg Ala Arg Thr Val Arg 35 40 45Phe Glu
Arg Ala Ala Glu Phe Leu Ala Ala Cys Ala Gly Gly Asp Leu 50 55 60Asp
Glu Ala Arg Leu Met Leu Arg Ala Ala Asp Pro Gly Pro Gly Ala65 70 75
80Glu Leu Asp Pro Ala Ala Pro Pro Pro Ala Arg Ala Val Leu Asp Ser
85 90 95Thr Asn Ala Asp Gly Ile Ser Ala Leu His Gln Ala Thr Met Asp
Tyr 100 105 110Lys Asp Asp Asp Asp Lys Val Asp Ser Arg Ala Ala Glu
Ser Asp Glu 115 120 125Ser Gly Leu Pro Ala Met Glu Ile Glu Cys Arg
Ile Thr Gly Thr Leu 130 135 140Asn Gly Val Glu Phe Glu Leu Val Gly
Gly Gly Glu Gly Thr Pro Glu145 150 155 160Gln Gly Arg Met Thr Asn
Lys Met Lys Ser Thr Lys Gly Ala Leu Thr 165 170 175Phe Ser Pro Tyr
Leu Leu Ser His Val Met Gly Tyr Gly Phe Tyr His 180 185 190Phe Gly
Thr Tyr Pro Ser Gly Tyr Glu Asn Pro Phe Leu His Ala Ile 195 200
205Asn Asn Gly Gly Tyr Thr Asn Thr Arg Ile Glu Lys Tyr Glu Asp Gly
210 215 220Gly Val Leu His Val Ser Phe Ser Tyr Arg Tyr Glu Ala Gly
Arg Val225 230 235 240Ile Gly Asp Phe Lys Val Met Gly Thr Gly Phe
Pro Glu Asp Ser Val 245 250 255Ile Phe Thr Asp Lys Ile Val Arg Ser
Asn Ala Thr Val Glu His Leu 260 265 270His Pro Met Gly Asp Asn Asp
Leu Asp Gly Ser Phe Thr Arg Thr Phe 275 280 285Ser Leu Arg Asp Gly
Gly Tyr Tyr Ser Ser Val Val Asp Ser His Met 290 295 300His Phe Lys
Ser Ala Ile His Pro Ser Ile Leu Gln Asn Gly Gly Pro305 310 315
320Met Phe Ala Phe Arg Arg Val Glu Glu Asp His Ser Asn Thr Glu Leu
325 330 335Gly Ile Val Glu Tyr Gln His Ala Phe Lys Thr Pro Asp Ala
Asp Ala 340 345 350Gly Glu Glu 3551821DNAArtificial
SequenceSYNTHESIZED 18ccactctgtg ctgaccactc t 211917DNAArtificial
SequenceSYNTHESIZED 19gcggcactcg atctcca 1720711DNAMus musculus
20gagcggctgc ggggcgggtg caagcacgtt tccgacttga gttgcctcaa gaggggcgtg
60ctgagccaga cctccatcgc gcactccggg gagtggaggg aaggagcgag ggctcagttg
120ggctgttttg gaggcaggaa gcacttgctc tcccaaagtc gctctgagtt
gttatcagta 180agggagctgc agtggagtag gcggggagaa ggccgcaccc
ttctccggag gggggagggg 240agtgttgcaa tacctttctg ggagttctct
gctgcctcct ggcttctgag gaccgccctg 300ggcctgggag aatcccttcc
ccctcttccc tcgtgatctg caactccagt ctttctagaa 360gatgggcggg
agtcttctgg gcaggcttaa aggctaacct ggtgtgtggg cgttgtcctg
420caggggaatt gaacaggtgt aaaattggag ggacaagact tcccacagat
tttcggtttt 480gtcgggaagt tttttaatag gggcaaataa ggaaaatggg
aggataggta gtcatctggg 540gttttatgca gcaaaactac aggttattat
tgcttgtgat ccgcctcgga gtattttcca 600tcgaggtaga ttaaagacat
gctcacccga gttttatact ctcctgcttg agatccttac 660tacagtatga
aattacagtg tcgcgagtta gactatgtaa gcagaatttt a 7112142RNAArtificial
SequenceSYNTHESIZED 21cuccagucuu ucuagaagau guuuuagagc uaugcuguuu
ug 422242RNAArtificial SequenceSYNTHESIZED 22ugaacaggug uaaaauugga
guuuuagagc uaugcuguuu ug 422342RNAArtificial SequenceSYNTHESIZED
23ugucgggaag uuuuuuaaua guuuuagagc uaugcuguuu ug 4224642DNARattus
rattus 24gggattcctc cttgagttgt ggcactgagg aacgtgctga acaagaccta
cattgcactc 60cagggagtgg atgaaggagt tggggctcag tcgggttgta ttggagacaa
gaagcacttg 120ctctccaaaa gtcggtttga gttatcatta agggagctgc
agtggagtag gcggagaaaa 180ggccgcaccc ttctcaggac gggggagggg
agtgttgcaa tacctttctg ggagttctct 240gctgcctcct gtcttctgag
gaccgccctg ggcctggaag attcccttcc cccttcttcc 300ctcgtgatct
gcaactggag tctttctgga agataggcgg gagtcttctg ggcaggctta
360aaggctaacc tggtgcgtgg ggcgttgtcc tgcagaggaa ttgaacaggt
gtaaaattgg 420aggggcaaga cttcccacag attttcgatt gtgttgttaa
gtattgtaat aggggcaaat 480aagggaaata gactaggcac tcacctgggg
ttttatgcag caaaactaca ggttattatt 540gcttgtgatc cgccctggag
aatttttcac cgaggtagat tgaagacatg cccacccaaa 600ttttaatatt
cttccacttg cgatccttgc tacagtatga aa 6422542RNAArtificial
SequenceSYNTHESIZED 25agggggaagg gaaucuucca guuuuagagc uaugcuguuu
ug 422642RNAArtificial SequenceSYNTHESIZED 26ucugcaacug gagucuuucu
guuuuagagc uaugcuguuu ug 422742RNAArtificial SequenceSYNTHESIZED
27aggcgggagu cuucugggca guuuuagagc uaugcuguuu ug 42
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