WO2014144761A2 - Increasing specificity for rna-guided genome editing - Google Patents

Increasing specificity for rna-guided genome editing Download PDF

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Publication number
WO2014144761A2
WO2014144761A2 PCT/US2014/029304 US2014029304W WO2014144761A2 WO 2014144761 A2 WO2014144761 A2 WO 2014144761A2 US 2014029304 W US2014029304 W US 2014029304W WO 2014144761 A2 WO2014144761 A2 WO 2014144761A2
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Prior art keywords
seq
sequence
target
dna
rna
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PCT/US2014/029304
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English (en)
French (fr)
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WO2014144761A3 (en
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J. Keith Joung
James ANGSTMAN
Jeffry D. Sander
Morgan Maeder
Shengdar TSAI
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General Hospital Corp
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General Hospital Corp
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First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=51537665&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2014144761(A2) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Application filed by General Hospital Corp filed Critical General Hospital Corp
Priority to US14/776,620 priority Critical patent/US9885033B2/en
Priority to EP14764117.9A priority patent/EP2970208A4/en
Priority to EP21151899.8A priority patent/EP3865586A1/en
Priority to CN202110920229.7A priority patent/CN113684205B/zh
Publication of WO2014144761A2 publication Critical patent/WO2014144761A2/en
Priority to CN201480076396.6A priority patent/CN106103706B/zh
Priority to KR1020167020111A priority patent/KR20160102056A/ko
Priority to CA2935032A priority patent/CA2935032C/en
Priority to EP21191144.1A priority patent/EP3985124A1/en
Priority to AU2014370416A priority patent/AU2014370416B2/en
Priority to EP14875819.6A priority patent/EP3090044B1/en
Priority to JP2016542968A priority patent/JP6721508B2/ja
Priority to US15/107,550 priority patent/US10526589B2/en
Anticipated expiration legal-status Critical
Publication of WO2014144761A3 publication Critical patent/WO2014144761A3/en
Priority to US15/870,659 priority patent/US10844403B2/en
Priority to JP2019218086A priority patent/JP7005580B2/ja
Priority to US16/735,146 priority patent/US20200165587A1/en
Priority to US17/099,503 priority patent/US11920152B2/en
Priority to AU2021203309A priority patent/AU2021203309B2/en
Priority to AU2023258349A priority patent/AU2023258349A1/en
Priority to US18/415,999 priority patent/US20240240207A1/en
Ceased legal-status Critical Current

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Definitions

  • RNA-guided genome editing e.g., editing using CRISPR/Cas9 systems.
  • CRISPR clustered, regularly interspaced, short palindromic repeats
  • Cas CRISPR-associated systems
  • the Cas9 nuclease from S. pyogenes can be guided via base pair complementarity between the first 20 nucleotides of an engineered gRNA and the complementary strand of a target genomic DNA sequence of interest that lies next to a protospacer adjacent motif (PAM), e.g., a PAM matching the sequence NGG or NAG (Shen et al, Cell Res (2013); Dicarlo et al, Nucleic Acids Res (2013); Jiang et al, Nat Biotechnol 31, 233-239 (2013); Jinek et al, Elife 2, e00471 (2013); Hwang et al, Nat Biotechnol 31, 227-229 (2013); Cong et al, Science 339, 819-823 (2013); Mali et al, Science 339, 823-826 (2013c); Cho et al, Nat Biotechnol 31 , 230-232 (2013); Jinek et al, Science 337, 816
  • PAM protospacer
  • CRISPR-Cas nucleases can tolerate up to five mismatches and still cleave; it is hard to predict the effects of any given single or combination of mismatches on activity. Taken together, these nucleases can show significant off-target effects but it can be challenging to predict these sites. Described herein are methods of genome editing using the CRISPR/Cas system, e.g., using Cas9 or Cas9-based fusion proteins.
  • the invention provides a synthetic guide ribonucleic acid, wherein: one or more of the nucleotides is modified, e.g., locked (2'-0-4'-C methylene bridge), is 5'-methylcytidine, is 2'-0-methyl-pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain; and/or wherein one or more of the nucleotides is a deoxyribonucleic acid.
  • one or more of the nucleotides is modified, e.g., locked (2'-0-4'-C methylene bridge), is 5'-methylcytidine, is 2'-0-methyl-pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain
  • one or more of the nucleotides is a deoxyribonucleic acid.
  • the invention provides a guide RNA molecule having a target complementarity region of 17-20 nucleotides, e.g., a sequence complementary to the complementary strand of 17-20 consecutive nucleotides of a target sequence, preferably a target sequence immediately 5 Of a protospacer adjacent motif (PAM), e.g., NGG, NAG, or NNGG, wherein one or more of the RNA nucleotides is modified, e.g., locked (2'-0-4'-C methylene bridge), is 5'-methylcytidine, is 2'-0-methyl- pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain, e.g., one or more of the nucleotides within the sequence X17-20, one or more of the nucleotides within the sequence X N , or one or more of the nucleotides within any sequence of the gRNA.
  • PAM protospacer adjacent motif
  • X is any sequence, wherein N (in the RNA) can be 0-200, e.g., 0-100, 0-50, or 0-20, that does not interfere with the binding of the ribonucleic acid to Cas9.
  • the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUUU, UUUUUUUUUUUUUU) at the 3' end of the molecule, as a result of the optional presence of one or more Ts used as a termination signal to terminate RNA PolIII transcription.
  • the RNA includes one or more, e.g., up to 3, e.g., one, two, or three, additional nucleotides at the 5' end of the RNA molecule that is not complementary to the target sequence.
  • the invention provides a ribonucleic acid comprising or consisting of the sequence:
  • X 17-20 is a sequence complementary to the complementary strand of 17-20 consecutive nucleotides of a target sequence (though in some embodiments this complementarity region may be longer than 20 nts, e.g., 21, 22, 23, 24, 25 or more nts), preferably a target sequence immediately 5 Of a protospacer adjacent motif (PAM), e.g., NGG, NAG, or NNGG, wherein one or more of the RNA nucleotides is modified, e.g., locked (2'-0-4'-C methylene bridge), is 5'-methylcytidine, is 2'-0- methyl-pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain, e.g., one or more of the nucleotides within the sequence X 17-20 , one or more of the nucleotides within the sequence X N , or one or more of the nucleotides within any sequence of the gRNA
  • X 17-20 identical to a sequence that naturally occurs adjacent to the rest of the RNA.
  • X N is any sequence, wherein N (in the RNA) can be 0-200, e.g., 0-100, 0-50, or 0-20, that does not interfere with the binding of the ribonucleic acid to Cas9.
  • the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUUU, UUUUUUUUUUUUUU) at the 3' end of the molecule, as a result of the optional presence of one or more Ts used as a termination signal to terminate RNA PolIII transcription.
  • the RNA includes one or more, e.g., up to 3, e.g., one, two, or three, additional nucleotides at the 5' end of the RNA molecule that is not complementary to the target sequence.
  • the invention provides hybrid nucleic acids comprising or consisting of the sequence:
  • X17-20 is a sequence complementary to the complementary strand of 17-20 consecutive nucleotides of a target sequence (though in some embodiments this complementarity region may be longer than 20 nts, e.g., 21, 22, 23, 24, 25 or more nts), preferably a target sequence immediately 5 Of a protospacer adjacent motif (PAM), e.g., NGG, NAG, or NNGG, wherein the nucleic acid is at least partially or wholly DNA, or is partially RNA and partially DNA.
  • PAM protospacer adjacent motif
  • X17-20 identical to a sequence that naturally occurs adjacent to the rest of the RNA.
  • X is any sequence, wherein N (in the RNA) can be 0-200, e.g., 0-100, 0-50, or 0-20, that does not interfere with the binding of the ribonucleic acid to Cas9.
  • the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUUUU, UUUUUUUUU) at the 3 ' end of the molecule, as a result of the optional presence of one or more Ts used as a termination signal to terminate RNA PolIII transcription.
  • the RNA includes one or more, e.g., up to 3, e.g., one, two, or three, additional nucleotides at the 5' end of the RNA molecule that is not complementary to the target sequence.
  • the invention provides DNA molecules encoding the ribonucleic acids described herein.
  • the invention provides methods for inducing a single or double-stranded break in a target region of a double-stranded DNA molecule, e.g., in a genomic sequence in a cell.
  • the methods include expressing in or introducing into the cell: a Cas9 nuclease or nickase; and
  • a guide RNA that includes one or more deoxyribonuclotides e.g., where the sequence may also be partially or wholly DNA but with thymine in place or uracil
  • a guide RNA that includes a sequence of 17-20 nucleotides that are
  • RNA includes one or more deoxyribonuclotides (e.g., where the defined sequence may also be partially or wholly DNA but with thymine in place or uracil), e.g., a hybrid nucleic acid as described herein; or (b) a guide RNA wherein one or more of the nucleotides is modified, e.g., locked (2'-0-4'-C methylene bridge), is 5'-methylcytidine, is 2'-0-methyl-pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain, e.g., a guide RNA that includes a sequence of 17-20 nucleotides that are complementary to a target sequence, preferably a target sequence immediately 5 Of a protospacer adjacent motif (PAM), e.g., NGG, NAG, or NNGG, wherein the guide RNA includes one or more deoxyribonuclotides (e.g., where the defined
  • the invention provides methods for inducing a single or double- stranded break in a target region of a double-stranded DNA molecule, e.g., in a genomic sequence in a cell.
  • the methods include expressing in or introducing into the cell:
  • a tracrRNA e.g., comprising the sequence of
  • a crRNA that includes or more deoxyribonuclotides e.g., wherein the sequence may also be partially or wholly DNA but with thymine in place or uracil
  • the target complementarity region is at least partially or wholly DNA
  • PAM protospacer adjacent motif
  • the crRNA includes one or more deoxyribonuclotides (e.g., where the defined sequence may also be partially or wholly DNA but with thymine in place or uracil), e.g., wherein the crRNA consists of the sequence: 5' - XI 7 -2OGUUUUAGAGCUAUGCUGUUUUG(XN)- 3' (SEQ ID
  • Xi 7 _2o GUUUUAGAGCUAUGCU (SEQ ID NO:7); where the Xi 7 _ 20 is at least partially or wholly DNA and is a sequence complementary to 17-20 consecutive nucleotides of a target sequence; or
  • the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUUU, UUUUUUUUUUUUUU) at the 3' end of the molecule, as a result of the optional presence of one or more Ts used as a termination signal to terminate RNA PolIII transcription.
  • the RNA includes one or more, e.g., up to 3, e.g., one, two, or three, additional nucleotides at the 5' end of the RNA molecule that is not complementary to the target sequence.
  • the invention provides methods for sequence- specifically inducing a pair of nicks in a double-stranded DNA molecule, e.g., in a genomic sequence in a cell.
  • the methods include expressing in the cell, or introducing into the cell or contacting the cell with, a Cas9-nickase as known in the art or described herein, and:
  • a tracrRNA and two crRNAs wherein one of the two crRNAs includes sequence that is complementary to one strand of the target sequence and the second of the two crR As is complementary to the other strand of the target sequence, such that using both crRNAs results in targeting both strands, and the Cas9-nickase cuts each strand.
  • the method includes contacting the cell with two nickases, wherein the first nickase comprises a Cas9 with a mutation at D10, E762, H983, or D986 and the second nickase comprises a Cas9 with a mutation at H840 or N863.
  • the invention provides three-part fusion guide nucleic acid comprising, in any order that preserves activity of each part: (1) a first sequence that is complementary to the complementary strand of a target genomic sequence, e.g., a first sequence of 17-20 or 17-25 consecutive nucleotides that is complementary to 17-20 or 17-25 consecutive nucleotides of the complementary strand of a target sequence; (2) a second sequence comprising all or part of a Cas9 guide RNA that forms a stem-loop sequence that is recognized by and binds to Cas9; and (3) a third sequence that binds to an RNA binding protein, e.g., MS2, CRISPR/Cas Subtype Ypest protein 4 (Csy4), or lambda N.
  • the first and second sequences comprise:
  • X 17-20 is a sequence complementary to 17-20 nts of a target sequence.
  • X N identical to a sequence that naturally occurs adjacent to the rest of the RNA.
  • X is any sequence, wherein N (in the RNA) can be 0-200, e.g., 0-100, 0-50, or 0-20, that does not interfere with the binding of the ribonucleic acid to Cas9.
  • the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUU, UU,UUUUU, U,UUUUUU, U,U,UUUUU, U, U, UUUUUUU, U, UUUUUUU, U, UUUUUUU,
  • the RNA includes one or more, e.g., up to 3, e.g., one, two, or three, additional nucleotides at the 5 ' end of the RNA molecule that is not
  • the invention provides tracrRNA molecule comprising a sequence
  • RNA binding protein e.g., MS2, Csy4 (e.g.,
  • the tracrRNA molecule may be truncated from its 3' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts. In another embodiment, the tracrRNA molecule may be truncated from its 5' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts. Alternatively, the tracrRNA molecule may be truncated from both the 5' and 3' end, e.g., by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 or 20 nts on the 5' end and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts on the 3' end. Additional exemplary tracrRNA sequences include:
  • the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUUUU, UUUUUUUUUU) at the 3 ' end of the molecule, as a result of the optional presence of one or more Ts used as a termination signal to terminate RNA PolIII transcription.
  • the RNA includes one or more, e.g., up to 3, e.g., one, two, or three, additional nucleotides at the 5 ' end of the RNA molecule that is not complementary to the target sequence.
  • the invention provides DNA molecules encoding the three- part fusion guide nucleic acids or the tracrRNA described herein.
  • the invention provides fusion proteins comprising an RNA binding protein, e.g., MS2, Csy4, or lambda N, linked to a catalytic domain of a Fokl nuclease or to a heterologous functional domain (HFD) as described herein, optionally with an intervening linker of 2-30, e.g., 5-20 nts, and DNA molecules encoding the fusion proteins.
  • an RNA binding protein e.g., MS2, Csy4, or lambda N
  • HFD heterologous functional domain
  • the fusion protein comprises a Fokl catalytic domain sequence fused to the N terminus of Csy4, with an intervening linker, optionally a linker of from 2-30 amino acids, e.g., 4-12 amino acids, e.g., Gly 4 Ser, (Gly 4 Ser)i_ 5 .
  • the HFD modifies gene expression, histones, or DNA, e.g., transcriptional activation domain, transcriptional repressors (e.g., silencers such as Heterochromatin Protein 1 (HP1), e.g., HPla or ⁇ , or a transcriptional repression domain, e.g., Krueppel-associated box (KRAB) domain, ERF repressor domain (ERD), or mSin3 A interaction domain (SID)), enzymes that modify the methylation state of DNA (e.g., DNA methyltransferase (DNMT) or Ten- Eleven Translocation (TET) proteins, e.g., TET1, also known as Tet Methylcytosine Dioxygenase 1), or enzymes that modify histone subunit (e.g., histone
  • transcriptional repressors e.g., silencers such as Heterochromatin Protein 1 (HP1), e.g., HPla or ⁇ ,
  • the invention provides methods for sequence-specifically inducing a break in a double-stranded DNA molecule, e.g., in a genomic sequence in a cell.
  • the methods include expressing in the cell, or contacting the cell with a fusion protein comprising an RNA binding protein, e.g., MS2, Csy4, or lambda N, linked to a catalytic domain of a Fokl nuclease, optionally with an intervening linker of 2-30, e.g., 5-20 nts,
  • the invention provides vectors comprising the DNA molecules described herein, and host cells expressing the vectors.
  • the invention provides methods for modifying a target region of a double-stranded DNA molecule, e.g., in a genomic sequence in a cell.
  • the methods include expressing in or introducing into the cell:
  • dCas9-HFD a dCas9-heterologous functional domain fusion protein
  • a guide RNA that includes one or more deoxyribonuclotides e.g., where the sequence may also be partially or wholly DNA but with thymine in place or uracil
  • a guide RNA that includes a sequence of 17-20 nucleotides that are
  • RNA complementary to the complementary strand of a target sequence, preferably a target sequence immediately 5 Of a protospacer adjacent motif (PAM), e.g., NGG, NAG, or NNGG, wherein the guide RNA includes one or more deoxyribonuclotides (e.g., where the defined sequence may also be partially or wholly DNA but with thymine in place or uracil), e.g., hybrid nucleic acid as described herein; or
  • PAM protospacer adjacent motif
  • a guide RNA wherein one or more of the nucleotides is modified, e.g., locked (2'-0-4'-C methylene bridge), is 5'-methylcytidine, is 2'-0-methyl-pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain
  • a guide RNA that includes a sequence of 17-20 nucleotides that are complementary to the complementary strand of a target sequence, preferably a target sequence immediately 5 Of a protospacer adjacent motif (PAM), e.g., NGG, NAG, or NNGG, wherein one or more of the nucleotides is modified, e.g., locked (2'-0-4'-C methylene bridge), is 5'-methylcytidine, is 2'-0-methyl-pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain, e.g., a guide RNA
  • the R A includes one or more, e.g., up to 3, e.g., one, two, or three, additional nucleotides at the 5' end of the RNA molecule that is not complementary to the target sequence.
  • the invention provides methods for modifying a target region of a double-stranded DNA molecule, e.g., in a genomic sequence in a cell.
  • the methods include expressing in or introducing into the cell:
  • dCas9-HFD a dCas9-heterologous functional domain fusion protein
  • a tracrRNA e.g., comprising the sequence of tracrRNA molecule comprising a sequence
  • a crRNA that includes or more deoxyribonuclotides e.g., wherein the sequence may also be partially or wholly DNA but with thymine in place or uracil
  • the target complementarity region is at least partially or wholly DNA
  • PAM protospacer adjacent motif
  • the crRNA includes one or more deoxyribonuclotides (e.g., where the defined sequence may also be partially or wholly DNA but with thymine in place or uracil), e.g., wherein the cr
  • Xi 7 - 2 o GUUUUAGAGCUAUGCU (SEQ ID NO:7); where the X 17 - 20 is at least partially or wholly DNA and is a sequence complementary to 17-20 consecutive nucleotides of a target sequence; or
  • a crRNAthat includes one or more nucleotides that are modified, e.g., locked (2'-0-4'-C methylene bridge), is 5'-methylcytidine, is 2'-0-methyl-pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain, e.g., wherein one or more of the nucleotides in the target complementarity region is modified, e.g., a crRNAthat includes a sequence of 17-20 nucleotides that are complementary to the complementary strand of a target sequence, preferably a target sequence immediately 5 Of a protospacer adjacent motif (PAM), e.g., NGG, NAG, or NNGG, wherein one or more of the nucleotides is modified, e.g., locked (2'-0-4'-C methylene bridge), is 5'-methylcytidine, is 2'-0-methyl-pseudouridine, or in which
  • the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUUU, UUUUUUUUUUUUUU) at the 3' end of the molecule, as a result of the optional presence of one or more Ts used as a termination signal to terminate RNA PolIII transcription.
  • the RNA includes one or more, e.g., up to 3, e.g., one, two, or three, additional nucleotides at the 5' end of the RNA molecule that is not complementary to the target sequence.
  • the dCas9-heterologous functional domain fusion protein comprises a HFD that modifies gene expression, histones, or DNA, e.g., transcriptional activation domain, transcriptional repressors (e.g., silencers such as Heterochromatin Protein 1 (HP1), e.g., HPla or ⁇ , or a transcriptional repression domain, e.g., Krueppel-associated box (KRAB) domain, ERF repressor domain (ERD), or mSin3A interaction domain (SID)), enzymes that modify the methylation state of DNA (e.g., DNA methyltransferase (DNMT) or Ten-Eleven Translocation (TET) proteins, e.g., TET1, also known as Tet Methylcytosine
  • DNMT DNA methyltransferase
  • TET1 Ten-Eleven Translocation
  • Dioxygenase 1 Dioxygenase 1
  • histone subunit e.g., histone
  • the heterologous functional domain is a transcriptional activation domain, e.g., a transcriptional activation domain from VP64 or NF-KB p65; an enzyme that catalyzes DNA demethylation, e.g., a TET; or histone modification (e.g., LSD1, histone methyltransferase, HDACs, or HATs) or a transcription silencing domain, e.g., from Heterochromatin Protein 1 (HP1), e.g., HP la or ⁇ ; or a biological tether, e.g., CRISPR/Cas Subtype Ypest protein 4 (Csy4), MS2,or lambda N protein.
  • a transcriptional activation domain e.g., a transcriptional activation domain from VP64 or NF-KB p65
  • an enzyme that catalyzes DNA demethylation e.g., a TET
  • histone modification e.g., LSD1, histone
  • Figure 1 Schematic illustrating a gRNA/Cas9 nuclease complex bound to its target DNA site. Scissors indicate approximate cleavage points of the Cas9 nuclease on the genomic DNA target site. Note the numbering of nucleotides on the guide RNA proceeds in an inverse fashion from 5' to 3'.
  • Figure 2B Schematic overview of the EGFP disruption assay. Repair of targeted Cas9-mediated double-stranded breaks in a single integrated EGFP-PEST reporter gene by error-prone NHEJ-mediated repair leads to frame-shift mutations that disrupt the coding sequence and associated loss of fluorescence in cells.
  • Figures 2C-F Activities of CRISPR RNA-guided nucleases (RGNs) with gRNAs bearing (C) single mismatches, (D) adjacent double mismatches, (E) variably spaced double mismatches, and (F) increasing numbers of adjacent mismatches assayed on three different target sites in the EGFP reporter gene sequence. Mean activities of replicates (see Online Methods) are shown, normalized to the activity of a perfectly matched gRNA. Error bars indicate standard errors of the mean. Positions mismatched in each gRNA are highlighted in grey in the grid below. Sequences of the three EGFP target sites were as follows:
  • FIG. 2G Mismatches at the 5' end of the gRNA make CRISPR/Cas more sensitive more 3' mismatches.
  • the gRNAs Watson-Crick base pair between the RNA&DNA with the exception of positions indicated with an "m" which are mismatched using the Watson-Crick transversion (i.e. EGFP Site#2 M18-19 is mismatched by changing the gRNA to its Watson-Crick partner at positions 18 & 19.
  • positions near the 5 ' of the gRNA are generally very well tolerated, matches in these positions are important for nuclease activity when other residues are mismatched. When all four positions are mismatched, nuclease activity is no longer detectable.
  • Figure 2H Efficiency of Cas9 nuclease activities directed by gRNAs bearing variable length complementarity regions ranging from 15 to 25 nts in a human cell- based U20S EGFP disruption assay. Expression of a gRNA from the U6 promoter requires the presence of a 5 ' G and therefore it was only possible to evaluate gRNAs harboring certain lengths of complementarity to the target DNA site (15, 17, 19, 20, 21, 23, and 25 nts).
  • Figure 3B Efficiencies of targeted indel mutations introduced at seven different human endogenous gene targets by matched standard and tru-RGNs.
  • Figure 3C DNA sequences of indel mutations induced by RGNs using a tru- gRNA or a matched full-length gRNA targeted to the EMXl site.
  • the portion of the target DNA site that interacts with the gRNA complementarity region is highlighted in grey with the first base of the PAM sequence shown in lowercase. Deletions are indicated by dashes highlighted in grey and insertions by italicized letters highlighted in grey. The net number of bases deleted or inserted and the number of times each sequence was isolated are shown to the right.
  • Figure 3D Efficiencies of precise HDR/ssODN-mediated alterations introduced at two endogenous human genes by matched standard and tru-RGNs.
  • %HDR was measured using a BamHl restriction digest assay (see the Experimental Procedures for Example 2).
  • Control gRNA empty U6 promoter vector.
  • FIG. 3E U20S.EGFP cells were transfected with variable amounts of full- length gRNA expression plasmids (top) or tru-gRNA expression plasmids (bottom) together with a fixed amount of Cas9 expression plasmid and then assayed for percentage of cells with decreased EGFP expression. Mean values from duplicate experiments are shown with standard errors of the mean. Note that the data obtained with tru-gRNA matches closely with data from experiments performed with full- length gRNA expression plasmids instead of tru-gRNA plasmids for these three EGFP target sites.
  • Figure 3F U20S.EGFP cells were transfected with variable amount of Cas9 expression plasmid together with variable amounts of full-length gRNA expression plasmids (top) or tru-gRNA expression plasmids (bottom) (amounts determined for each tru-gRNA from the experiments of Figure 3E). Mean values from duplicate experiments are shown with standard errors of the mean. Note that the data obtained with tru-gRNA matches closely with data from experiments performed with full- length gRNA expression plasmids instead of tru-gRNA plasmids for these three EGFP target sites. The results of these titrations determined the concentrations of plasmids used in the EGFP disruption assays performed in Examples 1 and 2.
  • FIG. 4 Schematic representation of gRNA-guided RGN and DNA-guided Cas9 nuclease.
  • the gRNA fusion RNA molecule can bind to both its on-target sequence (no asterisks) and a wide range of off-target sites (mismatches denoted by asterisks) and induce DNA cleavage. Because of the increased sensitivity of DNA- DNA duplexes to mismatches, a DNA-guided Cas9 nuclease system that uses a short DNA oligonucleotide with complementarity to a tracRNA may no longer be able to bind and cut at off-target sites, but may still function in genomic localization of Cas9. This may lead to a marked increase in Cas9-mediated nuclease activity over traditional RGNs.
  • Figure 5 Pairs of Cas9 RNA-guided nickases used to create paired nicks on opposing strands of DNA
  • Figure 7A Variant gRNAs bearing a Csy4 binding site can function to recruit
  • Figure 7B Three-part complex of catalytically inactive Cas9 nuclease (dCas9), gRNA with Csy4 recognition site, and FokI-Csy4 fusion.
  • Protospacer adjacent motif (PAM) sequences are facing Outward' in this configuration.
  • Figure 7C dCas9/gRNA/FokI-Csy4 pairs with spacer lengths of 15-16 bp showing the highest level of activity in an EGFP-disruption assay.
  • FIG. 7D T7 endonuclease I assay showing molecular evidence of nonhomologous end joining-mediated DNA double-stranded break repair in
  • RGNs CRISPR RNA-guided nucleases
  • off-target sites were seen for a number of RGNs, identification of these sites was neither comprehensive nor genome -wide in scale. For the six RGNs studied, only a very small subset of the much larger total number of potential off-target sequences in the human genome (sites that differ by three to six nucleotides from the intended target site) was examined. Although examining such large numbers of loci for off-target mutations by T7EI assay is neither a practical nor a cost-effective strategy, the use of high-throughput sequencing in future studies might enable the interrogation of larger numbers of candidate off-target sites and provide a more sensitive method for detecting bona fide off-target mutations.
  • RGN target site can be optimized; given that off-target sites that differ at up to five positions from the intended target site can be efficiently mutated by RGNs, choosing target sites with minimal numbers of off-target sites as judged by mismatch counting seems unlikely to be effective; thousands of potential off-target sites that differ by four or five positions within the 20 bp RNA:DNA complementarity region will typically exist for any given RGN targeted to a sequence in the human genome. It is also possible that the nucleotide content of the gRNA complementarity region might influence the range of potential off-target effects.
  • RNA:DNA hybrid influence the genome-wide specificities of RGNs.
  • RGNs genome-wide specificities of RGNs.
  • RGN-induced off-target effects might be to reduce the concentrations of gRNA and Cas9 nuclease expressed in the cell. This idea was tested using the RGNs for VEGFA target sites 2 and 3 in
  • CRISPR-Cas RNA-guided nucleases based on the S.
  • pyogenes Cas9 protein can have significant off-target mutagenic effects that are comparable to or higher than the intended on-target activity (Example 1). Such off-target effects can be problematic for research and in particular for potential therapeutic applications. Therefore, methods for improving the specificity of
  • RGNs RNA guided nucleases
  • Cas9 RGNs can induce high-frequency indel mutations at off-target sites in human cells (see also Cradick et al., 2013; Fu et al., 2013; Hsu et al., 2013; Pattanayak et al, 2013). These undesired alterations can occur at genomic sequences that differ by as many as five mismatches from the intended on- target site (see Example 1).
  • RNAs generally speaking come in two different systems: System 1, which uses separate crRNA and tracrRNAs that function together to guide cleavage by Cas9, and System 2, which uses a chimeric crRNA-tracrRNA hybrid that combines the two separate guide RNAs in a single system (referred to as a single guide RNA or sgRNA, see also Jinek et al., Science 2012; 337:816-821).
  • the tracrRNA can be variably truncated and a range of lengths has been shown to function in both the separate system (system 1) and the chimeric gRNA system (system 2).
  • tracrRNA may be truncated from its 3' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts.
  • the tracrRNA molecule may be truncated from its 5' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts.
  • the tracrRNA molecule may be truncated from both the 5' and 3' end, e.g., by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 or 20 nts on the 5' end and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts on the 3' end.
  • vectors complementary to a region that is within about 100-800 bp upstream of the transcription start site, e.g., is within about 500 bp upstream of the transcription start site, includes the transcription start site, or within about 100-800 bp, e.g., within about 500 bp, downstream of the transcription start site.
  • vectors are complementary to a region that is within about 100-800 bp upstream of the transcription start site, e.g., is within about 500 bp upstream of the transcription start site, includes the transcription start site, or within about 100-800 bp, e.g., within about 500 bp, downstream of the transcription start site.
  • plasmids encoding more than one gRNA are used, e.g., plasmids encoding, 2, 3, 4, 5, or more gRNAs directed to different sites in the same region of the target gene.
  • guide RNAs e.g., single gRNAs or crRNA and tracrRNA, that include one or more modified (e.g., locked) nucleotides or
  • RNA oligonucleotides such as locked nucleic acids (LNAs) have been demonstrated to increase the specificity of RNA-DNA hybridization by locking the modified oligonucleotides in a more favorable (stable) conformation.
  • LNAs locked nucleic acids
  • 2'-0-methyl RNA is a modified base where there is an additional covalent linkage between the 2' oxygen and 4' carbon which when incorporated into oligonucleotides can improve overall thermal stability and selectivity (formula I).
  • Guide RNAs as described herein may be synthetic guide RNA molecules wherein one, some or all of the nucleotides 5 ' region of the guide RNA
  • ribose phosphate backbone has been replaced by a polyamide chain (peptide nucleic acid), e.g., a synthetic ribonucleic acid.
  • one, some or all of the nucleotides of the gRNA sequence may be modified, e.g., locked (2'-0-4'-C methylene bridge), 5'- methylcytidine, 2'-0-methyl-pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain (peptide nucleic acid), e.g., a synthetic ribonucleic acid.
  • a polyamide chain peptide nucleic acid
  • exemplary modified or synthetic gRNAs may comprise, or consist of, the following sequences:
  • X17-20 is a sequence complementary to 17-20 nts of a target sequence, preferably a target sequence immediately 5' of a protospacer adjacent motif (PAM), e.g., NGG, NAG, or NNGG, and further wherein one or more of the nucleotides are locked, e.g., one or more of the nucleotides within the sequence X 17-20 , one or more of the nucleotides within the sequence X N , or one or more of the nucleotides within any sequence of the gRNA.
  • PAM protospacer adjacent motif
  • X17-20 is X17- 18 , e.g., is 17-18 nucleotides long; in some embodiments, the target complementarity can be longer, e.g., 17-20, 21, 22, 23, 24, 25, or more nucleotides long.
  • X N is any sequence, wherein N (in the RNA) can be 0-200, e.g., 0-100, 0-50, or 0-20, that does not interfere with the binding of the ribonucleic acid to Cas9.
  • the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUUUU, UUUUUUUUU) at the 3' end of the molecule, as a result of the optional presence of one or more Ts used as a termination signal to terminate RNA PolIII transcription.
  • U e.g., 1 to 8 or more Us
  • one or both can be synthetic and include one or more locked nucleotides, as dual gRNAs (e.g., the crRNA and tracrRNA found in naturally occurring systems) can also be modified.
  • dual gRNAs e.g., the crRNA and tracrRNA found in naturally occurring systems
  • a single tracrRNA would be used in conjunction with multiple different crRNAs expressed using the present system, e.g., the following:
  • the methods include contacting the cell with a tracrRNA comprising or consisting of the sequence
  • the tracrRNA molecule may be truncated from its 3' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts. In another embodiment, the tracrRNA molecule may be truncated from its 5 ' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts.
  • the tracrRNA molecule may be truncated from both the 5' and 3' end, e.g., by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 or 20 nts on the 5' end and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts on the 3' end.
  • Exemplary tracrRNA sequences in addition to SEQ ID NO: 8 include the following:
  • one or both can be synthetic and include one or more modified (e.g., locked) nucleotides.
  • the single guide RNAs or crRNAs or tracrRNAs includes one or more Adenine (A) or Uracil (U) nucleotides on the 3 ' end.
  • the methods described can include contacting the cell with a locked gRNA as described herein, and contacting the cell with or expressing in the cell a nuclease that can be guided by the locked gRNAs, e.g., a Cas9 nuclease, e.g., as described in Mali et al., a Cas9 nickase as described in Jinek et al., 2012; or a dCas9-heterofunctional domain fusion (dCas9-HFD) as described in U.S. Provisional Patent Applications USSN 61/799,647, Filed on March 15, 2013, USSN 61/838,148, filed on 6/21/2013, and PCT International Application No. PCT/US 14/27335, all of which are
  • RNA-DNA heteroduplexes can form a more promiscuous range of structures than their DNA-DNA counterparts.
  • DNA-DNA duplexes are more sensitive to mismatches, suggesting that a DNA- guided nuclease may not bind as readily to off-target sequences, making them comparatively more specific than RNA-guided nucleases.
  • an engineered Cas9-based RGN wherein a short DNA oligonucleotide replaces all or part of the complementarity region of a gRNA (for example, see Figure 4).
  • This DNA- based molecule could replace either all or part of the gRNA in a single gRNA system or alternatively might replace all of part of the crRNA in a dual crRNA/tracrRNA system.
  • Such a system that incorporates DNA into the complementarity region should more reliably target the intended genomic DNA sequences due to the general intolerance of DNA-DNA duplexes to mismatching compared to RNA-DNA duplexes.
  • Methods for making such duplexes are known in the art, See, e.g., Barker et al, BMC Genomics. 2005 Apr 22;6:57; and Sugimoto et al, Biochemistry. 2000 Sep 19;39(37): 11270-81.
  • described herein are hybrid guide DNA/RNAs consisting of the sequence:
  • X17-20 is a sequence complementary to 17-20 nts of a target sequence, preferably a target sequence immediately 5' of a protospacer adjacent motif (PAM), e.g., NGG, NAG, or NNGG, wherein the X17-20 is at least partially or wholly DNA, e.g., one or more of the nucleotides are deoxyribonucleotides (e.g., is all or partially DNA, e.g.
  • PAM protospacer adjacent motif
  • DNA/RNA hybrids e.g., one or more of the nucleotides within the sequence X 17-20 , one or more of the nucleotides within the sequence X N , or one or more of the nucleotides within any sequence of the gRNA is a deoxyribonucleotide.
  • X17-20 is X17-18, e.g., is 17-18 nucleotides long.
  • X N is any sequence, wherein N (in the RNA) can be 0-200, e.g., 0-100, 0-50, or 0-20, that does not interfere with the binding of the ribonucleic acid to Cas9.
  • the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUUUU, UUUUUUUUU) at the 3' end of the molecule, as a result of the optional presence of one or more Ts used as a termination signal to terminate RNA PolIII transcription.
  • U e.g., 1 to 8 or more Us
  • one or both can be synthetic and include one or more deoxyribonucleotides, as dual gRNAs (e.g., the crRNA and tracrRNA found in naturally occurring systems) can also be hybrids.
  • dual gRNAs e.g., the crRNA and tracrRNA found in naturally occurring systems
  • a single tracrRNA would be used in conjunction with multiple different crRNAs expressed using the present system, e.g., the following: (Xi 7 -2o)GUUUUAGAGCUA (SEQ ID NO:5);
  • the crRNA is used as the guide RNA in the methods and molecules described herein, and the tracrRNA can be expressed from the same or a different
  • the methods include contacting the cell with a tracrRNA comprising or consisting of the sequence
  • the tracrRNA molecule may be truncated from its 3' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts. In another embodiment, the tracrRNA molecule may be truncated from its 5 ' end by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts.
  • the tracrRNA molecule may be truncated from both the 5' and 3' end, e.g., by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 or 20 nts on the 5' end and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts on the 3' end.
  • Exemplary tracrRNA sequences in addition to SEQ ID NO: 8 include the following:
  • GGCACCGAGUCGGUGC SEQ ID NO: 17 or an active portion thereof.
  • tracrRNA (SEQ ID NO: 6) is used as a crRNA, the following tracrRNA is used:
  • tracrRNA is used as a crRNA, the following tracrRNA is used:
  • one or both can be synthetic and include one or more deoxyribonucleotides.
  • the guide RNA includes one or more Adenine (A) or
  • the RNA includes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU, UUUUU, UUUUU, UUUUUU, UUUUUU, UUUUUU, UUUUUUUU, UUUUUUUUU) at the 3' end of the molecule, as a result of the optional presence of one or more Ts used as a termination signal to terminate RNA PolIII transcription.
  • U e.g., 1 to 8 or more Us
  • the present system utilizes the Cas9 protein from S. pyogenes, either as encoded in bacteria or codon-optimized for expression in mammalian cells, containing mutations the nuclease portion of the protein partially catalytically inactive.
  • S. pyogenes either as encoded in bacteria or codon-optimized for expression in mammalian cells, containing mutations the nuclease portion of the protein partially catalytically inactive.
  • the wild type sequence of the S. pyogenes Cas9 that can be used in the methods and compositions described herein is set forth below.
  • a Cas9-nickase e.g., a Cas9 with a mutation at any of D10, E762, H983, D986, H840, or N863, that renders only one of the nuclease portions of the protein catalytically inactive; substitutions at these positions could be alanine (as they are in Nishimasu al, Cell 156, 935-949 (2014)) or they could be other residues, e.g., glutamine, asparagine, tyrosine, serine, or aspartate, e.gE762Q, H983N/H983Y, D986N, N863D/N863S/N863H D10A/D10N,
  • each of the two guide RNAs include sequences that are complementary to either strand of the target sequence, such that using both guide RNAs results in targeting both strands, and the Cas9-nickase cuts each strand singly on opposing strands of DNA.
  • the RGNickase like RGNs consisting of wildtype Cas9 is expected to cut the DNA target site approximately 3bp upstream of the PAM, with the D10A Cas9 cleaving the complementary DNA strand and the H840A Cas9 cleaving the non-complementary strand.
  • the two gRNA target sites may be overlapping or some distance away from each other, e.g., up to about 200 nts apart, e.g., less than 100, 50, 25, 10, 5, 4, or 2 nts apart.
  • Another method to improve the specificity of Cas9 is to use dCas9 together with a modified gRNA bearing extra RNA sequence on either the 5 ' or 3 ' end of the gRNA (or on the ends of the crRNA and/or tracrRNA if using a dual gRNA system) that is bound by an RNA-binding protein that is in turn fused to a heterologous functional domain (HFD), e.g., the Fokl nuclease domain.
  • HFD heterologous functional domain
  • RNA-binding protein-HFD e.g., Fokl nuclease domain
  • HFD/Fokl nuclease domains would dimerize, thereby resulting in introduction of a targeted double-stranded break in the DNA sequence between the two dCas9 binding sites.
  • FokI-Csy4 VP64-Csy4, TET1-Csy4, and so on could be used.
  • RNA-binding protein/RNA target sequences that could be used would include but are not limited to the lambda N, MS2 or Csy4 proteins.
  • the wild type and high- affinity sequences for MS2 are AAACAUGAGGAUUACCCAUGUCG (SEQ ID NO: 19) and AAAC AUG AGG AUC ACC C AUGUC G (SEQ ID NO:20), respectively (see Keryer-Bibens et al, supra, FIG. 2); the nutL and nutR BoxB sequences to which lambda N binds are GCCCUGAAGAAGGGC (SEQ ID NO:21) and GCCCUGAAAAAGGGC (SEQ ID NO:22), respectively.
  • the sequences to which Csy4 binds are GUUCACUGCCGUAUAGGCAG (SEQ ID NO:23) or
  • binding sites can be attached to 3 ' end of a gR A sequence and gR As harboring this additional Csy4 binding site can still direct Cas9 to cleave specific sequences in human cells and thus remain functional in the cell (Example 2 and Figure 7).
  • fusion guide nucleic acids comprising: (1) a first sequence of 17-20 nts that is complementary to the complementary strand of 17-20 consecutive nucleotides of a target sequence with an adjacent PAM sequence; (2) a second sequence comprising all or part of a Cas9 guide R A, e.g., all or part of GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCA ACUUGAAAAAGUGGCACCGAGTCGGUGCUUUU (SEQ ID NO: 15) or an active portion thereof,
  • RNA binding protein e.g., MS2, Csy4, or lambda N.
  • sequences can be arranged in any order so long as all of the parts retain their function, e.g., (l)-(2)-(3), or (3)-(l)-(2), or (3)- (2)-(l), or (l)-(3)-(2), or (2)-(l)-(3), or (2)-(3)-(l).
  • nucleotides there are additional nucleotides, e.g., up to 20 additional nucleotides, that act as a flexible linker between Csy4 and the gRNA; these nucleotides should not add any secondary or tertiary structure to the gRNA.
  • sequence 'GTTC has been shown to be unstructured and could be construed as 'linker' sequence.
  • the wild-type Csy4 binding sequence is used, which is: GUUCACUGCCGUAUAGGCAGCUAAGAAA (SEQ ID NO:24).
  • a truncated Csy4 binding sequence is used, which upon processing by Csy4 produces gRNAs of higher activity. This sequence is
  • fusion proteins comprising an RN A binding protein, e.g., MS2, Csy4, or lambda N, linked to a catalytic domain of a HFD, e.g., a Fokl nuclease as described above, optionally with an intervening linker of 2-30, e.g., 5-20 nts, as well as nucleic acids encoding the same.
  • RN A binding protein e.g., MS2, Csy4, or lambda N
  • a catalytic domain of a HFD e.g., a Fokl nuclease as described above
  • an intervening linker of 2-30, e.g., 5-20 nts, as well as nucleic acids encoding the same.
  • MS2 functions as a dimer, therefore the MS2 protein can include a fused single chain dimer sequence.
  • Acinetobacter baumannii AB0057 (Ab), Moritella sp. PE36 (MP1, MP01),
  • the Csy4 is from Pseudomonas aeruginosa.
  • Methods of using the fusions include contacting a cell with or expressing in a cell a pair of three-part fusion guide nucleic acids that include sequences
  • RNA-binding protein linked to a catalytic domain of a Fokl nuclease complementary to a single region of a target DNA
  • a Cas9 protein e.g., the inactive dCas9 protein from S.
  • pyogenes either as encoded in bacteria or codon-optimized for expression in mammalian cells, containing mutations at D10, E762, H983, D986, H840, or N863, e.g., D10A/D10N and H840A/H840N/H840Y, to render the nuclease portion of the protein catalytically inactive; substitutions at these positions could be alanine (as they are in Nishimasu al, Cell 156, 935-949 (2014)) or they could be other residues, e.g., glutamine, asparagine, tyrosine, serine, or aspartate, e.g., E762Q, H983N, H983Y, D986N, N863D, N863S, or N863H ( Figure 1C).).
  • the two gRNA target sites may be overlapping or some distance away from each other, e.g., up to about 200 nts apart, e.g
  • Fokl is a type lis restriction endonuclease that includes a DNA recognition domain and a catalytic (endonuclease) domain.
  • the fusion proteins described herein can include all of Fokl or just the catalytic endonuclease domain, i.e., amino acids 388-583 or 408-583 of GenBank Acc. No. AAA24927.1, e.g., as described in Li et al, Nucleic Acids Res. 39(1): 359-372 (2011); Cathomen and Joung, Mol. Ther. 16: 1200-1207 (2008), or a mutated form of Fokl as described in Miller et al. Nat
  • An exemplary nucleic acid sequence encoding Fokl is as follows:
  • the Fokl nuclease used herein is at least about 50% identical SEQ ID NO:33, e.g., to amino acids 388-583 or 408-583 of SEQ ID NO:33. These variant nucleases must retain the ability to cleave DNA.
  • the nucleotide sequences are about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identical to amino acids 388-583 or 408-583 of SEQ ID NO:4. In some embodiments, any differences from amino acids 388-583 or 408-583 of SEQ ID NO:4 are in non-conserved regions.
  • the sequences are aligned for optimal comparison purposes (gaps are introduced in one or both of a first and a second amino acid or nucleic acid sequence as required for optimal alignment, and non-homologous sequences can be disregarded for comparison purposes).
  • the length of a reference sequence aligned for comparison purposes is at least 50%> (in some embodiments, about 50%, 55%, 60%, 65%, 70%, 75%, 85%, 90%, 95%, or 100% of the length of the reference sequence is aligned).
  • the nucleotides or residues at corresponding positions are then compared. When a position in the first sequence is occupied by the same nucleotide or residue as the corresponding position in the second sequence, then the molecules are identical at that position.
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • the percent identity between two amino acid sequences is determined using the Needleman and Wunsch ((1970) J. Mol. Biol. 48:444-453) algorithm which has been incorporated into the GAP program in the GCG software package, using a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
  • transcriptional activation domains can be fused on the N or C terminus of the Cas9.
  • transcriptional repressors e.g., KRAB, ERD, SID, and others, e.g., amino acids 473-530 of the ets2 repressor factor (ERF) repressor domain (ERD), amino acids 1-97 of the KRAB domain of KOXl, or amino acids 1-36 of the Mad mSIN3 interaction domain (SID); see Beerli et al, PNAS USA 95:14628-14633 (1998)) or silencers such as
  • Heterochromatin Protein 1 (HPl, also known as swi6), e.g., HP la or ⁇ ; proteins or peptides that could recruit long non-coding RNAs (IncRNAs) fused to a fixed RNA binding sequence such as those bound by the MS2 coat protein, endoribonuclease Csy4, or the lambda N protein; enzymes that modify the methylation state of DNA (e.g., DNA methyltransferase (DNMT) or TET proteins); or enzymes that modify histone subunits (e.g., histone acetyltransferases (HAT), histone deacetylases (HDAC), histone methyltransferases (e.g., for methylation of lysine or arginine residues) or histone demethylases (e.g., for demethylation of lysine or arginine residues)) as are known in the art can also be used.
  • HAT histone acet
  • exemplary proteins include the Ten-Eleven- Translocation (TET) 1-3 family, enzymes that converts 5-methylcytosine (5-mC) to 5- hydroxymethylcytosine (5-hmC) in DNA.
  • TET Ten-Eleven- Translocation
  • Variant (1) represents the longer transcript and encodes the longer isoform (a).
  • Variant (2) differs in the 5' UTR and in the 3' UTR and coding sequence compared to variant 1.
  • the resulting isoform (b) is shorter and has a distinct C- terminus compared to isoform a.
  • all or part of the full-length sequence of the catalytic domain can be included, e.g., a catalytic module comprising the cysteine-rich extension and the 20GFeDO domain encoded by 7 highly conserved exons, e.g., the Tetl catalytic domain comprising amino acids 1580-2052, Tet2 comprising amino acids 1290-1905 and Tet3 comprising amino acids 966-1678.
  • sequence includes amino acids 1418-2136 of Tetl or the corresponding region in Tet2/3.
  • heterologous functional domain is a biological tether, and comprises all or part of (e.g., DNA binding domain from) the MS2 coat protein, endoribonuclease Csy4, or the lambda N protein. These proteins can be used to recruit RNA molecules containing a specific stem-loop structure to a locale specified by the dCas9 gRNA targeting sequences.
  • a dCas9 fused to MS2 coat protein, endoribonuclease Csy4, or lambda N can be used to recruit a long non-coding RNA (IncRNA) such as XIST or HOTAIR; see, e.g., Keryer-Bibens et al, Biol. Cell 100: 125-138 (2008), that is linked to the Csy4, MS2 or lambda N binding sequence.
  • the Csy4, MS2 or lambda N protein binding sequence can be linked to another protein, e.g., as described in Keryer-Bibens et al, supra, and the protein can be targeted to the dCas9 binding site using the methods and compositions described herein.
  • the Csy4 is catalytically inactive.
  • the fusion proteins include a linker between the dCas9 and the heterologous functional domains.
  • Linkers that can be used in these fusion proteins (or between fusion proteins in a concatenated structure) can include any sequence that does not interfere with the function of the fusion proteins.
  • the linkers are short, e.g., 2-20 amino acids, and are typically flexible (i.e., comprising amino acids with a high degree of freedom such as glycine, alanine, and serine).
  • the linker comprises one or more units consisting of GGGS (SEQ ID NO: 14) or GGGGS (SEQ ID NO: 15), e.g., two, three, four, or more repeats of the GGGS (SEQ ID NO: 14) or GGGGS (SEQ ID NO: 15) unit.
  • Other linker sequences can also be used.
  • Cas9 molecules of a variety of species can be used in the methods and compositions described herein. While the S. pyogenes and S. thermophilus Cas9 molecules are the subject of much of the disclosure herein, Cas9 molecules of, derived from, or based on the Cas9 proteins of other species listed herein can be used as well. In other words, while the much of the description herein uses S. pyogenes and S. thermophilus Cas9 molecules, Cas9 molecules from the other species can replace them. Such species include those set forth in the following table, which was created based on supplementary figure 1 of Chylinski et al, 2013.
  • the constructs and methods described herein can include the use of any of those Cas9 proteins, and their corresponding guide R As or other guide RNAs that are compatible.
  • the Cas9 from Streptococcus thermophilus LMD-9 CRISPR1 system has also been shown to function in human cells in Cong et al (Science 339, 819 (2013)).
  • Cas9 orthologs from N. meningitides are described in Hou et al, Proc Natl Acad Sci U S A. 2013 Sep 24;110(39): 15644-9 and Esvelt et al, Nat Methods. 2013 Nov;10(l 1): 1116-21. Additionally, Jinek et al.
  • the present system utilizes the Cas9 protein from S. pyogenes, either as encoded in bacteria or codon-optimized for expression in mammalian cells.
  • a catalytically inactive Cas9 (dCas9) containing mutations at (i) D10, E762, H983, or D986 and (i) H840 or N863, e.g., D 10A/D 1 ON and H840A/H840N/H840Y, to render the nuclease portion of the protein completely catalytically inactive; substitutions at these positions could be alanine (as they are in Nishimasu al, Cell 156, 935-949 (2014)) or they could be other residues, e.g., glutamine, asparagine, tyrosine, serine, or aspartate, e.g., E762Q, H983N, H983Y, D986N, N863D, N863S, or N863
  • a mutation at any of D10, E762, H983, D986, H840, or N863 can be introduced.
  • the wild type sequence of S. pyogenes Cas9 nuclease that can be used in the methods and compositions described herein is as follows.
  • PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGD (SEQ ID NO: 18)
  • the Cas9 nuclease used herein is at least about 50% identical to the sequence of S. pyogenes Cas9, i.e., at least 50%> identical to SEQ ID NO: 18.
  • the nucleotide sequences are about 50%>, 55%, 60%>, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identical to SEQ ID NO: 18.
  • any differences from SEQ ID NO: 18 are in non-conserved regions, as identified by sequence alignment of sequences set forth in Chylinski et al, R A Biology 10:5, 1-12; 2013 (e.g., in supplementary figure 1 and supplementary table 1 thereof); Esvelt et al, Nat Methods. 2013 Nov; 10(11):1116-21 and Fonfara et al, Nucl. Acids Res. (2014) 42 (4): 2577-2590. [Epub ahead of print 2013 Nov 22] doi: 10.1093/nar/gktl074.
  • the sequences are aligned for optimal comparison purposes (gaps are introduced in one or both of a first and a second amino acid or nucleic acid sequence as required for optimal alignment, and non-homologous sequences can be disregarded for comparison purposes).
  • the length of a reference sequence aligned for comparison purposes is at least 50% (in some embodiments, about 50%, 55%, 60%, 65%, 70%, 75%, 85%, 90%, 95%, or 100% of the length of the reference sequence is aligned).
  • the nucleotides or residues at corresponding positions are then compared. When a position in the first sequence is occupied by the same nucleotide or residue as the corresponding position in the second sequence, then the molecules are identical at that position.
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • the percent identity between two amino acid sequences is determined using the Needleman and Wunsch ((1970) J. Mol. Biol. 48:444-453 ) algorithm which has been incorporated into the GAP program in the GCG software package, using a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
  • the engineered proteins may be desirable to express the engineered proteins from a nucleic acid that encodes them.
  • the nucleic acid encoding the fusion protein or guide RNA can be cloned into an intermediate vector for transformation into prokaryotic or eukaryotic cells for replication and/or expression.
  • Intermediate vectors are typically prokaryote vectors, e.g., plasmids, or shuttle vectors, or insect vectors, for storage or manipulation of the nucleic acid encoding the fusion protein or guide RNA for production of the fusion protein or guide RNA.
  • the nucleic acid encoding the fusion protein or guide R A can also be cloned into an expression vector, for administration to a plant cell, animal cell, preferably a mammalian cell or a human cell, fungal cell, bacterial cell, or protozoan cell.
  • a sequence encoding a fusion protein or guide RNA is typically subcloned into an expression vector that contains a promoter to direct transcription.
  • Suitable bacterial and eukaryotic promoters are well known in the art and described, e.g., in Sambrook et al., Molecular Cloning, A Laboratory Manual (3d ed. 2001); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al, eds., 2010).
  • Bacterial expression systems for expressing the engineered protein are available in, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al, 1983, Gene 22:229-235). Kits for such expression systems are commercially available.
  • Eukaryotic expression systems for mammalian cells, yeast, and insect cells are well known in the art and are also commercially available.
  • the promoter used to direct expression of a fusion protein nucleic acid depends on the particular application. For example, a strong constitutive promoter is typically used for expression and purification of fusion proteins. In contrast, when the fusion protein is to be administered in vivo for gene regulation, either a constitutive or an inducible promoter can be used, depending on the particular use of the fusion protein. In addition, a preferred promoter for administration of the fusion protein can be a weak promoter, such as HSV TK or a promoter having similar activity.
  • the promoter can also include elements that are responsive to transactivation, e.g., hypoxia response elements, Gal4 response elements, lac repressor response element, and small molecule control systems such as tetracycline-regulated systems and the PvU-486 system (see, e.g., Gossen & Bujard, 1992, Proc. Natl. Acad. Sci. USA,
  • the expression vector typically contains a transcription unit or expression cassette that contains all the additional elements required for the expression of the nucleic acid in host cells, either prokaryotic or eukaryotic.
  • Atypical expression cassette thus contains a promoter operably linked, e.g., to the nucleic acid sequence encoding the fusion protein, and any signals required, e.g., for efficient polyadenylation of the transcript, transcriptional termination, ribosome binding sites, or translation termination.
  • Additional elements of the cassette may include, e.g., enhancers, and heterologous spliced intronic signals.
  • the particular expression vector used to transport the genetic information into the cell is selected with regard to the intended use of the fusion protein, e.g., expression in plants, animals, bacteria, fungus, protozoa, etc.
  • Standard bacterial expression vectors include plasmids such as pBR322 based plasmids, pSKF, pET23D, and commercially available tag- fusion expression systems such as GST and LacZ.
  • a preferred tag-fusion protein is the maltose binding protein (MBP).
  • MBP maltose binding protein
  • Such tag-fusion proteins can be used for purification of the engineered TALE repeat protein.
  • Epitope tags can also be added to recombinant proteins to provide convenient methods of isolation, for monitoring expression, and for monitoring cellular and subcellular localization, e.g., c-myc or FLAG
  • Expression vectors containing regulatory elements from eukaryotic viruses are often used in eukaryotic expression vectors, e.g., SV40 vectors, papilloma virus vectors, and vectors derived from Epstein-Barr virus.
  • eukaryotic vectors include pMSG, pAV009/A+, pMTO10/A+, pMAMneo-5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV40 early promoter, SV40 late promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.
  • the vectors for expressing the guide RNAs can include RNA Pol III promoters to drive expression of the guide RNAs, e.g., the HI, U6 or 7SK promoters. These human promoters allow for expression of gRNAs in mammalian cells following plasmid transfection. Alternatively, a T7 promoter may be used, e.g., for in vitro transcription, and the RNA can be transcribed in vitro and purified. Vectors suitable for the expression of short RNAs, e.g., siRNAs, shRNAs, or other small RNAs, can be used.
  • Some expression systems have markers for selection of stably transfected cell lines such as thymidine kinase, hygromycin B phosphotransferase, and dihydrofolate reductase. High yield expression systems are also suitable, such as using a
  • baculovirus vector in insect cells with the fusion protein encoding sequence under the direction of the polyhedrin promoter or other strong baculovirus promoters.
  • the elements that are typically included in expression vectors also include a replicon that functions in E. coli, a gene encoding antibiotic resistance to permit selection of bacteria that harbor recombinant plasmids, and unique restriction sites in nonessential regions of the plasmid to allow insertion of recombinant sequences.
  • Standard transfection methods are used to produce bacterial, mammalian, yeast or insect cell lines that express large quantities of protein, which are then purified using standard techniques (see, e.g., Colley et al, 1989, J. Biol. Chem., 264: 17619-22; Guide to Protein Purification, in Methods in Enzymology, vol. 182 (Deutscher, ed., 1990)). Transformation of eukaryotic and prokaryotic cells are performed according to standard techniques (see, e.g., Morrison, 1977, J. Bacteriol. 132:349-351; Clark-Curtiss & Curtiss, Methods in Enzymology 101 :347-362 (Wu et al, eds, 1983).
  • Any of the known procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, polybrene, protoplast fusion, electroporation, nucleofection, liposomes,
  • microinjection naked DNA, plasmid vectors, viral vectors, both episomal and integrative, and any of the other well-known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see, e.g., Sambrook et al., supra). It is only necessary that the particular genetic engineering procedure used be capable of successfully introducing at least one gene into the host cell capable of expressing the protein of choice.
  • the fusion protein includes a nuclear localization domain which provides for the protein to be translocated to the nucleus.
  • nuclear localization sequences are known, and any suitable NLS can be used.
  • many NLSs have a plurality of basic amino acids, referred to as a bipartite basic repeats (reviewed in Garcia-Bustos et al, 1991, Biochim. Biophys. Acta, 1071 :83-101).
  • An NLS containing bipartite basic repeats can be placed in any portion of chimeric protein and results in the chimeric protein being localized inside the nucleus.
  • a nuclear localization domain is incorporated into the final fusion protein, as the ultimate functions of the fusion proteins described herein will typically require the proteins to be localized in the nucleus. However, it may not be necessary to add a separate nuclear localization domain in cases where the DBD domain itself, or another functional domain within the final chimeric protein, has intrinsic nuclear translocation function.
  • the present invention includes the vectors and cells comprising the vectors.
  • RGNs CRISPR RNA-guided nucleases
  • Example 1 The following materials and methods were used in Example 1.
  • DNA oligonucleotides harboring variable 20 nt sequences for Cas9 targeting were annealed to generate short double-strand DNA fragments with 4 bp overhangs compatible with ligation into BsmBI-digested plasmid pMLM3636. Cloning of these annealed oligonucleotides generates plasmids encoding a chimeric +103 single-chain guide RNA with 20 variable 5 ' nucleotides under expression of a U6 promoter (Hwang et al, Nat Biotechnol 31 , 227-229 (2013); Mali et al, Science 339, 823-826 (2013).).
  • pMLM3636 and the expression plasmid pJDS246 (encoding a codon optimized version of Cas9) used in this study are both available through the non-profit plasmid distribution service Addgene (addgene.org/crispr-cas).
  • U20S.EGFP cells harboring a single integrated copy of an EGFP-PEST fusion gene were cultured as previously described (Reyon et al, Nat Biotech 30, 460- 465 (2012)).
  • 200,000 cells were Nucleofected with the indicated amounts of gRNA expression plasmid and pJDS246 together with 30 ng of a Td- tomato-encoding plasmid using the SE Cell Line 4D-NucleofectorTM X Kit (Lonza) according to the manufacturer's protocol. Cells were analyzed 2 days post- transfection using a BD LSRII flow cytometer. Transfections for optimizing gRNA/Cas9 plasmid concentration were performed in triplicate and all other transfections were performed in duplicate. PCR amplification and sequence verification of endogenous human genomic sites
  • PCR reactions were performed using Phusion Hot Start II high-fidelity DNA polymerase (NEB) with PCR primers and conditions listed in Table B. Most loci amplified successfully using touchdown PCR (98 °C, 10 s; 72-62 °C, -1 °C/cycle, 15 s; 72 °C, 30 s]10 cycles, [98 °C, 10 s; 62 °C, 15 s; 72 °C, 30 s]25 cycles). PCR for the remaining targets were performed with 35 cycles at a constant annealing temperature of 68 °C or 72 °C and 3% DMSO or 1M betaine, if necessary.
  • NEB Phusion Hot Start II high-fidelity DNA polymerase
  • PCR products were analyzed on a QIAXCEL capillary electrophoresis system to verify both size and purity. Validated products were treated with ExoSap-IT (Affymetrix) and sequenced by the Sanger method (MGH DNA Sequencing Core) to verify each target site.
  • ExoSap-IT Affymetrix
  • Sanger method MGH DNA Sequencing Core
  • Lipofectamine LTX reagent according to the manufacturer's instructions (Life Technologies). Genomic DNA was harvested from transfected U20S.EGFP,
  • HEK293, or K562 cells using the QIAamp DNA Blood Mini Kit (QIAGEN), according to the manufacturer's instructions.
  • QIAGEN QIAamp DNA Blood Mini Kit
  • EGFP enhanced green fluorescent protein
  • the activities of nucleases targeted to a single integrated EGFP reporter gene can be quantified by assessing loss of fiuorescence signal in human U20S.EGFP cells caused by inactivating frameshift insertion/deletion (indel) mutations introduced by error prone non-homologous end-joining (NHEJ) repair of nuclease-induced double- stranded breaks (DSBs) (Fig. 2B).
  • indel frameshift insertion/deletion
  • NHEJ error prone non-homologous end-joining
  • DSBs nuclease-induced double- stranded breaks
  • EGFP Site 2 GATGCCGT TCT TCTGCT TGTCGG SEQ I D NO : 2
  • Each of these gRNAs can efficiently direct Cas9-mediated disruption of EGFP expression (see Example le and 2a, and FIGs. 3E (top) and 3F (top)).
  • variant gRNAs were generated for each of the three target sites harboring Watson-Crick transversion mismatches at positions 1 through 19 (numbered 1 to 20 in the 3' to 5' direction; see Fig. 1) and the abilities of these various gRNAs to direct Cas9-mediated EGFP disruption in human cells tested (variant gRNAs bearing a substitution at position 20 were not generated because this nucleotide is part of the U6 promoter sequence and therefore must remain a guanine to avoid affecting expression.)
  • target site #1 was particularly sensitive to a mismatch at position 2 whereas target site #3 was most sensitive to mismatches at positions 1 and 8.
  • gRNA/DNA interface To test the effects of more than one mismatch at the gRNA/DNA interface, a series of variant gRNAs bearing double Watson-Crick transversion mismatches in adjacent and separated positions were created and the abilities of these gRNAs to direct Cas9 nuclease activity were tested in human cells using the EGFP disruption assay. All three target sites generally showed greater sensitivity to double alterations in which one or both mismatches occur within the 3 ' half of the gRNA targeting region. However, the magnitude of these effects exhibited site-specific variation, with target site #2 showing the greatest sensitivity to these double mismatches and target site #1 generally showing the least.
  • variant gRNAs were constructed bearing increasing numbers of mismatched positions ranging from positions 19 to 15 in the 5' end of the gRNA targeting region (where single and double mismatches appeared to be better tolerated).
  • gRNAs that target three different sites in the VEGFA gene, one in the EMX1 gene, one in the RNF2 gene, and one in the FANCF gene were used. These six gRNAs efficiently directed Cas9-mediated indels at their respective endogenous loci in human U20S.EGFP cells as detected by T7
  • Endonuclease I (T7EI) assay For each of these six RGNs, we then examined dozens of potential off-target sites (ranging in number from 46 to as many as 64) for evidence of nuclease-induced NHEJ-mediated indel mutations in U20S.EGFP cells. The loci assessed included all genomic sites that differ by one or two nucleotides as well as subsets of genomic sites that differ by three to six nucleotides and with a bias toward those that had one or more of these mismatches in the 5 ' half of the gRNA targeting sequence.
  • Example le Titration of gRNA- and Cas9-expressing plasmid amounts used for the EGFP disruption assay
  • gRNAs Single guide RNAs
  • EGFP SITES 1-3 Three different sequences located upstream of EGFP nucleotide 502, a position at which the introduction of frameshift mutations via non-homologous end- joining can robustly disrupt expression of EGFP (Maeder, M.L. et al, Mol Cell 31, 294-301 (2008); Reyon, D. et al, Nat Biotech 30, 460-465 (2012)).
  • a range of gRNA-expressing plasmid amounts (12.5 to 250 ng) was initially transfected together with 750 ng of a plasmid expressing a codon-optimized version of the Cas9 nuclease into our U20S.EGFP reporter cells bearing a single copy, constitutively expressed EGFP-PEST reporter gene. All three RGNs efficiently disrupted EGFP expression at the highest concentration of gRNA plasmid (250 ng) (Fig. 3E (top)).
  • RGNs for target sites #1 and #3 exhibited equivalent levels of disruption when lower amounts of gRNA-expressing plasmid were transfected whereas RGN activity at target site #2 dropped immediately when the amount of gRNA-expressing plasmid transfected was decreased (Fig. 3E (top)).
  • the amount of Cas9-encoding plasmid (range from 50 ng to 750 ng) transfected into our U20S.EGFP reporter cells was titrated EGFP disruption assayed. As shown in Fig. 3F (top), target site #1 tolerated a three-fold decrease in the amount of Cas9-encoding plasmid transfected without substantial loss of EGFP disruption activity. However, the activities of RGNs targeting target sites #2 and #3 decreased immediately with a three-fold reduction in the amount of Cas9 plasmid transfected (Fig. 3F (top)).
  • dCas9 is expressed together with a modified gRNA bearing extra RNA sequence on either or both of the 5' and/or 3' end of the gRNA that is bound by Csy4, an RNA-binding protein, as well as a fusion protein with Csy4 fused to the Fokl nuclease domain.
  • two dCas9 molecules would be targeted to adjacent DNA sequences by appropriate gRNAs and the Csy4-binding sequence on the two gRNA would interact with the Csy4-FokI nuclease domain fusion proteins.
  • the Fok nuclease domains would dimerize, resulting in introduction of a targeted double-stranded break in the DNA sequence
  • Csy4 RNA binding sites were attached to the 3 ' and 5 ' ends of a gRNA sequence and expressed with Cas9 in cells.
  • Multiplex gRNA encoding plasmids were constructed by ligating: 1) annealed oligos encoding the first target site, 2) phosphorylated annealed oligos encoding crRNA, tracrRNA, and Csy4-binding site, and 3) annealed oligos encoding the second targetsite, into a U6-Csy4site-gRNA plasmid backbone digested with BsmBI Type lis restriction enzyme.
  • the gRNAs can be encoded in multiplex gRNAs separated by Csy4 sites encoded on one transcript as well as individual gRNAs that have an additional Csy4 sequence.
  • the first N20 sequence represents the sequence complementary to one strand of the target genomic sequence
  • the second N20 sequence represents the sequence complementary to the other strand of the target genomic sequence.
  • a plasmid encoding the Csy4 recognition site containing gRNA was co- transfected with plasmid encoding Cas9 and Csy4 proteins separated by a '2A' peptide linkage.
  • the results showed that gRNAs with Csy4 sites fused to the 5' and 3 ' ends remained capable of directing Cas9-mediated cleavage in human cells using the U20S-EGFP disruption assay previously described.
  • Csy4 RNA binding sites can be attached to 3 ' end of a gRNA sequence and complexes of these Csy4 site- containing gRNAs with Cas9 remain functional in the cell (Figure 7A).
  • gRNA target sites that varied in the spacer length between the two sites (edge-to-edge distance between the N20NGG target sites).
  • orientation of the gRNA target sites were such that they either had their PAM sequences oriented "outward" from the spacer sequence in between or "inward” towards the spacer sequence in between.
  • gRNA/dCas9/FokI-Csy4 complexes to induce specific cleavage of DNA sequences that requires two gRNA binding sites, thereby increasing the specificity of the cleavage event.
  • Zinc Finger Targeter an engineered zinc finger/target site design tool. Nucleic Acids Res 35, W599-605. (2007).

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