Engineered CRISPR-Cas9 nucleases
Engineered CRISPR-Cas9 nucleases with improved specificity and their use in genomic engineering, epigenomic engineering, genome targeting, and genome editing.
1. A Staphylococcus aureus Cas9 (SaCas9):single guide RNA (sgRNA) complex comprising a SaCas9 protein that is at least 95% identical to SEQ ID NO: 2, with mutations at one, two, three, four, five, six, or more of the following positions: Y211, Y212, W229, Y230, R245, T392, N419, Y651, or R654.
2. The SaCas9:sgRNA complex of claim 1 , wherein the SaCas9 protein is fused to one or more of a nuclear localization sequence, cell penetrating peptide sequence, and/or affinity tag.
3. The SaCas9:sgRNA complex of claim 1 , wherein the SaCas9 protein comprises one or more of the following mutations: Y211A, Y212A, W229, Y230A, R245A, T392A, N419A, Y651A, and/or R654A.
4. The SaCas9:sgRNA complex of claim 1 , wherein the SaCas9 protein comprises mutations at N419 and/or R654, and optionally one, two, three, four or more of the additional mutations at Y211, Y212, W229, Y230, R245, T392, and Y651.
5. The SaCas9:sgRNA complex of claim 4 , wherein the SaCas9 protein comprises mutations at N419A/R654A, Y211A/R654A, Y211A/Y212A, Y211A/Y230A, Y211A/R245A, Y212A/Y230A, Y212A/R245A, Y230A/R245A, W229A/R654A, Y211A/Y212A/Y230A, Y211A/Y212A/R245A, Y211A/Y212A/Y651A, Y211A/Y230A/R245A, Y211A/Y230A/Y651A, Y211A/R245A/Y651A, Y211A/R245A/R654A, Y211A/R245A/N419A, Y211A/N419A/R654A, Y212A/Y230A/R245A, Y212A/Y230A/Y651A, Y212A/R245A/Y651A, Y230A/R245A/Y651A, R245A/N419A/R654A, T392A/N419A/R654A, R245A/T392A/N419A/R654A, Y211A/R245A/N419A/R654A, W229A/R245A/N419A/R654A, Y211A/R245A/T392A/N419A/R654A, or Y211A/W229A/R245A/N419A/R654A.
6. The SaCas9:sgRNA complex of claim 1 , wherein the SaCas9 protein further comprises mutations at N44; R45; R51; R55; K57; R59; R60; R61; H111; K114; R116; V164; R165; N169; R208; R209; T238; Y239; K248; Y256; R314; N394; Q414; L446; Q488A; N492A; Q495A; R497A; N498A; R499; Q500; K518; K523; K525; H557; R561; K572; R634; G655; N658; S662; N667; R686; K692; R694; H700; K751; D786; T787; L788; Y789; S790; R792; N804; Y868; K870; K878; K879; K881; T882; K886; N888, A889, Y897, R901; K906; L909; N985; N986; R991; and/or R1015.
7. The SaCas9:sgRNA complex of claim 1 , wherein the SaCas9 protein further comprises one or more of the following mutations: E782K; K929R; N968K; R1015H; E782K/N968K/R1015H (KKH variant); E782K/K929R/R1015H (KRH variant); or E782K/K929R/N968K/R1015H (KRLKH variant).
8. The SaCas9:sgRNA complex of claim 1 , wherein the SaCas9 protein further comprises mutations that decrease nuclease activity said mutations at H557 or N580 and at D10, E477, D556, H701, or D704.
9. The SaCas9:sgRNA complex of claim 8 , wherein the mutations at D10 are D10A or D10N, the mutation at D556 is D556A, the mutations at H557 are H557A, H557N, or H557Y and the mutation at N580 is N580A.
10. The SaCas9:sgRNA complex of claim 1 , wherein the SaCas9 protein is fused to a heterologous functional domain, with an optional intervening linker, wherein the linker does not interfere with activity of the fusion protein.
11. The SaCas9:sgRNA complex of claim 10 , wherein the heterologous functional domain is a transcriptional activation domain.
12. The SaCas9:sgRNA complex of claim 11 , wherein the transcriptional activation domain is from VP64 or NF-KB p65.
13. The SaCas9:sgRNA complex of claim 10 , wherein the heterologous functional domain is a transcriptional silencer or transcriptional repression domain.
14. The SaCas9:sgRNA complex of claim 13 , wherein the transcriptional repression domain is a Krueppel-associated box (KRAB) domain, ERF repressor domain (ERD), or mSin3A interaction domain (SID).
15. The SaCas9:sgRNA complex of claim 13 , wherein the transcriptional silencer is Heterochromatin Protein 1 (HP1).
16. The SaCas9:sgRNA complex of claim 15 , wherein the HP1 is HP1α or HP1β.
17. The SaCas9:sgRNA complex of claim 10 , wherein the heterologous functional domain is an enzyme that modifies the methylation state of DNA.
18. The SaCas9:sgRNA complex of claim 17 , wherein the enzyme that modifies the methylation state of DNA is a DNA methyltransferase (DNMT) or a TET protein.
19. The SaCas9:sgRNA complex of claim 18 , wherein the TET protein is TET1.
20. The SaCas9:sgRNA complex of claim 10 , wherein the heterologous functional domain is an enzyme that modifies a histone subunit.
21. The SaCas9:sgRNA complex of claim 20 , wherein the enzyme that modifies a histone subunit is a histone acetyltransferase (HAT), histone deacetylase (HDAC), histone methyltransferase (HMT), or histone demethylase.
22. The SaCas9:sgRNA complex of claim 10 , wherein the heterologous functional domain is a biological tether.
23. The SaCas9:sgRNA complex of claim 22 , wherein the biological tether is MS2, Csy4 or lambda N protein.
24. The SaCas9:sgRNA complex of claim 10 , wherein the heterologous functional domain is FokI.
25. A vector encoding the SaCas9 protein and the sgRNA of claim 1 .
26. A host cell comprising the nucleic acid of claim 25 .
27. A method of altering the genome of a cell, the method comprising expressing in the cell or contacting the cell with the SaCas9:sgRNA complex of claim 1 , wherein the sgRNA has a region complementary to a selected portion of the genome of the cell, whereby the genome of the cell is altered.
28. The method of claim 27 , wherein the SaCas9 protein comprises one or more of a nuclear localization sequence, cell penetrating sequence, and/or affinity tag.
29. A method of altering a double stranded DNA (dsDNA) molecule, the method comprising contacting the dsDNA molecule with the SaCas9:sgRNA complex of claim 1 , wherein the sgRNA has a region complementary to a selected portion of the dsDNA molecule, whereby the dsDNA molecule is altered.