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. An isolated Staphylococcus aureus Cas9 (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 isolated protein of claim 1 , comprising one or more of the following mutations: Y211A, Y212A, W229, Y230A, R245A, T392A, N419A, Y651A, and/or R654A.
3. The isolated protein of claim 1 , comprising 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.
4. The isolated protein of claim 3 , comprising 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.
5. The isolated protein of claim 1 , further comprising 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; L788Y789; S790; R792; N804; Y868; K870; K878; K879; K881; T882; K886; Y897N888; A889; R901; K906; L909; N985; N986; R991; and/or R1015.
6. The isolated protein of claim 1 , further comprising 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).
7. The isolated protein of claim 1 , further comprising mutations that decrease nuclease activity said mutations at H557 or N580 and at D10, E477, D556, H701, or D704.
8. The isolated protein of claim 7 , 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.
9. The isolated protein 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.
10. A fusion protein comprising the isolated protein of claim 1 , 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 fusion protein of claim 10 , wherein the heterologous functional domain is a transcriptional activation domain.
12. The fusion protein of claim 11 , wherein the transcriptional activation domain is from VP64 or NF-KB p65.
13. The fusion protein of claim 10 , wherein the heterologous functional domain is a transcriptional silencer or transcriptional repression domain.
14. The fusion protein 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 fusion protein of claim 13 , wherein the transcriptional silencer is Heterochromatin Protein 1 (HP1).
16. The fusion protein of claim 15 , wherein the HP1 is HP1α or HP1β.
17. The fusion protein of claim 10 , wherein the heterologous functional domain is an enzyme that modifies the methylation state of DNA.
18. The fusion protein of claim 17 , wherein the enzyme that modifies the methylation state of DNA is a DNA methyltransferase (DNMT) or a TET protein.
19. The fusion protein of claim 18 , wherein the TET protein is TET1.
20. The fusion protein of claim 10 , wherein the heterologous functional domain is an enzyme that modifies a histone subunit.
21. The fusion protein 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 fusion protein of claim 10 , wherein the heterologous functional domain is a biological tether.
23. The fusion protein of claim 22 , wherein the biological tether is MS2, Csy4 or lambda N protein.
24. The fusion protein of claim 10 , wherein the heterologous functional domain is FokI.
25. An isolated nucleic acid encoding the protein of claim 1 .
26. A vector comprising the isolated nucleic acid of claim 25 , optionally operably linked to one or more regulatory domains.
27. A host cell comprising the nucleic acid of claim 25 .
28. A method of altering the genome or epigenome of a cell, the method comprising expressing in the cell or contacting the cell with the isolated protein of claim 1 and a guide RNA having a region complementary to a selected portion of the genome of the cell.
29. A method of altering the genome or epigenome of a cell, the method comprising expressing in the cell or contacting the cell with the isolated fusion protein of claim 10 and a guide RNA having a region complementary to a selected portion of the genome of the cell.
30. A method of altering a double stranded DNA (dsDNA) molecule, the method comprising contacting the dsDNA molecule with the isolated protein of claim 1 , and a guide RNA having a region complementary to a selected portion of the dsDNA molecule.
31. The method of claim 30 , wherein the dsDNA molecule is in vitro.
32. A method of altering a double stranded DNA D (dsDNA) molecule, the method comprising contacting the dsDNA molecule with the fusion protein of claim 10 , and a guide RNA having a region complementary to a selected portion of the dsDNA molecule.