RNA-guided targeting of genetic and epigenomic regulatory proteins to specific genomic loci

1. A method of increasing expression of a target gene in a mammalian cell, the method comprising contacting the mammalian cell in vitro with an expression vector comprising a promoter operably linked to a nucleic acid encoding a fusion protein comprising a catalytically inactive S. pyogenes CRISPR associated 9 (Cas9) protein linked to a heterologous functional domain, and one or more expression vectors comprising a promoter operably linked to nucleic acid sequences encoding one or more guideRNAs directed to a promoter of the target gene,

wherein the catalytically inactive Cas9 protein comprises mutations at D10 and H840, and the heterologous functional domain is a transcriptional activation domain,

wherein the contacted mammalian cell expresses the Cas9 fusion protein and the one or more guideRNAs such that the expressed Cas9 fusion protein is directed to the promoter of the target gene by the expressed one or more guideRNAs, and wherein the transcriptional activation domain mediates the increased expression.

2. A method of increasing expression of a target gene in a mammalian cell in vitro, the method comprising expressing in the mammalian cell a fusion protein comprising a catalytically inactive S. pyogenes Cas9 protein linked to a heterologous functional domain, and expressing one or more guideRNAs directed to the target gene,

wherein the catalytically inactive Cas9 protein comprises mutations at D10 and H840, and the heterologous functional domain is a transcriptional activation domain,

wherein the expressed Cas9 fusion protein is directed to the target gene by the one or more guideRNAs, and wherein the transcriptional activation domain mediates the increased expression.

3. The method of claim 2 , wherein the transcriptional activation domain is a transcriptional activation domain selected from the group consisting of VP64 and NF-κB p65.

4. The method of claim 2 , wherein the heterologous functional domain is linked to the N terminus or the C terminus of the catalytically inactive Cas9 protein, with an optional intervening linker, wherein the linker does not interfere with activity of the fusion protein.

5. The method of claim 2 , further comprising one or both of a nuclear localization sequence and one or more epitope tags on the N-terminus, the C-terminus, or in between the catalytically inactive Cas9 protein and the heterologous functional domain, optionally with one or more intervening linkers.

6. The method of claim 5 , wherein the one or more epitope tags is selected from the group consisting of c-myc, 6His, and FLAG tags.

7. The method of claim 2 , wherein expressing the fusion protein in the mammalian cell comprises contacting the mammalian cell with an expression vector comprising a promoter operably linked to a nucleic acid encoding the fusion protein.

8. The method of claim 2 , wherein expressing the one or more guideRNAs directed to the target gene in the mammalian cell comprises contacting the mammalian cell with one or more expression vectors comprising a promoter operably linked to nucleic acid sequences encoding the one or more guideRNAs directed to the target gene.

9. A method of increasing expression of a target gene in a mammalian cell in vitro, the method comprising expressing in the mammalian cell a fusion protein comprising a catalytically inactive S. pyogenes Cas9 protein linked to a transcriptional activation domain, and expressing one or more guideRNAs directed to the target gene,

wherein the catalytically inactive Cas9 protein comprises mutations at D10 and H840, and the transcriptional activation domain is an enzyme that modifies the methylation state of DNA, and

wherein the expressed Cas9 fusion protein is directed to the target gene by the one or more guideRNAs, wherein the transcriptional activation domain mediates the increased expression.

10. The method of claim 9 , wherein the transcriptional activation domain is linked to the N terminus or the C terminus of the catalytically inactive Cas9 protein, with an optional intervening linker, wherein the linker does not interfere with activity of the fusion protein.

11. The method of claim 9 , further comprising one or both of a nuclear localization sequence and one or more epitope tags on the N-terminus, the C-terminus, or in between the catalytically inactive Cas9 protein and the transcriptional activation domain, optionally with one or more intervening linkers.

12. The method of claim 11 , wherein the one or more epitope tags is selected from the group consisting of c-myc, 6His, and FLAG tags.

13. The method of claim 9 , wherein expressing the fusion protein in the mammalian cell comprises contacting the mammalian cell with an expression vector comprising a promoter operably linked to a nucleic acid encoding the fusion protein.

14. The method of claim 9 , wherein expressing the one or more guideRNAs directed to the target gene in the mammalian cell comprises contacting the mammalian cell with one or more expression vectors comprising a promoter operably linked to nucleic acid sequences encoding the one or more guideRNAs directed to the target gene.

15. A method of increasing expression of a target gene in a mammalian cell in vitro, the method comprising expressing in the mammalian cell a fusion protein comprising a catalytically inactive S. pyogenes Cas9 protein linked to a transcriptional activation domain, and expressing one or more guideRNAs directed to the target gene,

wherein the catalytically inactive Cas9 protein comprises mutations at D10 and H840, and the transcriptional activation domain is an enzyme that modifies histones, and

wherein the expressed Cas9 fusion protein is directed to the target gene by the one or more guideRNAs, wherein the transcriptional activation domain mediates the increased expression.

16. The method of claim 15 , wherein the transcriptional activation domain is linked to the N terminus or the C terminus of the catalytically inactive Cas9 protein, with an optional intervening linker, wherein the linker does not interfere with activity of the fusion protein.

17. The method of claim 15 , further comprising one or both of a nuclear localization sequence and one or more epitope tags on the N-terminus, the C-terminus, or in between the catalytically inactive Cas9 protein and the transcriptional activation domain, optionally with one or more intervening linkers.

18. The method of claim 17 , wherein the one or more epitope tags is selected from the group consisting of c-myc, 6His, and FLAG tags.

19. The method of claim 15 , wherein expressing the fusion protein in the mammalian cell comprises contacting the mammalian cell with an expression vector comprising a promoter operably linked to a nucleic acid encoding the fusion protein.

20. The method of claim 15 , wherein expressing the one or more guideRNAs directed to the target gene in the mammalian cell comprises contacting the mammalian cell with one or more expression vectors comprising a promoter operably linked to nucleic acid sequences encoding the one or more guideRNAs directed to the target gene.