RNA-Guided Transcriptional Regulation

Abstract

Methods of modulating expression of a target nucleic acid in a cell are provided including introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to DNA, wherein the DNA includes the target nucleic acid, introducing into the cell a second foreign nucleic acid encoding a nuclease-null Cas9 protein that binds to the DNA and is guided by the one or more RNAs, introducing into the cell a third foreign nucleic acid encoding a transcriptional regulator protein or domain, wherein the one or more RNAs, the nuclease-null Cas9 protein, and the transcriptional regulator protein or domain are expressed, wherein the one or more RNAs, the nuclease-null Cas9 protein and the transcriptional regulator protein or domain co-localize to the DNA and wherein the transcriptional regulator protein or domain regulates expression of the target nucleic acid.

1 . A method of inserting a donor nucleic acid sequence into a cell using homologous recombination comprising
 providing to the cell two guide RNAs with each guide RNA having a spacer sequence, a tracr mate sequence and a tracr sequence, and with a portion of the tracr sequence being hybridized to the tracr mate sequence and with the tracr mate sequence and the tracr sequence being linked by a linker nucleic acid sequence and with each spacer sequence being complementary to an adjacent site in a DNA target nucleic acid,   providing to the cell a donor nucleic acid sequence,   providing to the cell a Cas9 protein nickase, and   wherein each of the two guide RNAs co-localize with the Cas9 protein nickase to the DNA target nucleic acid resulting in an offset nick with 5′-overhangs or 3′-overhangs, and   wherein the donor nucleic acid sequence is inserted into the target nucleic acid at the offset nick using homologous recombination.   
     
     
         2 . The method of  claim 1   wherein the two guide RNAs are provided to the cell by introducing into the cell a first foreign nucleic acid encoding the two guide RNAs,   wherein the Cas9 protein nickase is provided to the cell by introducing into the cell a second foreign nucleic acid encoding the Cas9 protein, and   wherein the two guide RNAs and the Cas9 protein nickase are expressed.   
     
     
         3 .- 11 . (canceled) 
     
     
         12 . The method of  claim 1  wherein the target nucleic acid is genomic DNA, mitochondrial DNA, viral DNA or exogenous DNA. 
     
     
         13 .- 24 . (canceled) 
     
     
         25 . The method of  claim 1  wherein the tracr sequence is between 90 to 500 nucleotides. 
     
     
         26 . The method of  claim 1  wherein the tracr sequence is between 90 to 200 nucleotides. 
     
     
         27 . The method of  claim 1  wherein the tracr sequence is between 100 to 200 nucleotides. 
     
     
         28 . A method of altering a target nucleic acid in a cell comprising
 providing to the cell two or more RNAs with each RNA being complementary to an adjacent site in the target nucleic acid,   providing to the cell a Cas9 protein nickase and being guided by the two or more RNAs, and   wherein the two or more RNAs and the Cas9 protein nickase co-localize to the DNA target nucleic acid and nick the target nucleic acid resulting in two or more adjacent nicks.   
     
     
         29 . The method of  claim 28   wherein the two or more RNAs are provided to the cell by introducing into the cell a first foreign nucleic acid encoding the two or more RNAs,   wherein the Cas9 protein nickase is provided to the cell by introducing into the cell a second foreign nucleic acid encoding the Cas9 protein, and   wherein the two or more RNAs and the Cas9 protein nickase are expressed and wherein the Cas9 protein nickase co-localizes with the two or more RNAs to the target nucleic acid and nicks the DNA target nucleic acid resulting in two or more adjacent nicks.   
     
     
         30 . The method of  claim 28  wherein the two or more adjacent nicks are on the same strand of the double stranded DNA. 
     
     
         31 . The method of  claim 28  wherein the two or more adjacent nicks are on the same strand of the double stranded DNA and result in homologous recombination. 
     
     
         32 . The method of  claim 28  wherein the two or more adjacent nicks are on different strands of the double stranded DNA. 
     
     
         33 . The method of  claim 28  wherein the two or more adjacent nicks are on different strands of the double stranded DNA and create double stranded breaks. 
     
     
         34 . The method of  claim 28  wherein the two or more adjacent nicks are on different strands of the double stranded DNA and create double stranded breaks resulting in nonhomologous end joining. 
     
     
         35 . The method of  claim 28  wherein the two or more adjacent nicks are on different strands of the double stranded DNA and are offset with respect to one another. 
     
     
         36 . The method of  claim 28  wherein the two or more adjacent nicks are on different strands of the double stranded DNA and are offset with respect to one another and create double stranded breaks. 
     
     
         37 . The method of  claim 28  wherein the two or more adjacent nicks are on different strands of the double stranded DNA and are offset with respect to one another and create double stranded breaks resulting in nonhomologous end joining. 
     
     
         38 . The method of  claim 28  further including introducing into the cell a third foreign nucleic acid encoding a donor nucleic acid sequence wherein the two or more nicks results in homologous recombination of the target nucleic acid with the donor nucleic acid sequence. 
     
     
         39 . The method of  claim 28  wherein the target nucleic acid is genomic DNA, mitochondrial DNA, viral DNA or exogenous DNA.