Compositions and methods for promoting homology directed repair

Abstract

This application provides improved methods of genome editing. Cas9 molecules can be used to create a break in a genomic region of interest. To increase the likelihood that the break is repaired by HDR (homology-directed repair), the cell can be contacted with molecules that bring a template nucleic acid in close proximity to the break, under conditions that allow the cell to repair the break using the template nucleic acid.

1 . A Cas9 fusion molecule comprising:
 a Cas9 molecule linked to   a template binding domain.   
     
     
         2 . The Cas9 fusion molecule of  claim 1 , wherein the template binding domain comprises a specific affinity for a template binding domain partner. 
     
     
         3 .- 9 . (canceled) 
     
     
         10 . The Cas9 fusion molecule of  claim 1 , wherein the Cas9 molecule is covalently or non-covalently linked to the template binding domain. 
     
     
         11 .- 17 . (canceled) 
     
     
         18 . The Cas9 fusion molecule of  claim 1 , wherein said Cas9 fusion molecule comprises at least two template binding domains. 
     
     
         19 . The Cas9 fusion molecule of  claim 1 , wherein the template binding domain comprises a protein, a nucleic acid, or a small molecule. 
     
     
         20 . (canceled) 
     
     
         21 . The Cas9 fusion molecule of  claim 1 , wherein the template binding domain comprises a protein, and wherein the protein comprises a DNA binding domain. 
     
     
         22 . The Cas9 fusion molecule of  claim 21 , wherein the protein comprises a repressor protein, or a fragment of a repressor protein. 
     
     
         23 . The Cas9 fusion molecule of  claim 22 , wherein the repressor protein, or the fragment of the repressor protein, is a TetR repressor, or a fragment of the TetR repressor; a LacI repressor, or a fragment of the LacI repressor; a Gal4 repressor, or a fragment of the Gal4 repressor; or a repressor protein C1, or a fragment of the repressor protein C1. 
     
     
         24 . The Cas9 fusion molecule of  claim 1 , further comprising a linker between the Cas9 molecule and the template binding domain. 
     
     
         25 .- 34 . (canceled) 
     
     
         35 . The Cas9 fusion molecule of  claim 1 , wherein the Cas9 molecule is an eaCas9 molecule or an eiCas9 molecule. 
     
     
         36 .- 51 . (canceled) 
     
     
         52 . A Cas9 system comprising a Cas9 fusion molecule of  claim 1  and a nucleic acid template system comprising:
 a template binding domain partner and 
 a template nucleic acid. 
 
     
     
         53 . The Cas9 system of  claim 52 , wherein the template binding domain of the Cas9 fusion molecule is bound to the template binding domain partner. 
     
     
         54 . The Cas9 system of  claim 53 , wherein the template binding domain of the Cas9 fusion molecule is covalently or non-covalently bound to the template binding domain partner. 
     
     
         55 . (canceled) 
     
     
         56 . The Cas9 system of  claim 52 , wherein the template binding domain partner is linked to the template nucleic acid. 
     
     
         57 .- 65 . (canceled) 
     
     
         66 . The Cas9 system of  claim 52 , wherein the template binding domain comprises a protein, a small molecule, or a nucleic acid, and wherein the template binding domain partner comprises a small molecule, a protein, or a nucleic acid. 
     
     
         67 .- 75 . (canceled) 
     
     
         76 . The Cas9 system of  claim 52 , wherein the template binding domain partner is a DNA sequence recognized by a DNA binding protein. 
     
     
         77 . The Cas9 system of  claim 76 , wherein the DNA sequence recognized by the DNA binding protein is selected from a Tet-O sequence, a Lac operon O1 sequence, a UAS sequence, or an Operator L and R sequence. 
     
     
         78 . (canceled) 
     
     
         79 . The Cas9 system of  claim 76 , wherein the DNA binding protein comprises a TetR repressor, or a fragment of the TetR repressor, and the DNA comprises at least one Tet-O sequence. 
     
     
         80 .- 93 . (canceled) 
     
     
         94 . The Cas9 system of  claim 52 , wherein the nucleic acid template system comprises a double stranded nucleic acid sequence or a single stranded nucleic acid sequence. 
     
     
         95 .- 106 . (canceled) 
     
     
         107 . The Cas9 system of  claim 52 , wherein the template nucleic acid comprises about 50-500 nucleotides of homology with a target nucleic acid. 
     
     
         108 .- 114 . (canceled) 
     
     
         115 . The Cas9 system of  claim 52 , further comprising a gRNA. 
     
     
         116 .- 117 . (canceled) 
     
     
         118 . A cell, or a population of cells, comprising the Cas9 system of  claim 52 . 
     
     
         119 . A cell, or a population of cells, comprising the Cas9 fusion molecule of  claim 1 . 
     
     
         120 . A nucleic acid encoding the Cas9 fusion molecule of  claim 1 . 
     
     
         121 . A vector comprising a nucleic acid of  claim 120 . 
     
     
         122 .- 123 . (canceled) 
     
     
         124 . A method of altering a nucleic acid at a target position in a cell, or a population of cells, the method comprising contacting the cell with the Cas9 system of  claim 115 ,
 wherein the gRNA molecule and Cas9 fusion molecule interact with the nucleic acid, resulting in a cleavage event, wherein the cleavage event is repaired by at least one DNA repair pathway, and   wherein the sequence of the nucleic acid after the cleavage event is different than the sequence of the nucleic acid prior to the cleavage event,   thereby altering the nucleic acid at the target position in the cell, or in the population of cells.   
     
     
         125 . The method of  claim 124 , further comprising contacting the cell, or the population of cells, with a second gRNA molecule,
 wherein the second gRNA molecule and the Cas9 fusion molecule interact with the nucleic acid, resulting in a second cleavage event.   
     
     
         126 .- 145 . (canceled) 
     
     
         146 . The method of  claim 125 , wherein the cell, or population of cells, is from a subject suffering from a disease or disorder selected from the group consisting of a blood disease, an immune disease, a neurological disease, a cancer, an infectious disease, a genetic disease, a disorder caused by aberrant mtDNA, a metabolic disease, a disorder caused by aberrant cell cycle, a disorder caused by aberrant angiogenesis, a disorder cause by aberrant DNA damage repair, or a pain disorder. 
     
     
         147 . (canceled) 
     
     
         148 . The method of  claim 125 , wherein the cell, or population of cells, is from a subject having at least one mutation at the target position. 
     
     
         149 .- 156 . (canceled) 
     
     
         157 . A cell, or a population of cells, altered by the method of  claim 125 . 
     
     
         158 . A pharmaceutical composition comprising the cell, or the population of cells, of  claim 157 . 
     
     
         159 . A pharmaceutical composition comprising the Cas9 system of  claim 115 . 
     
     
         160 . (canceled) 
     
     
         161 . A method of treating a subject suffering from a disease or disorder, the method comprising contacting a cell, or a population of cells, from the subject with the Cas9 system of  claim 115 ,
 wherein the gRNA molecule and the Cas9 fusion molecule interact with a nucleic acid at a target position, resulting in a cleavage event,   wherein the cleavage event is repaired by at least one DNA repair pathway, and   wherein the sequence of the nucleic acid after the cleavage event is different than the sequence of the nucleic acid prior to the cleavage event,   thereby treating the subject suffering from the disease or disorder.   
     
     
         162 .- 164 . (canceled)