Methods and compostions for targeted genomic deletion

A method for creating a targeted deletion of specific length and specific borders in a region of interest in a genomic locus in a host cell, the method comprising

• introducing first and second nucleases and a donor polynucleotide into the host cell, wherein
• (i) the first and second nucleases each comprise a 5′DNA-binding domain and a 3′ DNA binding domain and two catalytic domains;
• (ii) the first nuclease binds to target sequences 5 to the target sequences in the region of interest bound by the second nuclease;
• (iii) the 5′ DNA-binding domain binds to a target sequence 5′ to the target sequence bound by the 3′ DNA-binding domain,
• (iv);
• the first nuclease binds to target sequences 5′ to the target sequences in the region of interest and the second nuclease binds to target sequences 3′ in the region of interest;
• (v) the donor polynucleotide comprises the target sequences for the 5′ DNA binding domain of the first nuclease and target sequences for the 3′ DNA binding domain of the second nuclease and regions of homology to the genomic locus and further wherein the donor polynucleotide includes a deletion relative to the target sequence of specific length and specific borders, wherein the deletion extends between the target sequence 5′ DNA binding domain in of the first nuclease and target sequence for the 3′ DNA binding domain of the second nuclease;
• and
• (vi) the donor polynucleotide is introduced into the genomic locus such that a targeted deletion of specific length and specific borders is generated in the genomic locus.