Methods and compositions for targeted cleavage and recombination

A method of targeted mutation of a non-coding sequence in a region of interest in cellular chromatin in an isolated plant or mammalian cell containing a region of interest in cellular chromatin, the method comprising:

• (a) selecting first and second nucleotide sequences in the region of interest;
• (b) engineering first and second zinc finger binding domains to bind to the first and second nucleotide sequences;
• (c) expressing a first fusion protein in the isolated cell, the first fusion protein comprising the first engineered zinc finger binding domain and a first FokI cleavage half-domain;
• and
• (d) expressing a second fusion protein in the cell, the second fusion protein comprising the second zinc finger binding domain and a second FokI cleavage half-domain
• wherein the first and second fusion proteins cleave cellular chromatin and mutate the non-coding sequence in the region of interest and further wherein one of the cleavage half-domains comprises an alteration in amino acid 490 of the wild-type dimerization interface of the cleavage half-domain.