DNA binding specificities of the long zinc finger recombination protein PRDM9.

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Genome Biol 2013 Apr 24; 14(4):R35




BACKGROUND: Meiotic recombination ensures proper segregation of homologous chromosomes and creates genetic variation. In many organisms recombination occurs at limited sites, termed hotspots, whose positions in mammals are determined by PRDM9, a long array zinc finger and chromatin modifier protein. Determining the rules governing the DNA binding of PRDM9 is a major issue in understanding how it functions. RESULTS: We show that mouse PRDM9 protein variants bind hotspot DNA sequences in a manner that is specific for both PRDM9 and DNA haplotype and that in vitro binding parallels in vivo biological activity. Examining four hotspots, three activated by Prdm9Cst and one activated by Prdm9Dom2, we found that all binding sites required the full array of 11 or 12 contiguous fingers, depending on the allele, and that there was little sequence similarity between the binding sites of the three Prdm9Cst activated hotspots. The binding specificity of each position in the Hlx1 binding site, activated by Prdm9Cst, was tested by mutating each nucleotide to its three alternatives. The 31 positions along the binding site varied considerably in the ability of alternative bases to support binding, which also implicates a role for additional binding to the DNA phosphate backbone. CONCLUSIONS: These results, which provide the first detailed mapping of PRDM9-DNA binding and, to our knowledge, the most detailed analysis yet of DNA binding by a long zinc finger array, make clear that the binding specificities of PRDM9, and possibly other long array zinc finger proteins, are unusually complex. Genome Biol 2013 Apr 24; 14(4):R35