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

Genome Biology

Petko M Petkov²  Kenneth Paigen²  Michael Walker²  Christopher L Baker²  Emil D Parvanov¹  Timothy Billings² 

[1] National Centre for Biomolecular Research and Department of Biology, Masaryk University, Brno 625 00, Czech Republic;Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA

关键词: zinc-finger proteins;    EMSA;    DNA binding;    PRDM9;    recombination hotspots;   

Others  :  866864
DOI  :  10.1186/gb-2013-14-4-r35

 received in 2013-02-25, accepted in 2013-04-24,  发布年份 2013

【 摘 要 】

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 PR domain member 9 (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

Mouse PRDM9 protein variants bind to hotspot DNA sequences in a manner that is specific for both PRDM9 and DNA haplotypes, and that in vitro binding parallels its in vivo biological activity. Examining four hotspots, three activated by Prdm9^Cst and one activated by Prdm9^Dom2, 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 Prdm9^Cst activated hotspots. The binding specificity of each position in the Hlx1 binding site, activated by Prdm9^Cst, 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 binding to DNA 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.

【 授权许可】

   
2013 Billings et al.; licensee BioMed Central Ltd.

【 图 表 】

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