DNA binding specificities of the long zinc-finger recombination protein PRDM9
DNA binding specificities of the long zinc-finger recombination protein PRDM9
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DOI：
10.1186/gb-2013-14-4-r35
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发表时间：
2013-01-01
期刊：
影响因子：
12.3
通讯作者：
Petkov, Petko M.
中科院分区：
文献类型：
--
作者：
Billings, Timothy;Parvanov, Emil D.;Petkov, Petko M.
背景：减数分裂重组确保同源染色体的正确分离并产生遗传变异。在许多生物体中，重组发生在称为“热点”的有限位点，其在哺乳动物中的位置由 PR 结构域成员 9 (PRDM9)（一种长阵列锌指和染色质修饰蛋白）决定。确定控制 PRDM9 DNA 结合的规则是了解其功能的一个主要问题。结果：小鼠 PRDM9 蛋白变体以 PRDM9 和 DNA 单倍型特异的方式与热点 DNA 序列结合，并且体外结合与其体内生物活性平行。检查四个热点，其中三个由 Prdm9(Cst) 激活，一个由 Prdm9(Dom2) 激活，我们发现所有结合位点都需要 11 或 12 个连续手指的完整阵列，具体取决于等位基因，并且三个 Prdm9(Cst) 激活热点的结合位点之间几乎没有序列相似性。通过将每个核苷酸突变为其三个替代方案，测试了由 Prdm9(Cst) 激活的 Hlx1 结合位点中每个位置的结合特异性。结合位点上的 31 个位置在替代碱基支持结合的能力方面差异很大，这也暗示了与 DNA 磷酸主链的额外结合的作用。结论：这些结果提供了 PRDM9 与 DNA 结合的第一个详细图谱，并且据我们所知，是长锌指阵列对 DNA 结合的最详细分析，清楚地表明 PRDM9 以及可能的其他长阵列锌指蛋白的结合特异性异常复杂。
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.