A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis.
A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis.
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DOI：
10.7554/elife.28383
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发表时间：
2017-10-26
期刊：
影响因子：
7.7
通讯作者：
Myers SR
中科院分区：
文献类型：
--
作者：
Altemose N;Noor N;Bitoun E;Tumian A;Imbeault M;Chapman JR;Aricescu AR;Myers SR
PRDM 9结合定位人类和小鼠中几乎所有的减数分裂重组位点。然而，大多数PRDM 9结合的基因座不会成为重组热点。为了探索影响结合和后续重组结果的因素，我们在转染的人细胞系中绘制了人PRDM 9结合位点，并测量了PRDM 9诱导的组蛋白修饰。这些数据揭示了PRDM 9的不同DNA结合模式。我们还发现，人PRDM 9经常结合启动子，尽管它们的重组率低，它可以激活包括CTCFL和VCX在内的少数基因的表达。此外，我们确定了特定的序列基序，预测一致的，本地化的减数分裂重组抑制周围的一个子集的PRDM 9结合位点。这些基序与KRAB-ZNF蛋白结合、TRIM 28募集和特异性组蛋白修饰密切相关。最后，我们证明，除了结合DNA，PRDM 9的锌指也介导其多聚化，我们表明，一对高度分歧的等位基因优先形成同源多聚体。人类细胞的每个染色体有两个副本：一个来自母亲，一个来自父亲。当细胞分裂形成性细胞时，如精子或卵细胞，母亲和父亲的染色体并排排列，并交换了一些DNA。这个过程被称为基因重组，创造了不同版本的基因，并确保我们都是独特的-或遗传多样性。脱水是一个复杂的过程，主要由一种称为PRDM 9的蛋白质控制。该蛋白质在染色体上的特定位点结合DNA，并指导其他蛋白质在附近进行重组。然而，并非所有的PRDM 9的结合位点都是已知的，并且并非所有PRDM 9结合的区域都经历重组。直到现在，人们还不明白为什么在精细尺度上会出现这种情况。为了进一步研究这一点，Altemose等人在实验室培养的人肾细胞中激活了PRDM 9的人类版本。结果表明，PRDM 9通常结合在基因的起始位点附近，尽管这些区域在人类中很少发生重组。当PRDM 9结合在这些位点附近时，它有时会打开基因，这表明它也可能有助于调节基因的活性。此外，一组特定的DNA结合蛋白，称为KRAB-ZNF蛋白，似乎在它们结合的任何地方都抑制重组，这解释了为什么一些PRDM 9结合位点不重组。最后，Altemose等人发现PRDM 9与DNA结合的部分也可以与PRDM 9蛋白的其他拷贝结合。这种自我结合的能力可能在重组过程中将母本和父本染色体在正确的位点结合在一起方面发挥作用。总之，这些结果为重组过程提供了新的线索，重组过程是新物种形成的驱动力，也是繁殖力的关键。下一步将是在生殖器官组织中进一步研究这些结果。这将使我们更好地理解塑造人类进化的力量。
PRDM9 binding localizes almost all meiotic recombination sites in humans and mice. However, most PRDM9-bound loci do not become recombination hotspots. To explore factors that affect binding and subsequent recombination outcomes, we mapped human PRDM9 binding sites in a transfected human cell line and measured PRDM9-induced histone modifications. These data reveal varied DNA-binding modalities of PRDM9. We also find that human PRDM9 frequently binds promoters, despite their low recombination rates, and it can activate expression of a small number of genes including CTCFL and VCX. Furthermore, we identify specific sequence motifs that predict consistent, localized meiotic recombination suppression around a subset of PRDM9 binding sites. These motifs strongly associate with KRAB-ZNF protein binding, TRIM28 recruitment, and specific histone modifications. Finally, we demonstrate that, in addition to binding DNA, PRDM9's zinc fingers also mediate its multimerization, and we show that a pair of highly diverged alleles preferentially form homo-multimers. Human cells have two copies of each chromosome: one from the mother, and one from the father. When cells divide to form sex cells, such as sperm or egg cells, the maternal and paternal chromosomes line up next to each other and swap some of their DNA. This process, known as genetic recombination, creates different versions of genes and ensures that we are all unique – or genetically diverse. Recombination is a complex process that is largely controlled by a protein called PRDM9. This protein binds DNA at particular spots on the chromosome and directs other proteins to carry out recombination nearby. However, not all of PRDM9’s binding sites are known, and not all regions that PRDM9 binds to undergo recombination. Until now, it was not understood why this is the case at fine scales. To investigate this further, Altemose et al. activated the human version of PRDM9 in human kidney cells grown in the laboratory. The results showed that PRDM9 often bound near the start sites of genes, although these regions rarely undergo recombination in humans. When PRDM9 bound near these sites, it sometimes turned the gene on, which suggests that it may also help to regulate the activity of genes. Moreover, a specific group of DNA-binding proteins, called KRAB-ZNF proteins, appear to suppress recombination wherever they bind, which explains why some PRDM9 binding sites do not recombine. Lastly, Altemose et al. discovered that the part of PRDM9 that binds to DNA can also bind to other copies of PRDM9 proteins. This self-binding ability might play a role in bringing together the maternal and paternal chromosomes at the correct spots during recombination. Together, these results shed new light on the recombination process, which is a driving force in the formation of new species and essential for fertility. A next step will be to study these results further in tissues of the reproductive organs. This will provide a better understanding of the forces that shape human evolution.