Genomic and chromatin features shaping meiotic double-strand break formation and repair in mice

The SPO11-generated DNA double-strand breaks (DSBs) that initiate meiotic recombination occur non-randomly across genomes, but mechanisms shaping their distribution and repair remain incompletely understood. Here, we expand on recent studies of nucleotide-resolution DSB maps in mouse spermatocytes. We find that trimethylation of histone H3 lysine 36 around DSB hotspots is highly correlated, both spatially and quantitatively, with trimethylation of H3 lysine 4, consistent with coordinated formation and action of both PRDM9-dependent histone modifications. In contrast, the DSB-responsive kinase ATM contributes independently of PRDM9 to controlling hotspot activity, and combined action of ATM and PRDM9 can explain nearly two-thirds of the variation in DSB frequency between hotspots. DSBs were modestly underrepresented in most repetitive sequences such as segmental duplications and transposons. Nonetheless, numerous DSBs form within repetitive sequences in each meiosis and some classes of repeats are preferentially targeted. Implications of these findings are discussed for evolution of PRDM9 and its role in hybrid strain sterility in mice. Finally, we document the relationship between mouse strain-specific DNA sequence variants within PRDM9 recognition motifs and attendant differences in recombination outcomes. Our results provide further insights into the complex web of factors that influence meiotic recombination patterns.

介导减数分裂重组起始的、由SPO11产生的DNA双链断裂（DNA double-strand breaks, DSBs）在基因组中呈非随机分布，但其调控其分布与修复的分子机制尚未完全阐明。本研究拓展了近期针对小鼠精母细胞核苷酸分辨率DSB图谱的相关研究。我们发现，DSB热点区域周围的组蛋白H3赖氨酸36三甲基化，在空间分布与定量水平上均与组蛋白H3赖氨酸4三甲基化呈现高度相关性，这与PRDM9依赖的两类组蛋白修饰的协同形成与功能作用相一致。与之相对，响应DSB的激酶ATM可独立于PRDM9调控热点活性，且ATM与PRDM9的联合作用可解释热点间DSB频率差异的近三分之二。多数重复序列区域（如片段重复与转座子）的DSB发生频率略有偏低，但每个减数分裂周期中仍有大量DSB形成于重复序列内部，且部分重复序列家族存在靶向偏好性。本文讨论了上述发现对PRDM9进化的启示，以及其在小鼠杂交菌株不育中的作用。此外，我们还记录了PRDM9识别基序内的小鼠品系特异性DNA序列变异，及其伴随的重组结局差异。本研究结果进一步揭示了影响减数分裂重组模式的复杂调控网络。