Data_Sheet_2_Cataloging Human PRDM9 Allelic Variation Using Long-Read Sequencing Reveals PRDM9 Population Specificity and Two Distinct Groupings of Related Alleles.CSV

The PRDM9 protein determines sites of meiotic recombination in humans by directing meiotic DNA double-strand breaks to specific loci. Targeting specificity is encoded by a long array of C2H2 zinc fingers that bind to DNA. This zinc finger array is hypervariable, and the resulting alleles each have a potentially different DNA binding preference. The assessment of PRDM9 diversity is important for understanding the complexity of human population genetics, inheritance linkage patterns, and predisposition to genetic disease. Due to the repetitive nature of the PRDM9 zinc finger array, the large-scale sequencing of human PRDM9 is challenging. We, therefore, developed a long-read sequencing strategy to infer the diploid PRDM9 zinc finger array genotype in a high-throughput manner. From an unbiased study of PRDM9 allelic diversity in 720 individuals from seven human populations, we detected 69 PRDM9 alleles. Several alleles differ in frequency among human populations, and 32 alleles had not been identified by previous studies, which were heavily biased to European populations. PRDM9 alleles are distinguished by their DNA binding site preferences and fall into two major categories related to the most common PRDM9-A and PRDM9-C alleles. We also found that it is likely that inter-conversion between allele types is rare. By mapping meiotic double-strand breaks (DSBs) in the testis, we found that small variations in PRDM9 can substantially alter the meiotic recombination landscape, demonstrating that minor PRDM9 variants may play an under-appreciated role in shaping patterns of human recombination. In summary, our data greatly expands knowledge of PRDM9 diversity in humans.

PRDM9蛋白（PRDM9 protein）可通过引导减数分裂DNA双链断裂（DNA double-strand breaks，DSBs）至特定基因座，决定人类减数分裂重组（meiotic recombination）的发生位点。其靶向特异性由结合DNA的长阵列C2H2锌指（C2H2 zinc fingers）编码。该锌指阵列具有高度可变性，由此产生的等位基因（alleles）各自具备潜在不同的DNA结合偏好。对PRDM9多样性的评估，对于理解人类群体遗传学（population genetics）、遗传连锁模式以及遗传病易感性的复杂机制具有重要意义。鉴于PRDM9锌指阵列的重复序列特性，大规模测序人类PRDM9基因仍颇具挑战。为此，我们开发了长读长测序（long-read sequencing）策略，以高通量（high-throughput）方式推断二倍体PRDM9锌指阵列基因型。我们对来自7个人群的720名个体开展了PRDM9等位基因多样性的无偏研究，共检测到69个PRDM9等位基因。多个等位基因在不同人群中的频率存在显著差异，其中32个等位基因未被此前以欧洲人群为主要研究对象的相关研究鉴定出来。PRDM9等位基因以其DNA结合位点偏好性作为区分特征，可分为两大类别，与最常见的PRDM9-A和PRDM9-C等位基因相关。我们还发现，不同等位基因类型之间的相互转换可能较为罕见。通过在睾丸组织中绘制减数分裂DSBs的图谱，我们发现PRDM9的微小变异可显著改变减数分裂重组景观，这表明少量PRDM9变异在塑造人类重组模式中可能发挥了未被充分重视的作用。综上，本研究的数据极大拓展了学界对人类PRDM9多样性的认知。