Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria.
Genome Res. 2023 Dec 27;33(12):2094-2107. doi: 10.1101/gr.277865.123.
Paternal genomes are compacted during spermiogenesis and decompacted following fertilization. These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog , whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically associating domains (TADs) at the mid-blastula transition (MBT). Why cohesin assembles TADs only at this stage is unknown. We first analyzed genome architecture in frog sperm and compared it to human and mouse. Our results indicate that sperm genome organization is conserved between frogs and humans and occurs without formation of TADs. TADs can be detected in mouse sperm samples, as reported, but these structures might originate from somatic chromatin contaminations. We therefore discuss the possibility that the absence of TADs might be a general feature of vertebrate sperm. To analyze sperm genome remodeling upon fertilization, we reconstituted male pronuclei in egg extracts. In pronuclei, chromatin compartmentalization increases, but cohesin does not accumulate at CTCF sites and assemble TADs. However, if pronuclei are formed in the presence of exogenous CTCF, CTCF binds to its consensus sites, and cohesin accumulates at these and forms short-range chromatin loops, which are preferentially anchored at CTCF's N terminus. These results indicate that TADs are only assembled at MBT because before this stage CTCF sites are not occupied and cohesin only forms short-range chromatin loops.
父系基因组在精子发生过程中被压缩，在受精后解压缩。这些过程对于遗传至关重要，但尚未完全理解。我们在青蛙中分析了这些过程，其精子可以在体外的卵提取物中组装成功能性核。在这种提取物中，黏连蛋白将 DNA 挤出成环，但在体内，黏连蛋白仅在中胚层转变（MBT）时组装拓扑关联域（TAD）。为什么黏连蛋白仅在这个阶段组装 TAD 尚不清楚。我们首先分析了青蛙精子中的基因组结构，并将其与人类和小鼠进行了比较。我们的结果表明，青蛙和人类之间的精子基因组组织是保守的，并且在不形成 TAD 的情况下发生。正如报道的那样，可以在小鼠精子样本中检测到 TAD，但这些结构可能来自体细胞染色质污染。因此，我们讨论了 TAD 缺失可能是脊椎动物精子的一般特征的可能性。为了分析受精后精子基因组重塑，我们在卵提取物中重建了雄性核。在核中，染色质区室化增加，但黏连蛋白不会在 CTCF 位点积累并组装 TAD。然而，如果在存在外源 CTCF 的情况下形成核，则 CTCF 结合到其保守位点，并且黏连蛋白在这些位点积累并形成短程染色质环，这些环优先锚定在 CTCF 的 N 端。这些结果表明，TAD 仅在 MBT 时组装，因为在此阶段之前，CTCF 位点未被占据，并且黏连蛋白仅形成短程染色质环。
