Analysis of genome architecture during SCNT reveals a role of cohesin in repressing minor ZGA

Somatic cell nuclear transfer (SCNT) can reprogram a somatic nucleus to a totipotent state. However, the re-organization of three-dimensional chromatin structure in this process remains poorly understood. Here, using low-input Hi-C we revealed that during SCNT, the transferred nucleus first enters a mitotic-like state (premature chromatin condensation). Unlike fertilized embryos, SCNT embryos show stronger TADs at the 1-cell stage. TADs become weaker at the 2-cell stage, followed by gradual consolidation. Compartments A/B are markedly weak in 1-cell SCNT embryos, before becoming strengthened at the 2-cell stage and onward. Somatic chromatin compartments, TAD boundaries, and transcriptomes, with a few exceptions, are largely reset to embryonic patterns by the 8-cell stage. Unexpectedly, pre-depleting cohesin in donor cells facilitates minor zygotic genome activation (ZGA) and SCNT development. These data reveal multi-step reprogramming of 3D chromatin architecture during SCNT and support dual roles of cohesin in TAD formation and minor ZGA repression.体细胞核移植（Somatic cell nuclear transfer, SCNT）可将体细胞核重编程至全能性状态。然而，该过程中三维染色质结构的重组织机制仍未得到充分阐释。本研究通过低起始量Hi-C技术发现，在体细胞核移植过程中，供体核首先进入有丝分裂样状态（即早熟染色质凝集）。与受精胚胎相比，体细胞核移植胚胎在1细胞期的拓扑关联结构域（Topologically Associating Domains, TAD）信号更强；在2细胞期，TAD信号逐渐减弱，随后逐步趋于稳定整合。A/B区室在1细胞期的体细胞核移植胚胎中显著弱化，直至2细胞期及之后才得以强化。除少数例外情况外，体源性染色质区室、TAD边界及转录组在8细胞期已基本重编程为胚胎样模式。令人意外的是，在供体细胞中预先耗竭黏连蛋白（cohesin）可促进小合子基因组激活（minor zygotic genome activation, ZGA）以及体细胞核移植胚胎的发育。本研究数据揭示了体细胞核移植过程中三维染色质构象的多步重编程过程，并证实黏连蛋白在TAD形成与小合子基因组激活抑制中发挥双重功能。