Somatic cell nuclear transfer (SCNT) can reprogram a somatic nucleus to a totipotent state. However, the re-organization of 3D chromatin structure in this process remains poorly understood. 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 topologically associating domains (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 and become increasingly strengthened afterward. By the 8-cell stage, somatic chromatin architecture is largely reset to embryonic patterns. Unexpectedly, we found cohesin represses minor zygotic genome activation (ZGA) genes (2-cell-specific genes) in pluripotent and differentiated cells, and pre-depleting cohesin in donor cells facilitates minor ZGA and SCNT. 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（SCNT）可以将体细胞核重新编程为全能状态。然而，对于这一过程中 3D 染色质结构的重组仍然知之甚少。使用低输入 Hi-C，我们发现，在 SCNT 过程中，转移的核首先进入有丝分裂样状态（染色质过早凝结）。与受精胚胎不同，SCNT 胚胎在 1 细胞阶段表现出更强的拓扑关联域 (TAD)。 TAD 在 2 细胞阶段变得较弱，随后逐渐整合。 1 细胞 SCNT 胚胎中的 A/B 区室明显较弱，随后逐渐增强。到了 8 细胞阶段，体细胞染色质结构很大程度上重置为胚胎模式。出乎意料的是，我们发现粘连蛋白抑制多能细胞和分化细胞中的次要合子基因组激活（ZGA）基因（2细胞特异性基因），而预耗尽供体细胞中的粘连蛋白则有利于次要ZGA和SCNT。这些数据揭示了 SCNT 期间 3D 染色质结构的多步重编程，并支持粘连蛋白在 TAD 形成和轻微 ZGA 抑制中的双重作用。