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.

体细胞核转移（SCNT）可以将体细胞核重编程为全能状态。但是，在此过程中对3D染色质结构的重组仍知之甚少。使用低输入的Hi-C，我们揭示出，在SCNT期间，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细胞阶段显示出更强的拓扑关联域（TAD）。TAD在2单元阶段变得更弱，然后逐渐合并。隔室A / B在1细胞SCNT胚胎中明显弱，此后逐渐增强。到了8细胞阶段，体细胞染色质结构已很大程度上重置为胚胎模式。不料，我们发现粘着蛋白可抑制多能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），而供体细胞中的预消耗粘着蛋白可促进次要ZGA和SCNT。这些数据揭示了SCNT过程中3D染色质体系的多步重编程，并支持黏着蛋白在TAD形成和较小的ZGA抑制中的双重作用。