Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA

Abstract

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. 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 1cell 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.

Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription

“…By contrast, switched compartment regions tend to have intermediate gene density [29]. We now confirmed such results in additional mouse cells (MEF vs. cumulus cells [29,30]) and human cells (hESC vs trophectoderm [31]) ( Fig. 9d).…”

“…b Hi-C heatmap shown the compartmentalization of the C19Q region in EpiGo-KRAB (dCas9) cells. All the data processing and display are the same as a have the highest and lowest gene densities respectively [29]. By contrast, switched compartment regions tend to have intermediate gene density [29].…”

Rebooting the Epigenomes during Mammalian Early Embryogenesis

“…Such relaxed chromatin in early embryos is also conserved among fly, human ( Chen et al., 2019a ; Hug et al., 2017 ), and fish ( Nakamura et al., 2018 ; Kaaij et al., 2018 ). Similar relaxed chromatin organization was also found in SCNT mouse embryos, although at a slightly late stage (2-cell) ( Chen et al., 2020 ; Zhang et al., 2020 ). This extraordinary conservation during evolution raises a possibility that such relaxed chromatin states may very likely have important functions.…”

“…This extraordinary conservation during evolution raises a possibility that such relaxed chromatin states may very likely have important functions. Interestingly, our recent study revealed that cohesin, the core architectural protein required for TADs ( Rowley and Corces, 2018 ), can repress minor ZGA genes such as Zscan4 in mESCs and differentiated neurons, and its removal facilitates minor ZGA and promotes SCNT development ( Zhang et al., 2020 ). It remains to be determined whether this is also true in fertilized mouse embryos.…”

Relaxed 3D genome conformation facilitates the pluripotent to totipotent state transition in embryonic stem cells

“…Therefore, disruption of TAD boundary loops in ESCs may facilitate the contacts between 2C enhancers that are likely sporadically activated in ESCs and the promoters of nearby 2C genes, thus promoting their expression, which in turn fully activates the 2C-like transcriptional program. Consistently, a recent study showed that cohesin pre-depletion in donor cells could enhance SCNT efficiency at least partially through up-regulation of the minor ZGA genes in donor cells, many of which are also 2C-specific genes (Zhang et al, 2020).…”