Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos

Abstract

The oocyte cytoplasm can reprogram the somatic cell nucleus into a totipotent state, but with low efficiency. The spatiotemporal chromatin organization of somatic cell nuclear transfer (SCNT) embryos remains elusive. Here, we examine higher order chromatin structures of mouse SCNT embryos using a low-input Hi-C method. We find that donor cell chromatin transforms to the metaphase state rapidly after SCNT along with the dissolution of typical 3D chromatin structure. Intriguingly, the genome undergoes a mitotic metaphase-like to meiosis metaphase II-like transition following activation. Subsequently, weak chromatin compartments and topologically associating domains (TADs) emerge following metaphase exit. TADs are further removed until the 2-cell stage before being progressively reestablished. Obvious defects including stronger TAD boundaries, aberrant super-enhancer and promoter interactions are found in SCNT embryos. These defects are partially caused by inherited H3K9me3, and can be rescued by Kdm4d overexpression. These observations provide insight into chromatin architecture reorganization during SCNT embryo development.

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.…”

Insights into epigenetic patterns in mammalian early embryos

“…Moreover, a recent study by our group revealed spatiotemporally dynamic chromatin reorganization in SCNT embryos (Chen et al, 2020 ). Both aberrant TADs and compartment A/B organization are observed throughout early SCNT embryo development.…”

“…Moreover, overexpression of KDM4A also drastically increased the blastocyst rate of human SCNT and improves the derivation of human ntESC, with the similar mechanism as in mice (Chung et al, 2015 ). Our recent study also shows that H3K9me3 in donor cells also prevent the removal of topologically associated domains (TADs) during SCNT (Chen et al, 2020 ). These findings suggest that some H3K9me3, mainly associated with heterochromatin, is resistant to the cell conversion methods and presents as a barrier to reprogramming to pluripotency that impairs both the efficiency of reprogramming and the quality of embryogenesis.…”

“…These epigenetic abnormalities of pre-implantation SCNT embryos are highly correlated with subsequent placenta overgrowth and embryonic lethality (Miri et al, 2013 ; Okae et al, 2014b ; Inoue et al, 2017b ). Intriguingly, the upregulation of clustered miRNAs of Sfmbt2 , one of the H3K27me3-dependent imprinted genes (Matoba et al, 2018 ; Chen et al, 2020 ), has recently been identified as the major cause of placental hyperplasia in SCNT mice (Inoue et al, 2020 ). These observations highlight the crucial function of H3K27me3-imprinted genes in both pre-implantation and postimplantation embryos, although the detailed molecular mechanisms and consequences of intergenerational epigenetic inheritance remain elusive.…”

Chromatin accessibility dynamics during cell fate reprogramming

“…On the other hand, vitamin c (Vc) induces demethylation of H3K9me3 by stimulating the activity of the histone demethylase Kdm3/4 and enhances the efficiency of somatic cell reprogramming (Wang et al , 2011). H3K9me3 is also a blockade in somatic cell nuclear transfer (SCNT) mediated reprogramming (Jullien et al , 2010; Matoba et al , 2014), indeed, injection of H3K9me3 demethylase Kdm4 mRNA into enucleated oocytes could greatly improve SCNT efficiency (Matoba et al , 2014; Chung et al , 2015; Liu et al , 2016; Liu et al , 2018; Chen et al , 2020b). Those results suggest that H3K9me3 is associated with closed chromatin to maintain cell identity, thus being an obstacle for somatic reprogramming.…”