Insights into epigenetic patterns in mammalian early embryos

Abstract

Mammalian fertilization begins with the fusion of two specialized gametes, followed by major epigenetic remodeling leading to the formation of a totipotent embryo. During the development of the pre-implantation embryo, precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality, but the underlying molecular mechanisms remain elusive. For the past few years, unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development, taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies. The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals, including DNA methylation, histone modifications, chromatin accessibility and 3D chromatin organization.

Keywords: DNA methylation; early embryo development; epigenetic reprogramming; histone modifications.

Figure 1

Epigenome reprogramming of histone modifications and chromatin accessibility during early mouse embryo development. H3K4me3: After fertilization, H3K4me3 in the paternal genome is rapidly depleted but re-established during major ZGA. By contrast, noncanonical H3K4me3 with broad domains in both promoters and distal regions is found in MII oocytes and is replaced by canonical H3K4me3 at the late 2-cell stage (ZGA). Broad ncH3K4me3 domains are correlated with partial DNA methylation domains (PMDs). Broad promoter H3K4me3 domains are much more abundant in early embryos than in MII oocytes or derived cell lines and are associated with high levels of gene expression. During ZGA, chromatin accessibility is observed at both the TSS and TES sites of active genes. Transposable elements (TEs) are also accessible and are enriched in distal H3K4me3. Developmental genes are primed to be active until the blastocyst stage, marked by bivalent H3K4me3/H3K27me3. H3K27me3: During mouse early embryo development, H3K27me3 in promoter regions exhibits a widespread loss at the 2-cell stage, a caused by the global erasure of H3K27me3 in the paternal genome and the selective depletion of promoter H3K27me3 in the maternal genome. H3K27me3 and DNA methylation are negatively correlated with H3K4me3. H3K27me3 also appears in non-promoter regions in a highly pervasive and promiscuous manner. H3K9me3: H3K9me3 peaks mainly fall in LTRs in early embryos. The number of H3K9me3-marked LTRs gradually increases and remains high during pre-implantation development. Most of the parental H3K9me3 regions are established de novo upon fertilization. Promoter H3K9me3 marks are erased upon fertilization and are reestablished postimplantation. Most LTR-enriched H3K9me3 domains are progressively established after the 4-cell stage and are responsible for LTR silencing. During the early cleavage stage, H3K9me3 domains overlap with H3K27me3-marked facultative heterochromatin. Maternal-specific H3K9me3 regions are much more abundant than paternal-specific regions during early embryogenesis, but this divergence gradually diminishes. Transposable elements: Mouse endogenous retrovirus type L (MERVL), a member of the ERV3 family member, is expressed in both 2-cell-like ESCs and cleavage-stage embryos, where it drives the expression of many transcripts specific to ZGA and totipotency. Upon fertilization, LINE1 is actively transcribed, with the increase in LINE1 RNA reaching its highest level at the 2-cell stage. LINE1 is essential for Dux silencing, the synthesis of rRNA, exit from the 2-cell stage and chromatin remodeling over accessible regions during pre-implantation embryo development. Chromatin accessibility: Open chromatin exists around both the promoters and transcription end sites (TES) of actively transcribed genes at the 2-cell stage. The transient and active transcription of transposable elements is probably associated with increased chromatin accessibility at the 2-cell stage of early embryos

Figure 2

Dynamic histone modifications and chromatin accessibility during human pre-implantation embryogenesis. H3K4me3: H3K4me3 shows sharp peaks at promoters in human GV oocytes. During early human embryogenesis, wider promoter H3K4me3 marks are easily observable at the 4-cell stage (pre-ZGA), and 53% of these marks remain at the 8-cell stage (peri-ZGA) and are preferentially activated. The remainder of these sites (~ 47%), where H3K4me3 is lost, are in the promoters of genes related to development and differentiation, which remain inactive during ZGA. Weaker (compared to promoter H3K4me3) but widespread distal H3K4me3 marks are observed in pre-ZGA embryos, which indicates the de novo deposition of H3K4me3, and are decreased at the 8-cell stage. Distal H3K4me3 is deposited in CpG-rich and hypomethylated regions. Most of the distal H3K4me3 marks overlap with cis-regulatory elements and are highly chromatin accessible at the 4-cell stage. H3K27me3: H3K27me3 in human GV oocytes is deposited in the promoters of developmental genes and partially methylated domains. Human embryos at the ZGA stage (8-cell stage) show almost no H3K27me3 signals, indicating the global erasure of H3K27me3 in the maternal genome. The inaccessible cis-regulatory elements located in distal chromatin regions near developmental genes are correlated with H3K27me3 in the human ICM. Chromatin accessibility: Widespread accessible chromatin regions also highly overlap with cis-regulatory elements and transposable elements in human early embryos. High chromatin accessibility exists in distal regions enriched in transcription factor binding sites, overlapping with hypomethylated DNA regions in oocytes. Distal accessible chromatin at the 4-cell stage is also enriched for distal H3K4me3. These distal regions become inaccessible after the 8-cell stage

Figure 3

The higher-order chromatin organization in the gametes and pre-implantation embryos of mouse and human. Mouse: 3D chromatin: MII oocytes lacks TADs and compartments given its mitotic. PADs and their compartmental interactions appear to emerge only on the maternal allele in early 2-cell embryos, and begin to fade away in the 8-cell embryos. By contrast, sperm present frequent extra-long-range interactions (> 4 Mb) and inter-chromosomal interactions. Upon fertilization, the higher-order structures of both parental chromatins are obscure at the zygotic and ZGA stages but are spatially separated from each other with distinct compartmentalization. The gradual establishment of the parental chromatin organization occurs throughout the development of pre-implantation embryos, with slow consolidation of TADs and the A/B compartments. Such allele separation and compartmentalization are maintained until the 8-cell stage. Human: Human sperm lack TADs and expression of the chromatin regulator CTCF. Consistent with findings in mice, TADs and A/B compartmentalization are gradually established during human embryogenesis. CTCF is highly expressed at the ZGA stage of human embryos, which coincides with the time at which TADs are observed