GSE125318
Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency
Around implantation, the epiblast transits from naïve to primed pluripotency, before giving rise to the three germ layers. How chromatin is reconfigured during this developmental window remains poorly understood. We performed a genome-wide investigation of chromatin landscapes during this period. We find that enhancers in ectoderm are already pre-accessible in embryonic day 6.5 (E6.5) Epi when cells enter a primed pluripotent state. Unexpectedly, strong H3K4me3 emerges at developmental gene promoters in E6.5 epiblast and positively correlates with H3K27me3, thus establishing bivalency. These genes also show enhanced spatial interactions. Both the strong bivalency and spatial clustering are virtually absent in preimplantation embryos and are markedly reduced in fate-committed lineages. Finally, we show that KMT2B is essential for establishing bivalent H3K4me3 at E6.5 but becomes partially dispensable later. Its deficiency leads to impaired activation of developmental genes and subsequent embryonic lethality. Thus, our data characterize lineage-specific chromatin reconfiguration and a unique chromatin state for primed pluripotency. Overall design: To determine the dynamics of chromatin states during gastrulation in mouse early embryos, male (DBA2) and female (C57BL/6N) were mated and multiple lineages were separated from embryos, including epiblast (Epi) and visceral endoderm (VE) at embryonic day 6.5 (E6.5), ectoderm (Ect), primitive streak (PS), mesoderm (Mes) and endoderm (End) at E7.5. We then conducted miniATAC-seq and STAR ChIP-seq for H3K4me3, H3K27ac, and H3K27me3 in these tissues. We also performed RNA-seq, ChIP-seq, MethylC-seq, and sisHi-C in E6.5Epi and/or E8.5 head tissues to determine the chromatin configuration in embryos upon loss of Kmt2b.