H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq]

Facultative heterochromatin is formed by Polycomb repressive complex 2 (PRC2)-deposited H3K27 tri-methylation (H3K27me3) and PRC1-deposited H2AK119 mono-ubiquitylation (H2AK119ub1). How it is newly established after fertilization remains unclear. To delineate the establishment kinetics, here we profiled the temporal dynamics of H3K27 di-methylation (H3K27me2), which represents the de novo PRC2 catalysis, in mouse preimplantation embryos. H3K27me2 is newly deposited at CpG islands (CGIs), the paternal X-chromosome (Xp), and putative enhancers during the 8-cell-to-morula transition, all of which follow H2AK119ub1 deposition. We found that JARID2, a PRC2.2-specific accessory protein possessing an H2AK119ub1-binding ability, colocalizes with SUZ12 at CGIs and Xp in morula embryos. Upon JARID2 depletion, SUZ12 chromatin binding and H3K27me2 deposition were attenuated and H3K27 acetylation was increased at putative enhancers in morulae, and subsequently H3K27me3 failed to be deposited in blastocysts. These data reveal that facultative heterochromatin is established by PRC2.2-driven stepwise H3K27 methylation along pre-deposited H2AK119ub1 during early embryogenesis. Overall design: H3K27me2 and H3K36me3 Carrier DNA assisted ChIP-seq (CATCH-seq) and JARID2 and H3K36me3 CUT&RUN were performed in WT mouse ES cells, oocytes and B6/PWK F1 hybrid preimplantation embryos. H3K27me2, H3K27me3 and H3K27ac CATCH-seq and SUZ12 CUT&RUN were performed in BDF1/PWK F1 hybrid Jarid2 CTR and KO morula and blastocyst embryos. H3K27me2 CATCH-seq with spike-in was performed in BDF1/BDF1 F1 WT preimplantation embryos. H3K27me3 CUT&RUN was performed in BDF1/BDF1 WT and Jarid2 overexpressed 2-cell embryos. H3K27me3 CATCH-seq was performed in BDF1/PWK hybrid WT and Jarid2 overexpressed morula embryos.