Establishing Polycomb regulatory landscapes in human early development

H2AK119ub (H2Aub) and H3K27me3, which are deposited by the Polycomb group (PcG) complexes PRC1 and PRC2, respectively, cooperatively repress developmental genes. However, in human preimplantation embryos, H3K27me3 undergoes genome-wide erasure and subsequent restoration. How H3K27me3 is reestablished and whether PcG complexes still regulate gene repression in human embryos remain unknown. Here, we profiled H2Aub dynamics from human gametes to blastocysts. H2Aub emerges in GC-rich regions as early as the two-cell stage, progressively accumulates at both active and inactive genes, and further culminates at PcG targets in later stages. H3K27me3 is weakly correlated with H2Aub in oocytes and two-cell embryos but colocalizes with H2Aub at H3K4me3-depleted, inactive PcG targets in blastocysts. Loss of H2Aub abolishes H3K27me3 reestablishment at PcG targets causing moderate derepression, accompanied by ectopic H3K27me3 deposition and impaired embryonic development. Finally, H2Aub and DNA methylation cooperatively maintain H3K27me3 patterning in human embryonic stem cells. Therefore, H2Aub-dependent H3K27me3 deposition underlies the earliest establishment of Polycomb repression in humans.