Parallel PRC2/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells. Parallel PRC2/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells

The transcriptional repressors Polycomb Repressive Complex 1 (PRC1) and PRC2 are required to maintain cell fate during embryonic development. PRC1 and PRC2 catalyse distinct histone modifications, establishing repressive chromatin at shared targets. Loss of PRC1, but not PRC2, from mouse embryonic stem cells (mESCs) triggers exit from pluripotency. How PRC2 and PRC1, which consists of distinct “variant PRC1” (vPRC1) and “canonical PRC1” (cPRC1) complexes, cooperate to silence genes and support mESC self-renewal is unclear. Here, we report that independent pathways composed of vPRC1 and cPRC1/PRC2 repress shared target genes. Individual loss of vPRC1, cPRC1, or PRC2 disrupts only one pathway and does not impair mESC pluripotency. However, loss of both pathways leads to mESC differentiation and activation of a subset of poised target genes co-occupied by relatively high levels of PRC1/PRC2. Thus, parallel pathways explains the differential requirements for PRC1 and PRC2, and provides robust silencing of poised, lineage-specific genes. Overall design: 198 samples in total: 102 ChIP-Seq (80x2 replicates each , 1x3 replicates Input, 1x3 replicates Cbx7 in Eed-null), 96 RNA-Seq (32x3 replicates each)

多梳抑制复合体1（Polycomb Repressive Complex 1, PRC1）与多梳抑制复合体2（Polycomb Repressive Complex 2, PRC2）作为转录抑制因子，在胚胎发育过程中对维持细胞命运不可或缺。PRC1与PRC2催化不同类型的组蛋白修饰，在共同靶位点建立抑制性染色质状态。从小鼠胚胎干细胞（mouse embryonic stem cells, mESCs）中敲除PRC1（而非PRC2）会触发细胞退出多能性状态。目前尚不明确PRC2，以及由变异型PRC1（variant PRC1, vPRC1）和经典型PRC1（canonical PRC1, cPRC1）复合体组成的PRC1，是如何协同发挥基因沉默作用并维持mESC自我更新的。本研究表明，vPRC1与cPRC1/PRC2分别构成独立通路，共同抑制共享靶基因。单独敲除vPRC1、cPRC1或PRC2仅会破坏其中一条通路，并不会损害mESC的多能性。但同时丧失两条通路则会导致mESC分化，并激活一部分由较高水平PRC1/PRC2共同结合的预启动靶基因。综上，平行通路机制解释了PRC1与PRC2的差异化需求，并为预启动谱系特异性基因的稳定沉默提供了可靠保障。实验整体设计：样本总量共计198份，其中包含102份染色质免疫共沉淀测序（ChIP-Seq）样本（含80组各2个生物学重复、1组输入样本3个重复、1组Eed敲除细胞中Cbx7的ChIP-Seq样本3个重复），以及96份RNA测序（RNA-Seq）样本（32组各3个生物学重复）