Variant PRC2.1 and PRC2.2 co-operate to direct H3K27 methylations in ESCs [RNA-seq]. Variant PRC2.1 and PRC2.2 co-operate to direct H3K27 methylations in ESCs [RNA-seq]

Polycomb repressive complex 2 (PRC2) is composed of EED, SUZ12, and EZH1/2, and mediates mono-, di- and tri-methylation of Histone H3 at Lysine 27. While, two subcomplexes defined by their specific accessory proteins, termed PRC2.1 (Polycomb-like proteins 1-3, EPOP and PALI1/2) and PRC2.2 (AEBP2 and JARID2) exist, little is known about their differential functions. Here, we show that PRC2.1 and PRC2.2 share the majority of their target genes in mouse embryonic stem cells (ESCs). While loss of all three Polycomb-like proteins (PHF1, MTF2, PHF19) leads to eviction of EPOP and PALI1 from chromatin, PRC2.2 specific components are maintained together with SUZ12 and H3K27me3 at broad Polycomb domains. We show that PRC2.2 localises to PRC1 mediated H2AK119ub1 at these broad Polycomb domains to maintain H3K27me3, even in the absence of PRC2.1. Taken together, these data establish that PRC2.1 and PRC2.2 co-operate to direct H3K27me3, but have independent recruitment mechanisms. Overall design: RNA seq analysis of Pcl1-3 WT and Pcl1-3 TKO mouse embryonic stem cells and at three time points (Day 2, Day 4 and Day 8) during embryoid body differentiation (EB). 20 samples are included. Biological duplicates are present.

多梳抑制复合体2（Polycomb repressive complex 2, PRC2）由EED、SUZ12及EZH1/2构成，能够介导组蛋白H3（Histone H3）赖氨酸27位的单甲基化、二甲基化与三甲基化修饰。目前已依据附属蛋白的特异性将PRC2划分为两个亚复合体：分别为携带多梳样蛋白1-3、EPOP与PALI1/2的PRC2.1，以及携带AEBP2与JARID2的PRC2.2，但二者的功能分化机制仍不明晰。本研究证实，在小鼠胚胎干细胞（embryonic stem cells, ESCs）中，PRC2.1与PRC2.2共享绝大多数靶基因。当三种核心多梳样蛋白（PHF1、MTF2、PHF19）完全缺失时，EPOP与PALI1会从染色质上解离，但PRC2.2的特异性组分仍可与SUZ12及H3K27me3共同保留在宽泛的多梳结构域内。研究进一步发现，即便在PRC2.1缺失的情况下，PRC2.2也能够定位至这些宽泛多梳结构域中由PRC1介导的H2AK119ub1位点，以维持H3K27me3的水平。综上，本研究表明PRC2.1与PRC2.2可协同调控H3K27me3的建立，但二者具备独立的招募机制。实验设计：本研究对Pcl1-3野生型（wild-type, WT）与Pcl1-3三重敲除（triple knockout, TKO）的小鼠胚胎干细胞，以及拟胚体分化（embryoid body, EB）过程中第2天、第4天、第8天三个时间点的样本开展RNA测序（RNA-seq）分析。本次数据集共纳入20个样本，并设置了生物学重复。