Uncoupling histone H3K4 trimethylation from developmental gene expression via an epigenetic equilibrium of Polycomb, COMPASS and DNA methylation

The COMPASS family catalyzes histone H3 lysine 4 (H3K4) methylation and its members are essential for regulating developmental gene expression. MLL2/COMPASS methylates H3K4 on many genes but only a subset lose expression upon MLL2 loss. To understand MLL2 -dependent transcriptional regulation, we performed a CRISPR screen in mouse embryonic stem cells (mESCs) and found that MLL2 protects developmental genes from repression by repelling PRC2 and DNA methylation machineries from these loci. Repression in the absence of MLL2 is relieved by inhibition of PRC2 and DNA methyltransferases, demonstrating that prevention of active repression and not H3K4me3 underlies their transcriptional state. DNA demethylation on such loci leads to reactivation of MLL2-dependent genes not only by removing DNA methylation but also by opening up previously CpG methylated regions for PRC2 recruitment, diluting PRC2 at Polycomb-repressed genes. These findings reveal how the context and function of these three epigenetic modifiers can orchestrate transcriptional decisions.

COMPASS家族能够催化组蛋白H3赖氨酸4（H3K4）甲基化，其成员在调控发育基因的表达过程中发挥必需作用。MLL2/COMPASS可对大量基因位点的H3K4实施甲基化修饰，但仅当MLL2缺失时，其中部分基因才会出现表达水平下调。为阐明MLL2依赖型转录调控的分子机制，我们在小鼠胚胎干细胞（mESCs）中开展了CRISPR筛选实验，结果发现MLL2可通过将PRC2（多梳抑制复合体2）与DNA甲基化机制从发育基因位点逐出，从而保护这些基因免受转录抑制。在MLL2缺失的条件下，通过抑制PRC2与DNA甲基转移酶即可解除该转录抑制状态，这证实维持相关基因转录状态的核心在于阻断其主动被抑制的通路，而非依赖H3K4me3修饰。上述基因位点的DNA去甲基化不仅可通过移除DNA甲基化来激活MLL2依赖型基因，还能够开放此前被CpG甲基化的区域以招募PRC2，进而稀释多梳蛋白抑制基因位点处的PRC2富集度。本研究揭示了这三种表观遗传修饰因子的作用背景与功能如何协同调控转录决策。