KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation [ChIP-Seq]

Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. Here, we show that KDM5B, which demethylates lysine 4 of histone H3, co-localizes with H3K4me3 near promoters and enhancers of active genes in ES cells; its depletion leads to spreading of H3K4 methylation into gene bodies and enhancer shores, indicating that KDM5B functions to focus H3K4 methylation at promoters and enhancers. Spreading of H3K4 methylation to gene bodies and enhancer shores is linked to defects in gene expression programs and enhancer activity, respectively, during self-renewal and differentiation of KDM5B-depleted ES cells. KDM5B critically regulates H3K4 methylation at bivalent genes during differentiation in the absence of LIF or Oct4. We also show that KDM5B and LSD1, another H3K4 demethylase, co-regulate H3K4 methylation at active promoters but they retain distinct roles in demethylating gene body regions and bivalent genes. Our results provide global and functional insight into the role of KDM5B in regulating H3K4 methylation marks near promoters, gene bodies, and enhancers in ES cells and during differentiation.

胚胎干细胞（embryonic stem cells, ES）的多能性，部分由调控组蛋白H3赖氨酸4（histone H3 lysine 4, H3K4）甲基化的染色质修饰因子所调控。然而，H3K4去甲基化如何影响ES细胞功能，目前仍不明确。本研究显示，可催化组蛋白H3赖氨酸4去甲基化的KDM5B，在ES细胞中与活跃基因启动子及增强子区域附近的组蛋白H3赖氨酸4三甲基化（H3K4me3）共定位；敲低KDM5B会导致H3K4甲基化扩散至基因本体及增强子侧翼区域，表明KDM5B的功能是将H3K4甲基化限定在启动子与增强子区域内。H3K4甲基化向基因本体及增强子侧翼区域的扩散，分别与KDM5B敲低的ES细胞在自我更新与分化过程中的基因表达程序缺陷及增强子活性异常相关。在缺乏白血病抑制因子（leukemia inhibitory factor, LIF）或Oct4的分化体系中，KDM5B可精准调控二价基因区域的H3K4甲基化水平。本研究还发现，KDM5B与另一H3K4去甲基化酶LSD1可共同调控活跃启动子区域的H3K4甲基化，但二者在基因本体区域及二价基因的去甲基化过程中发挥截然不同的作用。本研究结果为解析KDM5B在ES细胞及分化进程中，调控启动子、基因本体及增强子附近H3K4甲基化标记的功能提供了全局性的认知。