Glutarylation of Histone H4 Lysine 91 Regulates Chromatin Dynamics

Chromatin is decorated with diverse histone posttranslational modifications (PTMs) that are involved in regulating chromatin structure and dynamics during various DNA-associated processes such as gene transcription, DNA replication and DNA damage repair. Here, we combine a chemical reporter with mass spectrometry to identify a new class of histone PTM, lysine glutarylation (Kglu), occurring at 27 lysine residues on human core histones. The characterization of an evolutionarily conserved Kglu mark at histone H4 lysine 91 (H4K91glu) using a semisynthetic glutarylated protein reveals that this negatively charged modification greatly destabilizes nucleosome by weakening the interactions between histone H2A/H2B dimers and H3/H4 tetramer in vitro. The replacement of H4K91 by glutamic acid in S. cerevisiae to mimic glutarylation influences chromatin structure and thereby results in a global up-regulation of transcription and defects in cell cycle progression, DNA damage repair and telomere silencing in vivo. In mammalian cells, H4K91glu is mainly enriched at promoter regions of highly expressed genes. A down-regulation of H4K91glu is tightly associated with chromatin condensation during mitosis and in response to DNA damage. The cellular dynamics of H4K91glu is controlled by Sirt7 as a deglutarylase and KAT2A as a glutaryltransferase. This study designates a new histone mark (Kglu) as a new regulatory mechanism for chromatin dynamics. ChIP-seq and RNA-seq

染色质上修饰有多种组蛋白翻译后修饰（posttranslational modifications, PTMs），这类修饰参与调控基因转录、DNA复制、DNA损伤修复等各类DNA相关过程中的染色质结构与动态变化。本研究结合化学报告分子与质谱技术，鉴定出一类全新的组蛋白翻译后修饰——赖氨酸戊二酰化（lysine glutarylation, Kglu），该修饰发生在人类核心组蛋白的27个赖氨酸残基位点。利用半合成戊二酰化组蛋白对进化保守的组蛋白H4赖氨酸91位点戊二酰化（H4K91glu）修饰进行表征后发现，这种带负电的修饰可通过削弱组蛋白H2A/H2B二聚体与H3/H4四聚体之间的相互作用，在体外显著降低核小体稳定性。在酿酒酵母（Saccharomyces cerevisiae, S. cerevisiae）中，将H4K91替换为谷氨酸以模拟戊二酰化修饰，会改变染色质结构，进而在体内引发全基因组转录上调、细胞周期进程异常、DNA损伤修复缺陷以及端粒沉默功能受损。在哺乳动物细胞中，H4K91glu主要富集于高表达基因的启动子区域。H4K91glu的表达下调与有丝分裂过程中的染色质浓缩以及DNA损伤应答过程密切相关。H4K91glu的细胞动态平衡由去戊二酰化酶Sirt7与戊二酰转移酶KAT2A共同调控。本研究将赖氨酸戊二酰化（Kglu）确立为一种全新的组蛋白修饰标记，为染色质动态调控提供了新的机制。本数据集包含染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq）与转录组测序（RNA sequencing, RNA-seq）相关数据。