Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation
Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation
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DOI：
10.1074/mcp.m115.054460
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发表时间：
2016-08-01
影响因子：
7
通讯作者：
Jensen, Ole N.
中科院分区：
文献类型：
--
作者：
Schwammle, Veit;Sidoli, Simone;Jensen, Ole N.
组蛋白是一种含有大量翻译后修饰的染色质组分。这种PTM介导多种生物学功能，包括调节DNA复制、转录和修复的酶读取器、写入器和擦除器的募集。单个组蛋白分子含有多个共存的PTM，其中一些表现出串扰，即协调或相互排斥的活动。在这里，我们提出了一个综合的实验和计算系统水平的分子表征组蛋白PTM和PTM串扰。使用在Polycomb抑制复合物2（PRC 2，Suz 12（-/-））、PRC 1（Ring 1A/B-/-）和（Dnmt 1/3a/3 B（-/-））的组分中敲除的野生型和工程小鼠胚胎干细胞（mESC），我们通过利用串联质谱的定量中间蛋白质组分析对组蛋白H3尾部（50 aa）进行了全面的PTM分析。我们表征了跨四条mESC线的组合PTM特征，然后应用统计数据分析来预测组蛋白H3 PTM之间的串扰。我们检测到一个过度代表性的正串扰（共依赖标记）之间的相邻的单甲基化和乙酰化的标志，和负串扰（互斥标记）之间的大多数的7个特征的二和三甲基化的赖氨酸残基的H3尾巴。我们报告了PTM相互作用的新特征，涉及迄今为止表征不佳的精氨酸甲基化和赖氨酸甲基化位点，包括H3 R2 me，H3 R8 me和H3 K37 me。通过组蛋白PTM和组蛋白修饰酶的共丰度聚类分析将H3数据与RNAseq数据整合，揭示了PTM和酶水平之间的相关性。我们的结论是，中下蛋白质组学是一个强大的工具，以确定保守的或动态的组蛋白标记之间的相互依赖性，这铺平了道路，详细的调查组蛋白代码。组蛋白H3 PTM数据可在CrossTalkDB存储库中公开获得，网址为http://crosstalkdb.bmb.sdu.dk。
Histones are abundant chromatin constituents carrying numerous post-translational modifications (PTMs). Such PTMs mediate a variety of biological functions, including recruitment of enzymatic readers, writers and erasers that modulate DNA replication, transcription and repair. Individual histone molecules contain multiple coexisting PTMs, some of which exhibit crosstalk, i.e. coordinated or mutually exclusive activities. Here, we present an integrated experimental and computational systems level molecular characterization of histone PTMs and PTM crosstalk. Using wild type and engineered mouse embryonic stem cells (mESCs) knocked out in components of the Polycomb Repressive Complex 2 (PRC2, Suz12(-/-)), PRC1 (Ring1A/B-/-) and (Dnmt1/3a/3b(-/-)) we performed comprehensive PTM analysis of histone H3 tails (50 aa) by utilizing quantitative middle-down proteome analysis by tandem mass spectrometry. We characterized combinatorial PTM features across the four mESC lines and then applied statistical data analysis to predict crosstalk between histone H3 PTMs. We detected an overrepresentation of positive crosstalk (codependent marks) between adjacent mono-methylated and acetylated marks, and negative crosstalk (mutually exclusive marks) among most of the seven characterized di-a nd tri-methylated lysine residues in the H3 tails. We report novel features of PTM interplay involving hitherto poorly characterized arginine methylation and lysine methylation sites, including H3R2me, H3R8me and H3K37me. Integration of the H3 data with RNAseq data by coabundance clustering analysis of histone PTMs and histone modifying enzymes revealed correlations between PTM and enzyme levels. We conclude that middle-down proteomics is a powerful tool to determine conserved or dynamic interdependencies between histone marks, which paves the way for detailed investigations of the histone code. Histone H3 PTM data is publicly available in the CrossTalkDB repository at http://crosstalkdb.bmb.sdu.dk.