Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation

被引：63

作者：

Schwammle, Veit ^{[1
,2
]}

Sidoli, Simone ^{[1
,2
,6
]}

Ruminowicz, Chrystian ^{[1
,2
]}

Wu, Xudong ^{[3
,4
,7
]}

Lee, Chung-Fan ^{[3
,4
]}

Helin, Kristian ^{[3
,4
,5
]}

Jensen, Ole N. ^{[1
,2
]}

机构：

[1] Univ Southern Denmark, Dept Biochem & Mol Biol, Ctr Epigenet, Campusvej 55, DK-5230 Odense M, Denmark

[2] Univ Southern Denmark, Dept Biochem & Mol Biol, VILLUM Ctr Bioanalyt Sci, Campusvej 55, DK-5230 Odense M, Denmark

[3] Univ Copenhagen, Biotech Res & Innovat Ctr, DK-2200 Copenhagen, Denmark

[4] Univ Copenhagen, Ctr Epigenet, DK-2200 Copenhagen, Denmark

[5] Univ Copenhagen, Danish Stem Cell Ctr Danstem, DK-2200 Copenhagen, Denmark

[6] Univ Penn, Perelman Med, Dept Biochem & Biophys, Epigenet Program, Philadelphia, PA 19104 USA

[7] Tianjin Med Univ, Dept Cell Biol, Tianjin 300070, Peoples R China

来源：

MOLECULAR & CELLULAR PROTEOMICS | 2016年 / 15卷 / 08期

基金：

新加坡国家研究基金会; 欧洲研究理事会;

关键词：

GROUP PROTEINS RING1A/B; EMBRYONIC STEM-CELLS; REPRESSIVE COMPLEX 2; MASS-SPECTROMETRY; TRANSCRIPTIONAL ACTIVATION; METHYLATION; PHOSPHORYLATION; HETEROCHROMATIN; PROTEOMICS; GENOME;

D O I：

10.1074/mcp.M115.054460

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2715 / 2729

页数：15