Systems level analysis of Histone H3 posttranslational modifications (PTMs) reveals features of PTM crosstalk in chromatin regulation

Veit Schwämmle, Simone Sidoli, Chrystian Ruminowicz, Xudong Wu, Chung Fan Lee, Kristian Helin, Ole N. Jensen

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

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- and 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.

Original languageEnglish (US)
Pages (from-to)2715-2729
Number of pages15
JournalMolecular and Cellular Proteomics
Volume15
Issue number8
DOIs
StatePublished - Aug 2016
Externally publishedYes

Fingerprint

Post Translational Protein Processing
Crosstalk
Histones
Chromatin
Histone Code
Methylation
Stem cells
Lysine
Polycomb Repressive Complex 2
Enzymes
Proteome
Transcription
Statistical Data Interpretation
Mass spectrometry
Arginine
Tandem Mass Spectrometry
DNA Replication
Repair
DNA Repair
Proteomics

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry
  • Molecular Biology

Cite this

Systems level analysis of Histone H3 posttranslational modifications (PTMs) reveals features of PTM crosstalk in chromatin regulation. / Schwämmle, Veit; Sidoli, Simone; Ruminowicz, Chrystian; Wu, Xudong; Lee, Chung Fan; Helin, Kristian; Jensen, Ole N.

In: Molecular and Cellular Proteomics, Vol. 15, No. 8, 08.2016, p. 2715-2729.

Research output: Contribution to journalArticle

Schwämmle, Veit ; Sidoli, Simone ; Ruminowicz, Chrystian ; Wu, Xudong ; Lee, Chung Fan ; Helin, Kristian ; Jensen, Ole N. / Systems level analysis of Histone H3 posttranslational modifications (PTMs) reveals features of PTM crosstalk in chromatin regulation. In: Molecular and Cellular Proteomics. 2016 ; Vol. 15, No. 8. pp. 2715-2729.
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