Integrating Proteomics and Targeted Metabolomics to Understand Global Changes in Histone Modifications

Johayra Simithy, Simone Sidoli, Benjamin A. Garcia

Research output: Contribution to journalReview article

5 Citations (Scopus)

Abstract

The chromatin fiber is the control panel of eukaryotic cells. Chromatin is mostly composed of DNA, which contains the genetic instruction for cell phenotype, and histone proteins, which provide the scaffold for chromatin folding and part of the epigenetic inheritance. Histone writers/erasers “flag” chromatin regions by catalyzing/removing covalent histone post-translational modifications (PTMs). Histone PTMs chemically contribute to chromatin relaxation or compaction and recruit histone readers to modulate DNA readout. The precursors of protein PTMs are mostly small metabolites. For instance, acetyl-CoA is used for acetylation, ATP for phosphorylation, and S-adenosylmethionine for methylation. Interestingly, PTMs such as acetylation can occur at neutral pH also without their respective enzyme when the precursor is sufficiently concentrated. Therefore, it is essential to differentially quantify the contribution of histone writers/erasers versus the effect of local concentration of metabolites to understand the primary regulation of histone PTM abundance. Aberrant phenotypes such as cancer cells have misregulated metabolism and thus the composition and the modulation of chromatin is not only driven by enzymatic tuning. In this review, the latest advances in mass spectrometry (MS) to analyze histone PTMs and the most adopted quantification methods for related metabolites, both necessary to understand PTM relative changes, are discussed.

Original languageEnglish (US)
Article number1700309
JournalProteomics
Volume18
Issue number18
DOIs
StatePublished - Sep 2018
Externally publishedYes

Fingerprint

Histone Code
Metabolomics
Proteomics
Histones
Post Translational Protein Processing
Chromatin
Metabolites
Acetylation
Phenotype
S-Adenosylmethionine
Acetyl Coenzyme A
Enzyme Precursors
Phosphorylation
Methylation
Protein Precursors
DNA
Eukaryotic Cells
Metabolism
Epigenomics
Scaffolds

Keywords

  • Acetyl-CoA
  • epigenetics
  • histone
  • metabolism
  • post-translational modifications

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Integrating Proteomics and Targeted Metabolomics to Understand Global Changes in Histone Modifications. / Simithy, Johayra; Sidoli, Simone; Garcia, Benjamin A.

In: Proteomics, Vol. 18, No. 18, 1700309, 09.2018.

Research output: Contribution to journalReview article

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