Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics

Monica Soldi, Alessandro Cuomo, Michael Bremang, Tiziana Bonaldi

Research output: Contribution to journalArticlepeer-review

Abstract

Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce a specific "chromatin landscape", with a regulatory effect on gene expression. Mass Spectrometry (MS) has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from "Bottom Up" to "Top Down" analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.

Original languageEnglish
Pages (from-to)5402-5431
Number of pages30
JournalInternational Journal of Molecular Sciences
Volume14
Issue number3
DOIs
Publication statusPublished - Mar 2013

Keywords

  • Chromatin
  • Combinatorial modifications
  • Epigenetics
  • Histone code readers
  • Histone post-translational modifications (hPTMs)
  • Histone variants
  • Mass spectrometry
  • Proteomics
  • SILAC

ASJC Scopus subject areas

  • Computer Science Applications
  • Molecular Biology
  • Catalysis
  • Inorganic Chemistry
  • Spectroscopy
  • Organic Chemistry
  • Physical and Theoretical Chemistry

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