Middle-down proteomics: a still unexploited resource for chromatin biology

Simone Sidoli, Benjamin A. Garcia

Research output: Contribution to journalReview article

23 Scopus citations

Abstract

Introduction: Analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has become a fundamental tool for the characterization of chromatin composition and dynamics. Histone PTMs benchmark several biological states of chromatin, including regions of active enhancers, active/repressed gene promoters and damaged DNA. These complex regulatory mechanisms are often defined by combinatorial histone PTMs; for instance, active enhancers are commonly occupied by both marks H3K4me1 and H3K27ac. The traditional bottom-up MS strategy identifies and quantifies short (aa 4–20) tryptic peptides, and it is thus not suitable for the characterization of combinatorial PTMs. Areas covered: Here, we review the advancement of the middle-down MS strategy applied to histones, which consists in the analysis of intact histone N-terminal tails (aa 50–60). Middle-down MS has reached sufficient robustness and reliability, and it is far less technically challenging than PTM quantification on intact histones (top-down). However, the very few chromatin biology studies applying middle-down MS resulting from PubMed searches indicate that it is still very scarcely exploited, potentially due to the apparent high complexity of method and analysis. Expert commentary: We will discuss the state-of-the-art workflow and examples of existing studies, aiming to highlight its potential and feasibility for studies of cell biologists interested in chromatin and epigenetics.

Original languageEnglish (US)
Pages (from-to)617-626
Number of pages10
JournalExpert Review of Proteomics
Volume14
Issue number7
DOIs
StatePublished - Jul 3 2017
Externally publishedYes

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Keywords

  • Chromatin
  • cross-talk
  • histones
  • mass spectrometry
  • middle-down
  • post-translational modifications
  • proteomics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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