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Mass Spectrometry and Epigenetics

  • Luciano Nicosia
  • Roberta Noberini
  • Monica Soldi
  • Alessandro Cuomo
  • Daniele Musiani
  • Valeria Spadotto
  • Tiziana BonaldiEmail author
Reference work entry

Abstract

Chromatin is a nucleoprotein complex composed of DNA and histone proteins. The concerted activity of chromatin-associated proteins, histone post-translational modifications, and DNA methylation induces epigenetic variations that regulate most of the physiological processes of eukaryotic cells, ranging from gene expression to DNA replication and repair. Epigenetics has also been shown to be tightly linked to cell metabolism. For instance, histone modifications are highly sensitive to the changes in the microenvironment and the local concentration of specific metabolites. Mass-spectrometry (MS)-based proteomics significantly contributed to the recent advances in the epigenetic field, by allowing the comprehensive analysis of histone post-translational modifications as well as the systematic identification of chromatin constituents.

In this chapter, we will provide a general overview of various MS-based experimental strategies developed to boost the epigenetic field, with references to the studies whereby chromatin biology was assessed in relation to cell metabolism.

Keywords

Mass spectrometry Histone post-translational modifications Chromatin Metabolism Epigenetics Stable isotope labeling with amino acids in cell culture Chromatin-associated proteins Histone modifying enzymes Proteomics Global post-translational modification profiling 

List of Abbreviations

AF-10

Antisecretor factor 10

ChIP

Chromatin immunoprecipitation

CID

Collision-induced dissociation

CRISPR

Clustered regularly interspaced short palindromic repeats

DDA

Data-dependent acquisition

ECD

Electron capture dissociation

ESC

Embryonic stem cell

ETD

Electron transfer dissociation

HAT

Histone acetyltransferase

HMCV

Cytomegalovirus

hmSILAC

Heavy-methyl SILAC

KAT

Lysine acetyl-transferase

LC

Liquid chromatography

LF

Label-free

MRM

Multiple reaction monitoring

MS

Mass-spectrometry

NPC

Neural progenitor cell

NSC

Neural stem cell

PTM

Post-translational modification

RA

Relative abundance

RP

Reversed-phase

SAM

S-adenosyl-methionine

SILAC

Stable isotope labeling with amino acids in cell culture

SRM

Selected reaction monitoring

TAL

Transcription activator-like

TF

Transcription factor

WCX-HILIC

Weak-cation exchange hydrophilic interaction liquid chromatography

XIC

MS-extracted ion chromatogram

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Luciano Nicosia
    • 1
  • Roberta Noberini
    • 2
  • Monica Soldi
    • 1
  • Alessandro Cuomo
    • 1
  • Daniele Musiani
    • 1
  • Valeria Spadotto
    • 1
  • Tiziana Bonaldi
    • 1
    Email author
  1. 1.Department of Experimental OncologyEuropean Institute of OncologyMilanItaly
  2. 2.Center for Genomic Science of IIT@SEMMIstituto Italiano di TecnologiaMilanItaly

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