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Mass Spectrometry and Epigenetics

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Handbook of Nutrition, Diet, and Epigenetics

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.

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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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Authors and Affiliations

  1. Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan, 20139, Italy

    Luciano Nicosia, Monica Soldi, Alessandro Cuomo, Daniele Musiani, Valeria Spadotto & Tiziana Bonaldi

  2. Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, Milan, 20139, Italy

    Roberta Noberini

Authors
  1. Luciano Nicosia
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  2. Roberta Noberini
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  3. Monica Soldi
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  4. Alessandro Cuomo
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  5. Daniele Musiani
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  6. Valeria Spadotto
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  7. Tiziana Bonaldi
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Corresponding author

Correspondence to Tiziana Bonaldi .

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Editors and Affiliations

  1. c/o Editorial Board 978-0-387-78665 , Heidelberg, Baden-Württemberg, Germany

    Vinood Patel

  2. Kings College , London, United Kingdom

    Victor Preedy

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Nicosia, L. et al. (2017). Mass Spectrometry and Epigenetics. In: Patel, V., Preedy, V. (eds) Handbook of Nutrition, Diet, and Epigenetics. Springer, Cham. https://doi.org/10.1007/978-3-319-31143-2_115-1

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  • DOI: https://doi.org/10.1007/978-3-319-31143-2_115-1

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