Integrated analysis of acetyl-CoA and histone modification via mass spectrometry to investigate metabolically driven acetylation

Simone Sidoli, Sophie Trefely, Benjamin A. Garcia, Alessandro Carrer

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Abstract

Acetylation is a highly abundant and dynamic post-translational modification (PTM) on histone proteins which, when present on chromatin-bound histones, facilitates the accessibility of DNA for gene transcription. The central metabolite, acetyl-CoA, is a substrate for acetyltransferases, which catalyze protein acetylation. Acetyl-CoA is an essential intermediate in diverse metabolic pathways, and cellular acetyl-CoA levels fluctuate according to extracellular nutrient availability and the metabolic state of the cell. The Michaelis constant (Km) of most histone acetyltransferases (HATs), which specifically target histone proteins, falls within the range of cellular acetyl-CoA concentrations. As a consequence, global levels of histone acetylation are often restricted by availability of acetyl-CoA. Such metabolic regulation of histone acetylation is important for cell proliferation, differentiation, and a variety of cellular functions. In cancer, numerous oncogenic signaling events hijack cellular metabolism, ultimately inducing an extensive rearrangement of the epigenetic state of the cell. Understanding metabolic control of the epigenome through histone acetylation is essential to illuminate the molecular mechanisms by which cells sense, adapt, and occasionally disengage nutrient fluctuations and environmental cues from gene expression. In particular, targeting metabolic regulators or even dietary interventions to impact acetyl-CoA availability and histone acetylation is a promising target in cancer therapy. Liquid chromatography coupled to mass spectrometry (LC-MS) is the most accurate methodology to quantify protein PTMs and metabolites. In this chapter, we present state-of-the-art protocols to analyze histone acetylation and acetyl-CoA. Histones are extracted and digested into short peptides (4–20 aa) prior to LC-MS. Acetyl-CoA is extracted from cells and analyzed using an analogous mass spectrometry-based procedure. Model systems can be fed with isotopically labeled substrates to investigate the metabolic preference for acetyl-CoA production and the metabolic dependence and turnover of histone acetylation. We also present an example of data integration to correlate changes in acetyl-CoA production with histone acetylation.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages125-147
Number of pages23
DOIs
StatePublished - Jan 1 2019
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1928
ISSN (Print)1064-3745

Fingerprint

Histone Code
Acetyl Coenzyme A
Acetylation
Histones
Mass Spectrometry
Liquid Chromatography
Proteins
Histone Acetyltransferases
Food
Acetyltransferases
Post Translational Protein Processing
Metabolic Networks and Pathways
Epigenomics
Chromatin
Cues

Keywords

  • Acetyl-CoA
  • Histones
  • Mass spectrometry
  • Metabolism
  • Proteomics

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Sidoli, S., Trefely, S., Garcia, B. A., & Carrer, A. (2019). Integrated analysis of acetyl-CoA and histone modification via mass spectrometry to investigate metabolically driven acetylation. In Methods in Molecular Biology (pp. 125-147). (Methods in Molecular Biology; Vol. 1928). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9027-6_9

Integrated analysis of acetyl-CoA and histone modification via mass spectrometry to investigate metabolically driven acetylation. / Sidoli, Simone; Trefely, Sophie; Garcia, Benjamin A.; Carrer, Alessandro.

Methods in Molecular Biology. Humana Press Inc., 2019. p. 125-147 (Methods in Molecular Biology; Vol. 1928).

Research output: Chapter in Book/Report/Conference proceedingChapter

Sidoli, S, Trefely, S, Garcia, BA & Carrer, A 2019, Integrated analysis of acetyl-CoA and histone modification via mass spectrometry to investigate metabolically driven acetylation. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1928, Humana Press Inc., pp. 125-147. https://doi.org/10.1007/978-1-4939-9027-6_9
Sidoli S, Trefely S, Garcia BA, Carrer A. Integrated analysis of acetyl-CoA and histone modification via mass spectrometry to investigate metabolically driven acetylation. In Methods in Molecular Biology. Humana Press Inc. 2019. p. 125-147. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9027-6_9
Sidoli, Simone ; Trefely, Sophie ; Garcia, Benjamin A. ; Carrer, Alessandro. / Integrated analysis of acetyl-CoA and histone modification via mass spectrometry to investigate metabolically driven acetylation. Methods in Molecular Biology. Humana Press Inc., 2019. pp. 125-147 (Methods in Molecular Biology).
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