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Combined Metabolic and Chemical (CoMetChem) Labeling Using Stable Isotopes – a Strategy to Reveal Site-Specific Histone Acetylation and Deacetylation Rates by LC-MS

preprint
revised on 19.02.2021, 21:56 and posted on 22.02.2021, 09:03 by Alienke van Pijkeren, Jörn Dietze, Alejandro Sánchez Brotons, Tim Lijster, Andrei Barcaru, Anna-Sophia Egger, Madlen Hotze, Frank J. Dekker, Peter Horvatovich, Barbro Melgert, Mathias Ziegler, Kathrin Thedieck, Ines Heiland, Rainer Bischoff, Marcel Kwiatkowski
Histone acetylation is an important, reversible post-translational protein modification and a hallmark of epigenetic regulation. However, little is known about the dynamics of this process, due to the lack of analytical methods that can capture site-specific acetylation and deacetylation reactions. We present a new approach that combines metabolic and chemical labeling (CoMetChem) using uniformly 13C-labeled glucose and stable isotope labeled acetic anhydride. Thereby, chemically equivalent, fully acetylated histone species are generated enabling accurate relative quantification of site-specific lysine acetylation in tryptic peptides using high-resolution mass spectrometry. We show that CoMetChem enables site-specific quantification of the incorporation or loss of lysine acetylation over time, allowing the determination of reaction rates for acetylation and deacetylation. Thus, the CoMetChem methodology provides a comprehensive description of site-specific acetylation dynamics.

Funding

REspiratory Science Promoted by International Research Exchanges 3

European Commission

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Systems Medicine of Metabolic-Signaling Networks: A New Concept for Breast Cancer Patient Stratification

European Commission

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Norwegian Research Foundation (ES633272)

Norwegian Research Foundation (302314)

Novel tools to read and write the epigenetic code in inflammation

European Research Council

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Netherlands Organization of Scientific Research (723.012.005)

Netherlands X-omics Initiative (project no: 184.034.019)

University of Innsbruck (project no:316826)

History

Email Address of Submitting Author

marcel.kwiatkowski@uibk.ac.at

Institution

University of Innsbruck

Country

Austria

ORCID For Submitting Author

0000-0002-5804-6031

Declaration of Conflict of Interest

No conflict of interest

Version Notes

Version 2.

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