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Fragment Ion Patchwork Quantification for Measuring Site-Specific Acetylation Degrees

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Rudolf Virchow Center for Experimental Biomedicine and §Research Center for Infectious Diseases, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
Department of Cell & Developmental Biology, Biocenter University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
Cite this: Anal. Chem. 2015, 87, 19, 9939–9945
Publication Date (Web):September 3, 2015
https://doi.org/10.1021/acs.analchem.5b02517
Copyright © 2015 American Chemical Society

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    Abstract

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    We introduce fragment ion patchwork quantification as a new mass spectrometry-based approach for the highly accurate quantification of site-specific acetylation degrees. This method combines 13C1-acetyl derivatization on the protein level, proteolysis by low-specificity proteases and quantification on the fragment ion level. Acetylation degrees are determined from the isotope patterns of acetylated b and y ions. We show that this approach allows to determine site-specific acetylation degrees of all lysine residues for all core histones of Trypanosoma brucei. In addition, we demonstrate how this approach can be used to identify substrate sites of histone acetyltransferases.

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    Cited By

    This article is cited by 6 publications.

    1. Francesca Zappacosta, Craig D. Wagner, Anthony Della Pietra, Sarah V. Gerhart, Kathryn Keenan, Susan Korenchuck, Chad J. Quinn, Olena Barbash, Michael T. McCabe, Roland S. Annan. A Chemical Acetylation-Based Mass Spectrometry Platform for Histone Methylation Profiling. Molecular & Cellular Proteomics 2021, 20 , 100067. https://doi.org/10.1016/j.mcpro.2021.100067
    2. Amelie J. Kraus, Jens T. Vanselow, Stephanie Lamer, Benedikt G. Brink, Andreas Schlosser, T. Nicolai Siegel. Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes. Nature Communications 2020, 11 (1) https://doi.org/10.1038/s41467-020-15274-0
    3. Juan-José Vasquez, Carolin Wedel, Raul O Cosentino, T Nicolai Siegel. Exploiting CRISPR–Cas9 technology to investigate individual histone modifications. Nucleic Acids Research 2018, 46 (18) , e106-e106. https://doi.org/10.1093/nar/gky517
    4. Elisabeth Limbeck, Jens T. Vanselow, Julian Hofmann, Andreas Schlosser, Angela Mally. Linking site-specific loss of histone acetylation to repression of gene expression by the mycotoxin ochratoxin A. Archives of Toxicology 2018, 92 (2) , 995-1014. https://doi.org/10.1007/s00204-017-2107-6
    5. Willy Vincent Bienvenut, Jean-Pierre Scarpelli, Johan Dumestier, Thierry Meinnel, Carmela Giglione. EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples. BMC Bioinformatics 2017, 18 (1) https://doi.org/10.1186/s12859-017-1595-y
    6. Pravin K. Jha, Mohd. Imran Khan, Anshul Mishra, Pradeep Das, Kislay K. Sinha, . HAT2 mediates histone H4K4 acetylation and affects micrococcal nuclease sensitivity of chromatin in Leishmania donovani. PLOS ONE 2017, 12 (5) , e0177372. https://doi.org/10.1371/journal.pone.0177372

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