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Characterization of histone acylations links chromatin modifications with metabolism

Author

Listed:
  • Johayra Simithy

    (Perelman School of Medicine, University of Pennsylvania)

  • Simone Sidoli

    (Perelman School of Medicine, University of Pennsylvania)

  • Zuo-Fei Yuan

    (Perelman School of Medicine, University of Pennsylvania)

  • Mariel Coradin

    (Perelman School of Medicine, University of Pennsylvania)

  • Natarajan V. Bhanu

    (Perelman School of Medicine, University of Pennsylvania)

  • Dylan M. Marchione

    (Perelman School of Medicine, University of Pennsylvania)

  • Brianna J. Klein

    (University of Colorado School of Medicine)

  • Gleb A. Bazilevsky

    (Perelman School of Medicine, University of Pennsylvania)

  • Cheryl E. McCullough

    (University of Pennsylvania)

  • Robert S. Magin

    (Perelman School of Medicine, University of Pennsylvania)

  • Tatiana G. Kutateladze

    (University of Colorado School of Medicine)

  • Nathaniel W. Snyder

    (Drexel University)

  • Ronen Marmorstein

    (Abramson Family Cancer Research Institute, and the Department of Chemistry, University of Pennsylvania)

  • Benjamin A. Garcia

    (Perelman School of Medicine, University of Pennsylvania)

Abstract

Over the last decade, numerous histone acyl post-translational modifications (acyl-PTMs) have been discovered, of which the functional significance is still under intense study. Here, we use high-resolution mass spectrometry to accurately quantify eight acyl-PTMs in vivo and after in vitro enzymatic assays. We assess the ability of seven histone acetyltransferases (HATs) to catalyze acylations on histones in vitro using short-chain acyl-CoA donors, proving that they are less efficient towards larger acyl-CoAs. We also observe that acyl-CoAs can acylate histones through non-enzymatic mechanisms. Using integrated metabolomic and proteomic approaches, we achieve high correlation (R 2 > 0.99) between the abundance of acyl-CoAs and their corresponding acyl-PTMs. Moreover, we observe a dose-dependent increase in histone acyl-PTM abundances in response to acyl-CoA supplementation in in nucleo reactions. This study represents a comprehensive profiling of scarcely investigated low-abundance histone marks, revealing that concentrations of acyl-CoAs affect histone acyl-PTM abundances by both enzymatic and non-enzymatic mechanisms.

Suggested Citation

  • Johayra Simithy & Simone Sidoli & Zuo-Fei Yuan & Mariel Coradin & Natarajan V. Bhanu & Dylan M. Marchione & Brianna J. Klein & Gleb A. Bazilevsky & Cheryl E. McCullough & Robert S. Magin & Tatiana G. , 2017. "Characterization of histone acylations links chromatin modifications with metabolism," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-01384-9
    DOI: 10.1038/s41467-017-01384-9
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    Cited by:

    1. Ziping Niu & Chen Chen & Siyu Wang & Congcong Lu & Zhiyue Wu & Aiyuan Wang & Jing Mo & Jianji Zhang & Yanpu Han & Ye Yuan & Yingao Zhang & Yong Zang & Chaoran He & Xue Bai & Shanshan Tian & Guijin Zha, 2024. "HBO1 catalyzes lysine lactylation and mediates histone H3K9la to regulate gene transcription," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Motohiro Sekiya & Kenta Kainoh & Takehito Sugasawa & Ryunosuke Yoshino & Takatsugu Hirokawa & Hiroaki Tokiwa & Shogo Nakano & Satoru Nagatoishi & Kouhei Tsumoto & Yoshinori Takeuchi & Takafumi Miyamot, 2021. "The transcriptional corepressor CtBP2 serves as a metabolite sensor orchestrating hepatic glucose and lipid homeostasis," Nature Communications, Nature, vol. 12(1), pages 1-19, December.

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