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Global profiling of regulatory elements in the histone benzoylation pathway

Author

Listed:
  • Duo Wang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Fuxiang Yan

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Ping Wu

    (Chinese Academy of Science)

  • Kexue Ge

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Muchun Li

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    ShanghaiTech University)

  • Tingting Li

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Ying Gao

    (Chinese Academy of Sciences)

  • Chao Peng

    (Chinese Academy of Science)

  • Yong Chen

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    ShanghaiTech University)

Abstract

Lysine benzoylation (Kbz) is a recently discovered post-translational modification associated with active transcription. However, the proteins for maintaining and interpreting Kbz and the physiological roles of Kbz remain elusive. Here, we systematically characterize writer, eraser, and reader proteins of histone Kbz in S. cerevisiae using proteomic, biochemical, and structural approaches. Our study identifies 27 Kbz sites on yeast histones that can be regulated by cellular metabolic states. The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex and NAD+-dependent histone deacetylase Hst2 could function as the writer and eraser of histone Kbz, respectively. Crystal structures of Hst2 complexes reveal the molecular basis for Kbz recognition and catalysis by Hst2. In addition, we demonstrate that a subset of YEATS domains and bromodomains serve as Kbz readers, and structural analyses reveal how YEATS and bromodomains recognize Kbz marks. Moreover, the proteome-wide screening of Kbz-modified proteins identifies 207 Kbz sites on 149 non-histone proteins enriched in ribosome biogenesis, glycolysis/gluconeogenesis, and rRNA processing pathways. Our studies identify regulatory elements for the Kbz pathway and provide a framework for dissecting the biological functions of lysine benzoylation.

Suggested Citation

  • Duo Wang & Fuxiang Yan & Ping Wu & Kexue Ge & Muchun Li & Tingting Li & Ying Gao & Chao Peng & Yong Chen, 2022. "Global profiling of regulatory elements in the histone benzoylation pathway," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29057-2
    DOI: 10.1038/s41467-022-29057-2
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    References listed on IDEAS

    as
    1. Liling Wan & Hong Wen & Yuanyuan Li & Jie Lyu & Yuanxin Xi & Takayuki Hoshii & Julia K. Joseph & Xiaolu Wang & Yong-Hwee E. Loh & Michael A. Erb & Amanda L. Souza & James E. Bradner & Li Shen & Wei Li, 2017. "ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia," Nature, Nature, vol. 543(7644), pages 265-269, March.
    2. He Huang & Di Zhang & Yi Wang & Mathew Perez-Neut & Zhen Han & Y. George Zheng & Quan Hao & Yingming Zhao, 2018. "Lysine benzoylation is a histone mark regulated by SIRT2," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    3. Haibo Wang & Christian Dienemann & Alexandra Stützer & Henning Urlaub & Alan C. M. Cheung & Patrick Cramer, 2020. "Structure of the transcription coactivator SAGA," Nature, Nature, vol. 577(7792), pages 717-720, January.
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