1. Biochemistry and Chemical Biology
  2. Chromosomes and Gene Expression
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Sumoylation of the human histone H4 tail inhibits p300-mediated transcription by RNA polymerase II in cellular extracts

  1. Calvin Jon A Leonen
  2. Miho Shimada
  3. Caroline E Weller
  4. Tomoyoshi Nakadai
  5. Peter L Hsu
  6. Elizabeth L Tyson
  7. Arpit Mishra
  8. Patrick M M Shelton
  9. Martin Sadilek
  10. R David Hawkins
  11. Ning Zheng
  12. Robert G Roeder  Is a corresponding author
  13. Champak Chatterjee  Is a corresponding author
  1. University of Washington, United States
  2. The Rockefeller University, United States
  3. University Washington, United States
Research Article
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Cite this article as: eLife 2021;10:e67952 doi: 10.7554/eLife.67952

Abstract

The post-translational modification of histones by the small ubiquitin-like modifier (SUMO) protein has been associated with gene regulation, centromeric localization and double-strand break repair in eukaryotes. Although sumoylation of histone H4 was specifically associated with gene repression, this could not be proven due to the challenge of site-specifically sumoylating H4 in cells. Biochemical crosstalk between SUMO and other histone modifications, such as H4 acetylation and H3 methylation, that are associated with active genes also remains unclear. We addressed these challenges in mechanistic studies using an H4 chemically modified at Lys12 by SUMO-3 (H4K12su) and incorporated into mononucleosomes and chromatinized plasmids for functional studies. Mononucleosome-based assays revealed that H4K12su inhibits transcription-activating H4 tail acetylation by the histone acetyltransferase p300, as well as transcription-associated H3K4 methylation by the extended catalytic module of the Set1/COMPASS histone methyltransferase complex. Activator- and p300-dependent in vitro transcription assays with chromatinized plasmids revealed that H4K12su inhibits both H4 tail acetylation and RNA polymerase II-mediated transcription. Finally, cell-based assays with a SUMO-H4 fusion that mimics H4 tail sumoylation confirmed the negative crosstalk between histone sumoylation and acetylation/methylation. Thus, our studies establish the key role for histone sumoylation in gene silencing and its negative biochemical crosstalk with active transcription-associated marks in human cells.

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All data generated or analyzed during this study are included in the manuscript and supporting files.

Article and author information

Author details

  1. Calvin Jon A Leonen

    Chemistry, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3003-9021
  2. Miho Shimada

    Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Caroline E Weller

    Chemistry, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Tomoyoshi Nakadai

    Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Peter L Hsu

    Pharmacology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Elizabeth L Tyson

    Pharmacology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Arpit Mishra

    Pharmacology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Patrick M M Shelton

    Chemistry, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Martin Sadilek

    Chemistry, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. R David Hawkins

    Medicine and Genome Sciences, University Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2997-9457
  11. Ning Zheng

    Pharmacology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Robert G Roeder

    The Rockefeller University, New York, United States
    For correspondence
    roeder@rockefeller.edu
    Competing interests
    The authors declare that no competing interests exist.
  13. Champak Chatterjee

    Chemistry, University of Washington, Seattle, United States
    For correspondence
    champak1@uw.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5772-4438

Funding

NIH NCI (R01CA234561)

  • Robert G Roeder

NIH NIDDK (R01DK071900)

  • Robert G Roeder

NIH NIGMS (R01GM110430)

  • Champak Chatterjee

NIH NIGMS (T32GM008268)

  • Calvin Jon A Leonen

NSF GRFP (DGH-1256082)

  • Caroline E Weller

NIH NICHD (R01HD097408)

  • Ning Zheng

NIH NIDDK (R01DK103667)

  • R David Hawkins

NIH NIAMS (R01AR065952)

  • R David Hawkins

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Hening Lin, Cornell University, United States

Publication history

  1. Received: February 27, 2021
  2. Preprint posted: April 8, 2021 (view preprint)
  3. Accepted: November 6, 2021
  4. Accepted Manuscript published: November 8, 2021 (version 1)
  5. Version of Record published: November 26, 2021 (version 2)

Copyright

© 2021, Leonen et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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