1. Biochemistry and Chemical Biology
  2. Chromosomes and Gene Expression
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Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling

  1. Jugal Mohapatra
  2. Kyuto Tashiro
  3. Ryan L Beckner
  4. Jorge Sierra
  5. Jessica A Kilgore
  6. Noelle S Williams
  7. Glen Liszczak  Is a corresponding author
  1. The University of Texas Southwestern Medical Center, United States
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Cite this article as: eLife 2021;10:e71502 doi: 10.7554/eLife.71502

Abstract

Serine ADP-ribosylation (ADPr) is a DNA damage-induced post-translational modification catalyzed by the PARP1/2:HPF1 complex. As the list of PARP1/2:HPF1 substrates continues to expand, there is a need for technologies to prepare mono- and poly-ADP-ribosylated proteins for biochemical interrogation. Here we investigate the unique peptide ADPr activities catalyzed by PARP1 in the absence and presence of HPF1. We then exploit these activities to develop a method that facilitates installation of ADP-ribose polymers onto peptides with precise control over chain length and modification site. Importantly, the enzymatically mono- and poly-ADP-ribosylated peptides are fully compatible with protein ligation technologies. This chemoenzymatic protein synthesis strategy was employed to assemble a series of full-length, ADP-ribosylated histones and show that ADPr at H2BS6 or H3S10 converts nucleosomes into robust substrates for the chromatin remodeler ALC1. We found ALC1 preferentially remodels 'activated' substrates within heterogeneous mononucleosome populations and asymmetrically ADP-ribosylated dinucleosome substrates, and that nucleosome serine ADPr is sufficient to stimulate ALC1 activity in nuclear extracts. Our study identifies a biochemical function for nucleosome serine ADPr and describes a new, highly modular approach to explore the impact that site-specific serine mono- and poly-ADPr have on protein function.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Supplementary Dataset is available online on dryad- https://doi.org/10.5061/dryad.z612jm6cc

The following data sets were generated

Article and author information

Author details

  1. Jugal Mohapatra

    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Kyuto Tashiro

    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Ryan L Beckner

    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Jorge Sierra

    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jessica A Kilgore

    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Noelle S Williams

    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Glen Liszczak

    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
    For correspondence
    glen.liszczak@utsouthwestern.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8194-5281

Funding

Cancer Prevention and Research Institute of Texas (RR180051)

  • Glen Liszczak

Welch Foundation (I-2039)

  • Glen Liszczak

American Cancer Society (UTSW-IRG-17-174-13)

  • Glen Liszczak

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

Reviewing Editor

  1. Geeta J Narlikar, University of California, San Francisco, United States

Publication history

  1. Received: June 21, 2021
  2. Preprint posted: July 7, 2021 (view preprint)
  3. Accepted: November 20, 2021
  4. Accepted Manuscript published: December 7, 2021 (version 1)
  5. Version of Record published: December 17, 2021 (version 2)
  6. Version of Record updated: January 24, 2022 (version 3)

Copyright

© 2021, Mohapatra 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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