High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors

  1. Mingrui Duan
  2. Smitha Sivapragasam
  3. Jacob S Antony
  4. Jenna Ulibarri
  5. John M Hinz
  6. Gregory MK Poon
  7. John J Wyrick  Is a corresponding author
  8. Peng Mao  Is a corresponding author
  1. University of New Mexico, United States
  2. Washington State University, United States
  3. Georgia State University, United States

Abstract

DNA base damage arises frequently in living cells and needs to be removed by base excision repair (BER) to prevent mutagenesis and genome instability. Both the formation and repair of base damage occur in chromatin and are conceivably affected by DNA-binding proteins such as transcription factors (TFs). However, to what extent TF binding affects base damage distribution and BER in cells is unclear. Here, we used a genome-wide damage mapping method, N-methylpurine-sequencing (NMP-seq), and characterized alkylation damage distribution and BER at TF binding sites in yeast cells treated with the alkylating agent methyl methanesulfonate (MMS). Our data shows that alkylation damage formation was mainly suppressed at the binding sites of yeast TFs Abf1 and Reb1, but individual hotspots with elevated damage levels were also found. Additionally, Abf1 and Reb1 binding strongly inhibits BER in vivo and in vitro, causing slow repair both within the core motif and its adjacent DNA. Repair of UV damage by nucleotide excision repair (NER) was also inhibited by TF binding. Interestingly, TF binding inhibits a larger DNA region for NER relative to BER. The observed effects are caused by the TF-DNA interaction, because damage formation and BER can be restored by depletion of Abf1 or Reb1 protein from the nucleus. Thus, our data reveal that TF binding significantly modulates alkylation base damage formation and inhibits repair by the BER pathway. The interplay between base damage formation and BER may play an important role in affecting mutation frequency in gene regulatory regions.

Data availability

New DNA sequencing data has been deposited to GEO under accession code GSE183622. All data generated or analyzed are included in the manuscript and supplemental file. Source data files containing the numerical data for Figure 1 and Figure 2 are uploaded. Source codes used for sequencing reads mapping to identify alkylation lesions and repair analysis at yeast Abf1 and Reb1 binding sites are also uploaded.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Mingrui Duan

    Department of Internal Medicine, University of New Mexico, Albuquerque, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2352-1840
  2. Smitha Sivapragasam

    School of Molecular Biosciences, Washington State University, Pullman, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5599-9988
  3. Jacob S Antony

    School of Molecular Biosciences, Washington State University, Pullman, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1481-9768
  4. Jenna Ulibarri

    Department of Internal Medicine, University of New Mexico, Albuquerque, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. John M Hinz

    School of Molecular Biosciences, Washington State University, Pullman, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Gregory MK Poon

    Department of Chemistry, Georgia State University, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. John J Wyrick

    School of Molecular Biosciences, Washington State University, Pullman, United States
    For correspondence
    jwyrick@wsu.edu
    Competing interests
    The authors declare that no competing interests exist.
  8. Peng Mao

    Department of Internal Medicine, University of New Mexico, Albuquerque, United States
    For correspondence
    pmao@salud.unm.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2068-1344

Funding

National Institute of Environmental Health Sciences (R21ES029302)

  • John J Wyrick
  • Peng Mao

National Institute of Environmental Health Sciences (R01ES032814)

  • John J Wyrick

National Institute of Environmental Health Sciences (R01ES028698)

  • John J Wyrick

National Science Foundation (MCB 2028902)

  • Gregory MK Poon

National Institute of General Medical Sciences (P20GM130422)

  • Peng Mao

National Cancer Institute (P30CA118100)

  • Mingrui Duan
  • Peng Mao

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

Reviewing Editor

  1. Wolf-Dietrich Heyer, University of California, Davis, United States

Publication history

  1. Received: September 15, 2021
  2. Preprint posted: September 24, 2021 (view preprint)
  3. Accepted: March 11, 2022
  4. Accepted Manuscript published: March 15, 2022 (version 1)
  5. Version of Record published: March 31, 2022 (version 2)

Copyright

© 2022, Duan 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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  1. Mingrui Duan
  2. Smitha Sivapragasam
  3. Jacob S Antony
  4. Jenna Ulibarri
  5. John M Hinz
  6. Gregory MK Poon
  7. John J Wyrick
  8. Peng Mao
(2022)
High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
eLife 11:e73943.
https://doi.org/10.7554/eLife.73943

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