Sae2/CtIP prevents R-loop accumulation in eukaryotic cells

  1. Nodar Makharashvili
  2. Sucheta Arora
  3. Yizhi Yin
  4. Qiong Fu
  5. Xuemei Wen
  6. Ji-Hoon Lee
  7. Chung-Hsuan Kao
  8. Justin WC Leung
  9. Kyle M Miller
  10. Tanya T Paull  Is a corresponding author
  1. The University of Texas at Austin, United States
  2. National Institutes of Health, United States
  3. University of Arkansas for Medical Sciences, United States

Abstract

The Sae2/CtIP protein is required for efficient processing of DNA double-strand breaks that initiate homologous recombination in eukaryotic cells. Sae2/CtIP is also important for survival of single-stranded Top1-induced lesions and CtIP is known to associate directly with transcription-associated complexes in mammalian cells. Here we investigate the role of Sae2/CtIP at single-strand lesions in budding yeast and in human cells and find that depletion of Sae2/CtIP promotes the accumulation of stalled RNA polymerase and RNA-DNA hybrids at sites of highly expressed genes. Overexpression of the RNA-DNA helicase Senataxin suppresses DNA damage sensitivity and R-loop accumulation in Sae2/CtIP-deficient cells, and a catalytic mutant of CtIP fails to complement this sensitivity, indicating a role for CtIP nuclease activity in the repair process. Based on this evidence, we propose that R-loop processing by 5' flap endonucleases is a necessary step in the stabilization and removal of nascent R-loop initiating structures in eukaryotic cells.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files. Sequencing data has been deposited in GEO (accession number GSE122782).

The following data sets were generated

Article and author information

Author details

  1. Nodar Makharashvili

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Sucheta Arora

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Yizhi Yin

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Qiong Fu

    Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Xuemei Wen

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Ji-Hoon Lee

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7387-935X
  7. Chung-Hsuan Kao

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Justin WC Leung

    Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Kyle M Miller

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Tanya T Paull

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
    For correspondence
    tpaull@utexas.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2991-651X

Funding

Howard Hughes Medical Institute

  • Sucheta Arora
  • Qiong Fu
  • Xuemei Wen
  • Ji-Hoon Lee
  • Chung-Hsuan Kao
  • Tanya T Paull

Cancer Prevention and Research Institute of Texas

  • Nodar Makharashvili
  • Yizhi Yin

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

Reviewing Editor

  1. Andrés Aguilera, CABIMER, Universidad de Sevilla, Spain

Publication history

  1. Received: October 11, 2018
  2. Accepted: November 30, 2018
  3. Accepted Manuscript published: December 7, 2018 (version 1)
  4. Version of Record published: December 17, 2018 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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  1. Nodar Makharashvili
  2. Sucheta Arora
  3. Yizhi Yin
  4. Qiong Fu
  5. Xuemei Wen
  6. Ji-Hoon Lee
  7. Chung-Hsuan Kao
  8. Justin WC Leung
  9. Kyle M Miller
  10. Tanya T Paull
(2018)
Sae2/CtIP prevents R-loop accumulation in eukaryotic cells
eLife 7:e42733.
https://doi.org/10.7554/eLife.42733

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