1. Biochemistry and Chemical Biology
  2. Chromosomes and Gene Expression
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The interplay of RNA:DNA hybrid structure and G-quadruplexes determines the outcome of R-loop-replisome collisions

  1. Charanya Kumar
  2. Sahil Batra
  3. Jack D Griffith
  4. Dirk Remus  Is a corresponding author
  1. Memorial Sloan Kettering Cancer Center, United States
  2. University of North Carolina at Chapel Hill, United States
Research Article
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Cite this article as: eLife 2021;10:e72286 doi: 10.7554/eLife.72286

Abstract

R-loops are a major source of genome instability associated with transcription-induced replication stress. However, how R-loops inherently impact replication fork progression is not understood. Here, we characterize R-loop-replisome collisions using a fully reconstituted eukaryotic DNA replication system. We find that RNA:DNA hybrids and G-quadruplexes at both co-directional and head-on R-loops can impact fork progression by inducing fork stalling, uncoupling of leading strand synthesis from replisome progression, and nascent strand gaps. RNase H1 and Pif1 suppress replication defects by resolving RNA:DNA hybrids and G-quadruplexes, respectively. We also identify an intrinsic capacity of replisomes to maintain fork progression at certain R-loops by unwinding RNA:DNA hybrids, repriming leading strand synthesis downstream of G-quadruplexes, or utilizing R-loop transcripts to prime leading strand restart during co-directional R-loop-replisome collisions. Collectively, the data demonstrates that the outcome of R-loop-replisome collisions is modulated by R-loop structure, providing a mechanistic basis for the distinction of deleterious from non-deleterious R-loops.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided.

Article and author information

Author details

  1. Charanya Kumar

    Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Sahil Batra

    Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4210-3991
  3. Jack D Griffith

    University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Dirk Remus

    Memorial Sloan Kettering Cancer Center, New York, United States
    For correspondence
    remusd@mskcc.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5155-181X

Funding

National Institute of General Medical Sciences (R01-GM127428)

  • Dirk Remus

National Institute of General Medical Sciences (R01-GM107239)

  • Dirk Remus

National Institutes of Health (P30 CA008748)

  • Dirk Remus

National Institute of Environmental Health Sciences (ES031635)

  • Jack D Griffith

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

Reviewing Editor

  1. Bruce Stillman, Cold Spring Harbor Laboratory, United States

Publication history

  1. Received: July 18, 2021
  2. Accepted: September 7, 2021
  3. Accepted Manuscript published: September 8, 2021 (version 1)

Copyright

© 2021, Kumar 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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