1. Chromosomes and Gene Expression

Rdh54/Tid1 inhibits Rad51-Rad54-mediated D-loop formation and limits D-loop length

  1. Shanaya Shital Shah
  2. Stella R Hartono
  3. Aurèle Piazza
  4. Vanessa C Som
  5. William Wright
  6. Frédéric Chédin
  7. Wolf-Dietrich Heyer  Is a corresponding author
  1. University of California, Davis, United States
  2. ENS Lyon, France
https://doi.org/10.7554/eLife.59112
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  1. Shanaya Shital Shah
  2. Stella R Hartono
  3. Aurèle Piazza
  4. Vanessa C Som
  5. William Wright
  6. Frédéric Chédin
  7. Wolf-Dietrich Heyer
(2020)
Rdh54/Tid1 inhibits Rad51-Rad54-mediated D-loop formation and limits D-loop length
eLife 9:e59112.
https://doi.org/10.7554/eLife.59112
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Abstract

Displacement loops (D-loops) are critical intermediates formed during homologous recombination. Rdh54 (a.k.a. Tid1), a Rad54 paralog in Saccharomyces cerevisiae, is well-known for its role with Dmc1 recombinase during meiotic recombination. Yet contrary to Dmc1, Rdh54/Tid1 is also present in somatic cells where its function is less understood. While Rdh54/Tid1 enhances the Rad51 DNA strand invasion activity in vitro, it is unclear how it interplays with Rad54. Here, we show that Rdh54/Tid1 inhibits D-loop formation by Rad51 and Rad54 in an ATPase-independent manner. Using a novel D-loop Mapping Assay, we further demonstrate that Rdh54/Tid1 uniquely restricts the lengths of Rad51-Rad54-mediated D-loops. The alterations in D-loop properties appear to be important for cell survival and mating-type switch in haploid yeast. We propose that Rdh54/Tid1 and Rad54 compete for potential binding sites within the Rad51 filament, where Rdh54/Tid1 acts as a physical roadblock to Rad54 translocation, limiting D-loop formation and D-loop length.

Data availability

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

Article and author information

Author details

  1. Shanaya Shital Shah

    Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
    Competing interests
    No competing interests declared.

  2. Stella R Hartono

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    No competing interests declared.

  3. Aurèle Piazza

    ENS Lyon, Lyon, France
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7722-0955

  4. Vanessa C Som

    Microbiology and Molecular Genetics, University of California, Davis, Belmont, United States
    Competing interests
    No competing interests declared.

  5. William Wright

    Microbiology & Molecular Genetics, University of California, Davis, Davis, United States
    Competing interests
    No competing interests declared.

  6. Frédéric Chédin

    Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
    Competing interests
    No competing interests declared.

  7. Wolf-Dietrich Heyer

    Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
    For correspondence
    wdHeyer@ucdavis.edu
    Competing interests
    Wolf-Dietrich Heyer, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7774-1953

Funding

National Institutes of Health (GM 58015)

  • Wolf-Dietrich Heyer

National Institutes of Health (CA 92276)

  • Wolf-Dietrich Heyer

National Institutes of Health (CA 93373)

  • Wolf-Dietrich Heyer

National Institutes of Health (GM 120607)

  • Frédéric Chédin

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

Copyright

© 2020, Shah 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. Shanaya Shital Shah
  2. Stella R Hartono
  3. Aurèle Piazza
  4. Vanessa C Som
  5. William Wright
  6. Frédéric Chédin
  7. Wolf-Dietrich Heyer
(2020)
Rdh54/Tid1 inhibits Rad51-Rad54-mediated D-loop formation and limits D-loop length
eLife 9:e59112.
https://doi.org/10.7554/eLife.59112

Share this article

https://doi.org/10.7554/eLife.59112

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Further reading

    1. Chromosomes and Gene Expression

    Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution

    Shanaya Shital Shah, Stella R Hartono ... Wolf-Dietrich Heyer
    Tools and Resources Updated

    Displacement loops (D-loops) are signature intermediates formed during homologous recombination. Numerous factors regulate D-loop formation and disruption, thereby influencing crucial aspects of DNA repair, including donor choice and the possibility of crossover outcome. While D-loop detection methods exist, it is currently unfeasible to assess the relationship between D-loop editors and D-loop characteristics such as length and position. Here, we developed a novel in vitro assay to characterize the length and position of individual D-loops with near base-pair resolution and deep coverage, while also revealing their distribution in a population. Non-denaturing bisulfite treatment modifies the cytosines on the displaced strand of the D-loop to uracil, leaving a permanent signature for the displaced strand. Subsequent single-molecule real-time sequencing uncovers the cytosine conversion patch as a D-loop footprint. The D-loop Mapping Assay is widely applicable with different substrates and donor types and can be used to study factors that influence D-loop properties.