ZCWPW1 is recruited to recombination hotspots by PRDM9, and is essential for meiotic double strand break repair

Abstract

During meiosis, homologous chromosomes pair and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, double-strand breaks (DSBs) initiate recombination within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have been identified. We identified Zcwpw1, containing H3K4me3 and H3K36me3 recognition domains, as having highly correlated expression with Prdm9. Here, we show that ZCWPW1 has co-evolved with PRDM9 and, in human cells, is strongly and specifically recruited to PRDM9 binding sites, with higher affinity than sites possessing H3K4me3 alone. Surprisingly, ZCWPW1 also recognises CpG dinucleotides. Male Zcwpw1 knockout mice show completely normal DSB positioning, but persistent DMC1 foci, severe DSB repair and synapsis defects, and downstream sterility. Our findings suggest ZCWPW1 recognition of PRDM9-bound sites at DSB hotspots is critical for synapsis, and hence fertility.

Data availability

Source data files are provided for Figures 1-5.Raw and processed data for ChIP-seq (Figures 5-8) are available on the GEO database (identifier GSE141516).Codes used for analysis are available at github.com/MyersGroup/Zcwpw1 and archived at Zenodo (DOI: 10.5281/zenodo.3559759).

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

Article and author information

Author details

  1. Daniel Wells

    Wellcome Centre for Human Genetics, Department of Statistics, University of Oxford, Oxford, United Kingdom
    For correspondence
    daniel.john.wells@outlook.com
    Competing interests
    The authors declare that no competing interests exist.
  2. Emmanuelle Bitoun

    Wellcome Centre for Human Genetics, Department of Statistics, University of Oxford, Oxford, United Kingdom
    For correspondence
    ebitoun@well.ox.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
  3. Daniela Moralli

    Wellcome Centre for Human Genetics, Department of Statistics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Gang Zhang

    Wellcome Centre for Human Genetics, Department of Statistics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Anjali Hinch

    Wellcome Centre for Human Genetics, Department of Statistics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Julia Jankowska

    Wellcome Centre for Human Genetics, Department of Statistics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Peter Donnelly

    Wellcome Centre for Human Genetics, Department of Statistics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  8. Catherine Green

    Wellcome Centre for Human Genetics, Department of Statistics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  9. Simon R Myers

    Wellcome Centre for Human Genetics, Department of Statistics, University of Oxford, Oxford, United Kingdom
    For correspondence
    myers@stats.ox.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2585-9626

Funding

Wellcome (098387/Z/12/Z)

  • Simon R Myers

Wellcome (212284/Z/18/Z)

  • Simon R Myers

Wellcome (109109/Z/15/Z)

  • Daniel Wells

Wellcome (095552/Z/11/Z)

  • Peter Donnelly

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

Reviewing Editor

  1. Bernard de Massy, CNRS UM, France

Ethics

Animal experimentation: All animal experiments received local ethical review approval from the University of Oxford Animal Welfare and Ethical Review Body (Clinical Medicine board) and were carried out in accordance with the UK Home Office Animals (Scientific Procedures) Act 1986. The specific protocols used were authorised by the UK Home Office under Project Licence PPL 3003437.

Version history

  1. Received: November 7, 2019
  2. Accepted: July 31, 2020
  3. Accepted Manuscript published: August 3, 2020 (version 1)
  4. Version of Record published: September 16, 2020 (version 2)

Copyright

© 2020, Wells 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. Daniel Wells
  2. Emmanuelle Bitoun
  3. Daniela Moralli
  4. Gang Zhang
  5. Anjali Hinch
  6. Julia Jankowska
  7. Peter Donnelly
  8. Catherine Green
  9. Simon R Myers
(2020)
ZCWPW1 is recruited to recombination hotspots by PRDM9, and is essential for meiotic double strand break repair
eLife 9:e53392.
https://doi.org/10.7554/eLife.53392

Share this article

https://doi.org/10.7554/eLife.53392

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    Meiotic crossovers result from homology-directed repair of DNA double-strand breaks (DSBs). Unlike yeast and plants, where DSBs are generated near gene promoters, in many vertebrates DSBs are enriched at hotspots determined by the DNA binding activity of the rapidly evolving zinc finger array of PRDM9 (PR domain zinc finger protein 9). PRDM9 subsequently catalyzes tri-methylation of lysine 4 and lysine 36 of Histone H3 in nearby nucleosomes. Here, we identify the dual histone methylation reader ZCWPW1, which is tightly co-expressed during spermatogenesis with Prdm9, as an essential meiotic recombination factor required for efficient repair of PRDM9-dependent DSBs and for pairing of homologous chromosomes in male mice. In sum, our results indicate that the evolution of a dual histone methylation writer/reader (PRDM9/ZCWPW1) system in vertebrates remodeled genetic recombination hotspot selection from an ancestral static pattern near genes towards a flexible pattern controlled by the rapidly evolving DNA binding activity of PRDM9.

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