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  2. Genetics and Genomics
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The histone modification reader ZCWPW1 links histone methylation to PRDM9-induced double strand break repair

  1. Tao Huang
  2. Shenli Yuan
  3. Lei Gao
  4. Mengjing Li
  5. Xiaochen Yu
  6. Jianhong Zhang
  7. Yingying Yin
  8. Chao Liu
  9. Chuanxin Zhang
  10. Gang Lu
  11. Wei Li
  12. Jiang Liu  Is a corresponding author
  13. Zi-Jiang Chen  Is a corresponding author
  14. Hongbin Liu  Is a corresponding author
  1. Shandong University, China
  2. Beijing Institute of Genomics, Chinese Academy of Sciences, China
  3. Institute of Zoology, Chinese Academy of Sciences, China
  4. Chinese University of Hong Kong, China
Research Article
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Cite this article as: eLife 2020;9:e53459 doi: 10.7554/eLife.53459

Abstract

The histone modification writer Prdm9 has been shown to deposit H3K4me3 and H3K36me3 at future double-strand break (DSB) sites during the very early stages of meiosis, but the reader of these marks remains unclear. Here, we demonstrate that Zcwpw1 is an H3K4me3 reader that is required for DSB repair and synapsis in mouse testes. We generated H3K4me3 reader-dead Zcwpw1 mutant mice and found that their spermatocytes were arrested at the pachytene-like stage, which phenocopies the Zcwpw1 knock–out mice. Based on various ChIP-seq and immunofluorescence analyses using several mutants, we found that Zcwpw1's occupancy on chromatin is strongly promoted by the histone-modification activity of PRDM9. Zcwpw1 localizes to DMC1-labelled hotspots in a largely Prdm9-dependent manner, where it facilitates completion of synapsis by mediating the DSB repair process. In sum, our study demonstrates the function of ZCWPW1 that acts as part of the selection system for epigenetics-based recombination hotspots in mammals.

Data availability

The raw sequencing data produced in this study (ChIP-seq data listed in Supplemental Table S1) and RNA-seq data have been deposited to the Genome Sequence Archive (https://bigd.big.ac.cn/gsa/s/CjjpbIjf) under accession number PRJCA001901.

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

Article and author information

Author details

  1. Tao Huang

    National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7086-570X

  2. Shenli Yuan

    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  3. Lei Gao

    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  4. Mengjing Li

    Department of Biochemistry and Molecular Biology, Shandong University, Jinan, China
    Competing interests
    The authors declare that no competing interests exist.

  5. Xiaochen Yu

    National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
    Competing interests
    The authors declare that no competing interests exist.

  6. Jianhong Zhang

    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  7. Yingying Yin

    National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
    Competing interests
    The authors declare that no competing interests exist.

  8. Chao Liu

    State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  9. Chuanxin Zhang

    National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
    Competing interests
    The authors declare that no competing interests exist.

  10. Gang Lu

    CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China
    Competing interests
    The authors declare that no competing interests exist.

  11. Wei Li

    State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6235-0749

  12. Jiang Liu

    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    For correspondence
    liuj@big.ac.cn
    Competing interests
    The authors declare that no competing interests exist.

  13. Zi-Jiang Chen

    National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
    For correspondence
    chenzijiang@hotmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6637-6631

  14. Hongbin Liu

    National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
    For correspondence
    hongbin_sduivf@aliyun.com
    Competing interests
    The authors declare that no competing interests exist.

Funding

National Key Research and Development Programs of China (2018YFC1003400)

  • Hongbin Liu

National Natural Science Foundation of China (31890780)

  • Hongbin Liu

Shandong University (2016WLJH50)

  • Hongbin Liu

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

Ethics

Animal experimentation: All mice were housed under controlled environmental conditions with free access to water and food, and illumination was on between 6 am and 6 pm. All experimental protocols were approved by the Animal Ethics Committee of the School of Medicine of Shandong University.

Reviewing Editor

  1. Bernard de Massy, CNRS UM, France

Publication history

  1. Received: November 8, 2019
  2. Accepted: May 5, 2020
  3. Accepted Manuscript published: May 6, 2020 (version 1)
  4. Version of Record published: June 24, 2020 (version 2)
  5. Version of Record updated: November 11, 2020 (version 3)

Copyright

© 2020, Huang 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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Further reading

    1. Genetics and Genomics

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

    Daniel Wells et al.
    Research Article Updated

    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.

    1. Developmental Biology
    2. Genetics and Genomics

    Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice

    Mohamed Mahgoub et al.
    Research Article Updated

    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.

    1. Genetics and Genomics

    Sexual Reproduction: Reading the epigenetic code for exchanging DNA

    Mathilde Biot, Bernard de Massy
    Insight

    Three independent studies show that a protein called ZCWPW1 is able to recognize the histone modifications that initiate the recombination of genetic information during meiosis.