ZCWPW1 is recruited to recombination hotspots by PRDM9, and is essential for meiotic double strand break repair
- University of Oxford, United Kingdom
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).
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ZCWPW1 and DMC1 ChIP-seq dataNCBI Gene Expression Omnibus, GSE141516.
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DMC1 SSDS ChIPseq from human testisNCBI Gene Expression Omnibus, GSE59836.
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H3K4me3 ChIPseq from mice testisNCBI Gene Expression Omnibus, GSE73833.
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SPO11 ChIPseq from mice testisNCBI Gene Expression Omnibus, GSE84689.
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DMC1 SSDS ChIPseq from WT B6 mouse testisNCBI Gene Expression Omnibus, GSE35498.
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PRDM9, H3K4me3 and H3K36me3 ChIPseq from HEK293 cellsNCBI Gene Expression Omnibus, GSE99407.
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whole-genome bisulfite sequencing (BS-seq) of HEK293 cellsNCBI Gene Expression Omnibus, GSE51867.
Article and author information
Author details
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
- 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
- Received: November 7, 2019
- Accepted: July 31, 2020
- Accepted Manuscript published: August 3, 2020 (version 1)
- 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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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
Further reading
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- Developmental Biology
- Genetics and Genomics
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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- Computational and Systems Biology
- Genetics and Genomics
To fully exploit the potential of single-cell functional genomics in the study of development and disease, robust methods are needed to simplify the analysis of data across samples, time-points and individuals. Here we introduce a model-based factor analysis method, SDA, to analyze a novel 57,600 cell dataset from the testes of wild-type mice and mice with gonadal defects due to disruption of the genes Mlh3, Hormad1, Cul4a or Cnp. By jointly analyzing mutant and wild-type cells we decomposed our data into 46 components that identify novel meiotic gene-regulatory programs, mutant-specific pathological processes, and technical effects, and provide a framework for imputation. We identify, de novo, DNA sequence motifs associated with individual components that define temporally varying modes of gene expression control. Analysis of SDA components also led us to identify a rare population of macrophages within the seminiferous tubules of Mlh3-/- and Hormad1-/- mice, an area typically associated with immune privilege.
