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

Abstract

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.

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

“…Consistent with this idea, ZCWPW1 binding is positively associated with levels of both H3K4me3 and H3K36me3 marks ( Figure 6—figure supplements 1 and 2 , tested separately, not necessarily ‘dual’ marks coincident within an individual cell, although locations of these marks in meiotic cells are rarely coincident except at hotspots [ Powers et al, 2016 ]). While we cannot rule out a direct interaction between ZCWPW1 and PRDM9, others have shown that dual modified peptides have a greater affinity to ZCWPW1 than peptides carrying the single modifications, supporting that the marks themselves are responsible for ZCWPW1’s recruitment ( Mahgoub et al, 2020 ). We examined transcription start sites, which possess H3K4me3 at high levels, but lack H3K36me3, observing some ZCWPW1 signal at these sites, but with a uniformly lower mean ZCWPW1 enrichment compared to those with evidence of PRDM9 binding (and hence both histone marks) ( Figure 6 ).…”

“…Like DMC1, RPA2 levels were also significantly elevated in the Zcwpw1 −/− mouse from zygotene onwards ( Figure 4—figure supplement 2 ). In Zcwpw1 −/− males, like in the Prdm9 −/− mutant, DSBs form and recruit RPA2, RAD51 and DMC1 in similar numbers ( Huang et al, 2020 ; Li et al, 2019a ; Mahgoub et al, 2020 ), but fail to repair efficiently, accompanied by asynapsis and meiotic arrest at pseudo-pachytene. Indeed, we observe late unrepaired DMC1 foci mainly on HORMAD2-positive asynapsed chromosomes ( Figure 4—figure supplement 3 ).…”

Programmed DNA Damage and Physiological DSBs: Mapping, Biological Significance and Perturbations in Disease States

“…ZCWPW1 is a factor that participates in repairing PRDM9-induced DSBs during meiosis. This study, made possible with NGS and END-seq, demonstrated the tight regulation that is ensued due to the collaboration between ZCWPW1 and PRDM9 [99].…”

PRDM9 activity depends on HELLS and promotes local 5-hydroxymethylcytosine enrichment

“…As no evidence of HELLS/TET interaction in meiotic cells is available, a PRDM9-dependent chromatin modification might be implicated in recruiting the putative TET activity. ZCWPW1, a reader of H3K4me3 and H3K36me3 that is required for efficient DSB repair ( Huang et al, 2020 ; Mahgoub et al, 2020 ; Wells et al, 2019 ), might be directly or indirectly involved in this recruitment.…”

“…In addition, these histone modifications may play a role in DSB repair. Indeed, ZCWPW1, a protein reader of H3K4me3 and H3K36me3, is required for efficient DSB repair ( Huang et al, 2020 ; Li et al, 2019 ; Mahgoub et al, 2020 ; Wells et al, 2019 ). Whatever their exact role, the presence of both histone modifications leads to a unique chromatin landscape at PRDM9 sites that is not present at promoters, where H3K36me3 is depleted ( Grey et al, 2017 ; Lam et al, 2019 ; Powers et al, 2016 ).…”