Abstract:In mouse and human meiosis, DNA double-strand breaks (DSBs) initiate homologous recombination and occur at specific sites called hotspots. The localization of these sites is determined by the sequence-specific DNA binding domain of the PRDM9 histone methyl transferase. Here, we performed an extensive analysis of PRDM9 binding in mouse spermatocytes. Unexpectedly, we identified a noncanonical recruitment of PRDM9 to sites that lack recombination activity and the PRDM9 binding consensus motif. These sites includ… Show more
“…2F-H). These data agree with previous observations showing that H3K4me3 and H3K36me3 modifications at hotspots are independent of and therefore precede SPO11 binding and subsequent DSB formation (Buard et al, 2009;Grey et al, 2017).…”
Section: Formation Of Open Chromatin At Hotspots Precedes Meiotic Dsbssupporting
confidence: 93%
“…To test for HELLS binding of hotspots in vivo, we used enriched germ cells from 12 dpp KI mice, since the PRDM9 Cst allele reliably results in increased hotspot detection and higher signal-to-noise in functional genomic experiments (Baker et al, 2014;Grey et al, 2017) ( Fig. 2A and S2).…”
Section: Hells Is Recruited To Recombination Hotspots Through Prdm9mentioning
Chromatin barriers prevent spurious interactions between regulatory elements and DNAbinding proteins. One such barrier, whose mechanism for overcoming is poorly understood, is access to recombination hotspots during meiosis. Here we show that the chromatin remodeler HELLS and DNA-binding protein PRDM9 function together to open chromatin at hotspots and provide access for the DNA double-strand break (DSB) machinery. Recombination hotspots are decorated by a unique combination of histone modifications, not found at other regulatory elements. HELLS is recruited to hotspots by PRDM9, and is necessary for both histone modifications and DNA accessibility at hotspots. In male mice lacking HELLS, DSBs are retargeted to other sites of open chromatin, leading to germ cell death and sterility. Together, these data provide a model for hotspot activation where HELLS and PRDM9 function as a pioneer complex to create a unique epigenomic environment of open chromatin, permitting correct placement and repair of DSBs.
“…2F-H). These data agree with previous observations showing that H3K4me3 and H3K36me3 modifications at hotspots are independent of and therefore precede SPO11 binding and subsequent DSB formation (Buard et al, 2009;Grey et al, 2017).…”
Section: Formation Of Open Chromatin At Hotspots Precedes Meiotic Dsbssupporting
confidence: 93%
“…To test for HELLS binding of hotspots in vivo, we used enriched germ cells from 12 dpp KI mice, since the PRDM9 Cst allele reliably results in increased hotspot detection and higher signal-to-noise in functional genomic experiments (Baker et al, 2014;Grey et al, 2017) ( Fig. 2A and S2).…”
Section: Hells Is Recruited To Recombination Hotspots Through Prdm9mentioning
Chromatin barriers prevent spurious interactions between regulatory elements and DNAbinding proteins. One such barrier, whose mechanism for overcoming is poorly understood, is access to recombination hotspots during meiosis. Here we show that the chromatin remodeler HELLS and DNA-binding protein PRDM9 function together to open chromatin at hotspots and provide access for the DNA double-strand break (DSB) machinery. Recombination hotspots are decorated by a unique combination of histone modifications, not found at other regulatory elements. HELLS is recruited to hotspots by PRDM9, and is necessary for both histone modifications and DNA accessibility at hotspots. In male mice lacking HELLS, DSBs are retargeted to other sites of open chromatin, leading to germ cell death and sterility. Together, these data provide a model for hotspot activation where HELLS and PRDM9 function as a pioneer complex to create a unique epigenomic environment of open chromatin, permitting correct placement and repair of DSBs.
“…This switch during evolution likely facilitated the independent evolution of KRAB domains and zinc finger arrays. It is believed that all extant KRAB-ZFPs evolved from the PRDM9 or PRDM7 gene [34], both of which contain a KRAB domain and a tandem array of C2H2 zinc fingers separated by a PR-SET domain that catalyzes histone H3K4 and H3K36 methylation (Figure 2) [35–38]. However, unlike most mammalian KRAB-ZFPs that interact with the co-repressor TRIM28, the KRAB domain of PRDM9 does not interact with TRIM28 but instead interacts with CXXC1, a component of the COMPASS complex that activates gene transcription [39].…”
Kruppel-associated box zinc finger proteins (KRAB-ZFPs) make up the largest family of transcription factors in humans. These proteins emerged in the last common ancestor of coelacanth and tetrapods and have expanded and diversified in the mammalian lineage. Although their mechanism of transcriptional repression has been well studied for over a decade, the DNA binding activities and the biological function of these proteins has been largely unexplored. Recent large scale ChIP-seq studies and loss-of-function experiments have revealed that KRAB-ZFPs play a major role in the recognition and transcriptional silencing of transposable elements (TEs), consistent with an “arms race model” of KRAB-ZFP evolution against invading TEs. However, this model is insufficient to explain the evolution of many KRAB-ZFPs that appear to domesticate TEs for novel host functions. We highlight some of the mammalian regulatory innovations driven by specific KRAB-ZFPs, including genomic imprinting, meiotic recombination hotspot choice, and placental growth.
“…During meiosis, PRDM9 binds sequences throughout the genome, as specified by its ZF array (reviewed in Ségurel et al, 2011), and the SET domain of PRDM9 makes H3K4me3 and H3K36me3 marks nearby (Eram et al, 2014; Powers et al, 2016). These actions ultimately serve to recruit SPO11 to initiate DSBs, by a mechanism that remains unknown but is associated with the presence of both histone marks (Grey et al, 2017; Getun et al, 2017) and may involve KRAB and SSXRD domains (Parvanov et al, 2017). 10.7554/eLife.24133.003Figure 1.Phylogenetic distribution and evolution of PRDM9 orthologs in vertebrates.Shown are the four domains: KRAB domain (in tan), SSXRD (in white), PR/SET (in light green) and ZF (in gray/dark green; the approximate structure of identified ZFs is also shown).…”
Studies of highly diverged species have revealed two mechanisms by which meiotic recombination is directed to the genome—through PRDM9 binding or by targeting promoter-like features—that lead to dramatically different evolutionary dynamics of hotspots. Here, we identify PRDM9 orthologs from genome and transcriptome data in 225 species. We find the complete PRDM9 ortholog across distantly related vertebrates but, despite this broad conservation, infer a minimum of six partial and three complete losses. Strikingly, taxa carrying the complete ortholog of PRDM9 are precisely those with rapid evolution of its predicted binding affinity, suggesting that all domains are necessary for directing recombination. Indeed, as we show, swordtail fish carrying only a partial but conserved ortholog share recombination properties with PRDM9 knock-outs.DOI:
http://dx.doi.org/10.7554/eLife.24133.001
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