Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm

Hinch, Anjali Gupta; Zhang, Gang; Becker, Philipp; Moralli, Daniela; Hinch, Robert; Davies, Benjamin; Bowden, Rory; Donnelly, Peter

doi:10.1126/science.aau8861

Cited by 115 publications

(222 citation statements)

References 69 publications

Supporting

Mentioning

184

Contrasting

Order By: Relevance

“…driven by expected WT ZCWPW1 recruitment levels at each hotspot (Supplementary Figure 15). ZCWPW1 therefore offers a (thus far) unique protein, linking PRDM9 binding with its downstream functions (Davies et al, 2016;Hinch et al, 2019;R. Li et al, 2019) in aiding rapid DSB processing/repair at hotspots whose homologue is bound by PRDM9.…”

Section: Discussionmentioning

confidence: 99%

“…This is thought to reflect a wider phenomenon of faster DSB repair occurring within those hotspots whose homologue is more strongly bound by PRDM9, i.e. those hotspots with a stronger H3K4me3 signal in the WT mouse (Davies et al, 2016;Hinch et al, 2019;R. Li et al, 2019).…”

Section: Dmc1 Persistencementioning

confidence: 99%

“…From mid-zygotene to early pachytene, as part of the recombinational repair process, DMC1 dissociates from the ssDNA and counts decrease until all breaks (except those on the XY chromosomes) are repaired in late pachytene (Moens et al, 2002). At DSB sites where the homologous chromosome is not bound by PRDM9, DMC1 signal is strongly elevated (Davies et al, 2016), suggesting delayed DSB repair, while fewer homologous recombination events occur (Hinch et al, 2019;R. Li et al, 2019), suggesting that (eventual) DSB repair may sometimes use a sister chromosome pathway.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Wells

Bitoun

Moralli

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

During meiosis, homologous chromosomes pair (synapse) and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, recombination initiates with double-strand breaks (DSBs) within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have yet been identified.We identified Zcwpw1, which possesses H3K4me3 and H3K36me3 recognition domains, as highly co-expressed 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 recognizes CpG dinucleotides, including within many Alu transposons.Male Zcwpw1 homozygous knockout mice show completely normal DSB positioning, but persistent DMC1 foci at many hotspots, particularly those more strongly bound by PRDM9, severe DSB repair and synapsis defects, and downstream sterility. Our findings suggest a model where ZCWPW1 recognition of PRDM9-bound sites on either the homologous, or broken, chromosome is critical for synapsis, and hence fertility. Graphical Abstract LegendIn humans and other species, recombination is initiated by double strand breaks at sites bound by PRDM9. Upon binding, PRDM9 deposits the histone marks H3K4me3 and H3K36me, but the functional importance of these marks has remained unknown. Here, we show that PRDM9 recruits ZCWPW1, a reader of both these marks, to its binding sites genome-wide. ZCWPW1 does not help position the breaks themselves, but is essential for their downstream repair and chromosome pairing, and ultimately meiotic success and fertility in mice.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Dmc1 Persistencementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Wells

Bitoun

Moralli

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The ability to target DSBs to open chromatin is critical for meiotic recombination. In mice, meiotic DSBs(Baker et al, 2014;Lange et al, 2016) and crossovers identified through single-sperm sequencing(Hinch et al, 2019) are concentrated within hotspot NDRs. In the absence of open chromatin at hotspots, by loss of either HELLS or PRDM9, SPO11 preferentially targets other regions of accessible chromatin to create DSBs, even when the effect of these ectopic breaks is usually blocked meiotic progress and infertility.…”

mentioning

confidence: 99%

HELLS and PRDM9 form a Pioneer Complex to Open Chromatin at Meiotic Recombination Hotspots

Spruce

Dlamini

Ananda

et al. 2019

Preprint

View full text Add to dashboard Cite

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.

show abstract

“…The advent of whole genome sequencing has permitted high resolution crossover maps, by identifying regions of the genome where parental haplotypes change in recombinant individuals (Kulathinal et al 2008;Rockman and Kruglyak 2009;Dumont et al 2011;Miller et al 2012;Comeron et al 2012) . More recently, single-cell sequencing technologies have further extended such high-throughput crossover detection directly from sperms (Hinch et al 2019) . While providing impressive resolution often at the level of individual bases, these approaches are difficult to scale, as each recombinant individual/cell requires a separate library preparation and/or barcode.…”

Section: Introductionmentioning

confidence: 99%

The theory and practice of measuring broad-range recombination rate from marker selected pools

Wei

Bachtrog

2019

Preprint

View full text Add to dashboard Cite

Recombination is the exchange of genetic material between homologous chromosomes via physical crossovers. Pioneered by T. H. Morgan and A. Sturtevant over a century ago, methods to estimate recombination rate and genetic distance require scoring large number of recombinant individuals between molecular or visible markers. While high throughput sequencing methods have allowed for genome wide crossover detection producing high resolution maps, such methods rely on large number of recombinants individually sequenced and are therefore difficult to scale. Here, we present a simple and scalable method to infer near chromosome-wide recombination rate from marker selected pools and the corresponding analytical software MarSuPial. Rather than genotyping individuals from recombinant backcrosses, we bulk sequence marker selected pools to infer the allele frequency decay around the selected locus; since the number of recombinant individuals increases proportionally to the genetic distance from the selected locus, the allele frequency across the chromosome can be used to estimate the genetic distance and recombination rate. We mathematically demonstrate the relationship between allele frequency attenuation, recombinant fraction, genetic distance, and recombination rate in marker selected pools. Based on available chromosome-wide recombination rate models of Drosophila , we simulated read counts and determined that nonlinear local regressions (LOESS) produce robust estimates despite the high noise inherent to sequencing data. To empirically validate this approach, we show that (single) marker selected pools closely recapitulate genetic distances inferred from scoring recombinants between double markers. We theoretically determine how secondary loci with viability impacts can modulate the allele frequency decay and how to account for such effects directly from the data. We generated the recombinant map of three wild derived strains which strongly correlates with previous genome-wide measurements. Interestingly, amidst extensive recombination rate

show abstract

Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm

Cited by 115 publications

References 69 publications

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

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

HELLS and PRDM9 form a Pioneer Complex to Open Chromatin at Meiotic Recombination Hotspots

The theory and practice of measuring broad-range recombination rate from marker selected pools

Contact Info

Product

Resources

About