Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA

Khil, Pavel P.; Smagulova, Fátima; Brick, Kevin; Camerini‐Otero, R. Daniel; Petukhova, Galina V.

doi:10.1101/gr.130583.111

Cited by 115 publications

(144 citation statements)

References 30 publications

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“…We previously developed a variant of chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) to map DSB sites using anti-DMC1 antibodies and sequencing-based detection of ssDNA (SSDS) (Smagulova et al 2011;Khil et al 2012). Here, we used this approach to map recombination initiation hot spots in inbred mouse strains with different Prdm9 alleles (Fig.…”

Section: High-resolution Genome-wide Maps Of Recombination Initiationmentioning

confidence: 99%

The evolutionary turnover of recombination hot spots contributes to speciation in mice

et al. 2016

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Meiotic recombination is required for the segregation of homologous chromosomes and is essential for fertility. In most mammals, the DNA double-strand breaks (DSBs) that initiate meiotic recombination are directed to a subset of genomic loci (hot spots) by sequence-specific binding of the PRDM9 protein. Rapid evolution of the DNA-binding specificity of PRDM9 and gradual erosion of PRDM9-binding sites by gene conversion will alter the recombination landscape over time. To better understand the evolutionary turnover of recombination hot spots and its consequences, we mapped DSB hot spots in four major subspecies of Mus musculus with different Prdm9 alleles and in their F1 hybrids. We found that hot spot erosion governs the preferential usage of some Prdm9 alleles over others in hybrid mice and increases sequence diversity specifically at hot spots that become active in the hybrids. As crossovers are disfavored at such hot spots, we propose that sequence divergence generated by hot spot turnover may create an impediment for recombination in hybrids, potentially leading to reduced fertility and, eventually, speciation.

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Section: High-resolution Genome-wide Maps Of Recombination Initiationmentioning

confidence: 99%

The evolutionary turnover of recombination hot spots contributes to speciation in mice

et al. 2016

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“…It was previously believed that ssDNA could not be detected by ChIP-Seq. However, several studies have recently shown that this is not the case; ssDNA is rendered double-stranded during the library preparation process through the formation of DNA hairpins that arise as a result of regions of microhomology (42)(43)(44). This allows the DNA to be amplified and detected by ChIP-Seq.…”

Section: Methodsmentioning

confidence: 99%

Quantitative genomic analysis of RecA protein binding during DNA double-strand break repair reveals RecBCD action in vivo

Cockram

Milana

Danos

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Understanding molecular mechanisms in the context of living cells requires the development of new methods of in vivo biochemical analysis to complement established in vitro biochemistry. A critically important molecular mechanism is genetic recombination, required for the beneficial reassortment of genetic information and for DNA double-strand break repair (DSBR). Central to recombination is the RecA (Rad51) protein that assembles into a spiral filament on DNA and mediates genetic exchange. Here we have developed a method that combines chromatin immunoprecipitation with next-generation sequencing (ChIP-Seq) and mathematical modeling to quantify RecA protein binding during the active repair of a single DSB in the chromosome of Escherichia coli. We have used quantitative genomic analysis to infer the key in vivo molecular parameters governing RecA loading by the helicase/ nuclease RecBCD at recombination hot-spots, known as Chi. Our genomic analysis has also revealed that DSBR at the lacZ locus causes a second RecBCD-mediated DSBR event to occur in the terminus region of the chromosome, over 1 Mb away.homologous recombination | mechanistic modelling | DNA repair | RecA | RecBCD

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“…For H3K4me3 and DMC1 ChIP-seq experiments, we used the protocols described by Buard et al (2009) and Khil et al (2012), respectively.…”

Section: Chip-seq Experiments and Analysismentioning

confidence: 99%

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

et al. 2017

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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 include gene promoters, where PRDM9 is recruited in a DSB-dependent manner. Another subset reveals DSB-independent interactions between PRDM9 and genomic sites, such as the binding sites for the insulator protein CTCF. We propose that these DSB-independent sites result from interactions between hotspot-bound PRDM9 and genomic sequences located on the chromosome axis.

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Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA

Cited by 115 publications

References 30 publications

The evolutionary turnover of recombination hot spots contributes to speciation in mice

The evolutionary turnover of recombination hot spots contributes to speciation in mice

Quantitative genomic analysis of RecA protein binding during DNA double-strand break repair reveals RecBCD action in vivo

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

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