Genome‐wide Analysis Reveals Novel Molecular Features of Mouse Recombination

Abstract

Meiotic recombination occurs at discrete genomic loci known as recombination hotspots. To date, the lack of scalable, genome wide assays has limited studies of hotspot formation.Recombination begins with the formation of DNA double‐stranded breaks (DSBs) by the meiosis specific SPO11. Strand resection from the DSB exposes single stranded 3′ overhangs which are bound by recombinases (RAD51, DMC1). We performed ChIP against DMC1 & RAD51, followed by Solexa sequencing (ChIP‐Seq) to generate the first direct map of DSB hotspots in a mammalian genome. We identified 9,874 DSB hotspots at high resolution, including a large cluster in the pseudo‐autosomal region, the site of an obligate recombination event.Mouse hotspots are over‐represented in genes, have a distinct DNA skew pattern and hotspot DNA encodes a preference for nucleosome binding which is manifested in‐vivo. A consensus motif, found at 73% of hotspots is highly similar to the predicted binding site for PRDM9, a histone methyltransferase implicated in hotspot formation. The motif quality also correlates with hotspot strength. ChIP‐Seq against H3K4me3 showed that testis‐specific H3K4me3 peaks are co‐centered with 94% of hotspots, alluding to a central role for this motif, for PRDM9 and for H3K4me3 in DSB formation.The Intramural Research Program of the NIDDK, NIH, supported this research.