Re-engineering meiotic recombination in the mouse. E. Hatton1, B. Davies*1, J. Hussin1, F. Pratto2, D. Biggs1, N. Altemose3, N. Hortin1, C. Preece1, D. Moralli1, A. Gupta-Hinch1, K. Brick2, C. Green1, D. Camerini-Otero2, S. Myers*1,3, P. Donnelly*1,3 1) Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; 2) National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, USA; 3) Department of Statistics, University of Oxford, Oxford, United Kingdom.

   PRDM9 is a zinc-finger DNA binding protein implicated in controlling the localisation of meiotic recombination events and displays a large diversity in its zinc-finger binding array within and between species. Here, we successfully replaced the zinc-finger array of Prdm9 in a C57BL/6 mouse strain by its human B allele counterpart, providing a precise assay to investigate PRDM9 binding properties and their consequences. We developed a new statistical approach for calling double-strand break (DSB) hotspots from ChipSeq data, which utilises asymmetries on the two DNA strands expected around real hotspots. Our results confirm that virtually all DSB hotspots are under PRDM9 control, and indicate that a change in its DNA recognition domain is sufficient to fully reset the hotspot landscape. Sequence motifs enriched within DSB hotspots in the humanized mouse closely match the consensus motif reported in humans, and more than 78% of the DSB hotspots contain such a motif. In the heterozygote mouse, the human allele dominates the mouse allele in specifying DSB hotspots, which suggests substantial differences in binding abilities between alleles and/or in efficiencies to access their target motifs: 69% of the DSB hotspots in the heterozygote are found in the humanized homozygote mouse, whereas only 26% are inherited from the wild type homozygote. We also compared the localisation of DSB hotspots with several genomic and epigenetic elements. In particular, we found that exons are enriched in DSB hotpots in both humanized and wild type mice. Overall, our results suggest that Prdm9 zinc-finger array plays a predominant role in the localisation at the fine genomic scale, but that broad scale properties of DSB hotspot maps are mainly independent of the zinc-finger array. Finally, we show that the replacement of the zinc-finger array of the C57BL/6 Prdm9 allele was sufficient to rescue fertility in a well-characterised M. m. musculus and M. m. domesticus cross, in which hybrid males are otherwise fully sterile.