PRDM9 Drives Evolutionary Erosion of Hotspots in <i>Mus musculus</i> through Haplotype-Specific Initiation of Meiotic Recombination

<div><p>Meiotic recombination generates new genetic variation and assures the proper segregation of chromosomes in gametes. PRDM9, a zinc finger protein with histone methyltransferase activity, initiates meiotic recombination by binding DNA at recombination hotspots and directing the position of DNA double-strand breaks (DSB). The DSB repair mechanism suggests that hotspots should eventually self-destruct, yet genome-wide recombination levels remain constant, a conundrum known as the hotspot paradox. To test if PRDM9 drives this evolutionary erosion, we measured activity of the <i>Prdm9</i>^Cst allele in two <i>Mus musculus</i> subspecies, <i>M.m. castaneus</i>, in which <i>Prdm9^Cst</i> arose, and <i>M.m. domesticus</i>, into which <i>Prdm9^Cst</i> was introduced experimentally. Comparing these two strains, we find that haplotype differences at hotspots lead to qualitative and quantitative changes in PRDM9 binding and activity. Using <i>Mus spretus</i> as an outlier, we found most variants affecting PRDM9^Cst binding arose and were fixed in <i>M.m. castaneus</i>, suppressing hotspot activity. Furthermore, <i>M.m. castaneus</i>×<i>M.m. domesticus</i> F1 hybrids exhibit novel hotspots, with large haplotype biases in both PRDM9 binding and chromatin modification. These novel hotspots represent sites of historic evolutionary erosion that become activated in hybrids due to crosstalk between one parent's <i>Prdm9</i> allele and the opposite parent's chromosome. Together these data support a model where haplotype-specific PRDM9 binding directs biased gene conversion at hotspots, ultimately leading to hotspot erosion.</p>