Large disruptions to mammalian spermatogenesis downstream of genetic perturbations in meiotic double-strand break repair

Fertility in mammalian species depends on the successful pairing of homologous chromosomes, mediated by formation of DNA double-strand breaks and a process of homology search involved in repairing these breaks. PRDM9, the most rapidly evolving mammalian protein, which specifies the positioning of breaks where it binds to DNA, also facilitates homology search and chromosome pairing in settings where it “symmetrically” binds the same locations on the two homologous copies of each chromosome. Here, we investigate the mechanisms by which mutations influencing binding patterns of this key early-acting protein impact fertility in hybrid mice with varying degrees of genome-wide PRDM9 binding (a)symmetry, and high levels of genetic diversity.

By gathering and statistically analyzing data comprising transcription and chromatin accessibility patterns in single nuclei from male germline tissue in these animals, we precisely delineate and quantify key molecular developments (both normal and pathological) in spermatogenesis. We find that these mice exhibit a wide spectrum of fertility. Asymmetry specifically at PRDM9 binding sites is necessary for asynapsis, which is otherwise unaffected by almost 1% sequence divergence genome-wide, but animals vary strongly in their sensitivity to this asymmetry. Indeed, we identify a locus containing Dmc1 and Mei1 on chromosome 15, which genetically controls (R ² =0.64) most of this sensitivity variation. We show that despite high levels of pachytene cell death some cells survive to complete one or both meiotic divisions. However, resulting cells exhibit abnormalities including aneuploidy of multiple chromosomes, especially the X/Y chromosomes, impacts likely to persist into offspring. They also show strongly perturbed crossover rates at multi-megabase scales, in contrast to previous studies finding PRDM9 alleles do not differ in broad-scale rates. These abnormalities occur not only as direct consequences of asynapsis: accompanying meiotic silencing of unpaired chromatin (MSUC) is implicated in disrupting the proper progression of meiosis. Beyond providing insights into male meiosis downstream of homology search and synapsis, this work highlights a clear mechanism by which common non-coding variation, through alterations in efficiency of early processes, can drive cascading effects on a complex trait like fertility.