ANKRD31 anchors meiotic double-strand break formation as a direct partner of REC114

Homologous recombination initiated by double-strand breaks (DSBs) is crucial for chromosome pairing and segregation during meiosis. Here we unveil mouse ANKRD31 as a lynchpin controlling DSB formation. Spermatocytes lacking ANKRD31 have altered DSB locations and fail to target DSBs to X and Y pseudoautosomal regions (PAR). They also have delayed and fewer recombination sites but, paradoxically, more total DSBs, indicating DSB dysregulation. Unrepaired DSBs and pairing failures—stochastic on autosomes, nearly absolute on X and Y—cause meiotic arrest and male sterility, while Ankrd31-deficient females have reduced oocyte reserves. A crystal structure defines direct ANKRD31–REC114 molecular contacts and reveals a surprising pleckstrin homology domain in REC114. In vivo, ANKRD31 recruits REC114 to the PAR and elsewhere. Our findings inform a model that ANKRD31 is a scaffold anchoring REC114 and other factors to specific genomic locations, promoting efficient and timely DSB formation but also suppressing formation of clustered DSBs. For ssDNA sequencing: Three samples of juvenile mice from same breeding colony (Ankrd31 knocknout, heterozygote, and wild type control); one sample of Ankrd31 knockout adult; one sample of wild type adult; two samples of wild type adult (one of which is a control using an irrelevant-antibody); and one sample from Prdm9 knockout adult. For H3K4me3 ChIPseq: two biological replicates each of wild type and Ankrd31 knockout.