A high-resolution meiotic crossover map from single-nucleus ATAC-seq reveals insights into the recombination landscape in mammalian sperm

Meiotic crossovers promote correct chromosome segregation and the shuffling of genetic diversity. However, the measurement of crossovers remains challenging, impeding our ability to decipher the molecular mechanisms that are necessary for their formation and regulation. Here we demonstrate a novel repurposing of the single-nucleus Assay for Transposase Accessible Chromatin with sequencing (snATAC-seq) as a simple and high-throughput method to identify and characterise meiotic crossovers from sperm nuclei. We first validate the feasibility of obtaining genome-wide coverage from snATAC-seq by using ATAC-seq on bulk haploid mouse sperm, ensuring adequate variant detection for haplotyping. Subsequently, we adapt droplet-based snATAC-seq for crossover detection, revealing over 25,000 crossovers in F1 hybrid mice. Comparison between wildtype and a hyper-recombinogenic Fancm-deficient mutant mouse model confirmed an increase in crossover rates in this genotype, however a distribution which was unchanged. We also find that regions with the highest rate of crossover formation are enriched for DMC1 and PRDM9, with a subset that is further enriched for DMC1 in Fancm-deficient mice. Our findings demonstrate the utility of snATAC-seq as a robust and scalable tool for high-throughput crossover detection, offering insights into meiotic crossover dynamics and elucidating the underlying molecular mechanisms. It is possible that the research presented here with snATAC-seq of haploid sperm could be extended into fertility-related diagnostics.