Meiotic recombination is essential for accurate chromosome segregation and genetic diversity in sexually reproducing organisms. Altered crossover frequency during meiosis is a leading cause human aneuploidy, including trisomy 21. However, the measurement of crossovers remains challenging, because it requires sequencing families or large pedigrees, limiting our ability to uncover the molecular mechanisms underlying crossover formation and regulation.
In this study, we present a novel application of single-nucleus ATAC-seq (snATAC-seq) for high-throughput mapping of meiotic crossovers in mammalian sperm from individuals. By optimized snATAC-seq to profile haploid sperm nuclei from hybrid (C57BL/6 x FVB) mice, we achieve robust, genome-wide detection of crossovers. Our analysis of over 3,000 sperm nuclei demonstrated the scalability and accuracy of this approach. In a hyper-recombinogenic Fancm-deficient mouse model, we observed increased crossover frequencies, predominantly through the non-interfering crossover pathway. Crossovers were enriched in genomic regions marked by PRDM9 and DMC1 binding, with a notable association between crossover hotspots and DMC1 recombination sites in Fancm mutants compared to wild type.
These findings establish snATAC-seq as a powerful tool for dissecting the regulation of meiotic recombination. This approach not only provides new insights into the role of Fancm in modulating crossover dynamics but also demonstrates the feasibility of sequencing individual sperm for high-resolution genetic studies.