Mapping Meiotic Recombination DNA Double‐Strand Breaks (DSBs) Hotspots —Methodological Advances and Challenges

Programmed DNA double‐strand breaks (DSBs) initiate meiotic recombination at discrete genomic hotspots, and their precise mapping is crucial for understanding the molecular regulation of genome stability and evolution. A variety of genome‐wide methods have been developed, each leveraging different biochemical principles — from direct capture of Spo11‐oligonucleotide covalent intermediates to sequencing protein‐bound single‐stranded DNA (ssDNA), in situ DNA end labeling, and chromatin immunoprecipitation (ChIP). Direct approaches such as Spo11‐oligo mappin, CC‐seq and in situ DNA end labeling (END‐seq) achieve nucleotide‐resolution detection of the initial cleavage site, but typically require large amounts of starting material. ChIP ssDNA‐based methods (e.g., ChIP‐SSDS) enrich for recombinase associated proteins‐ bound (DMC1, RAD51, RPA) intermediates, reflecting an indirect proxy of DSB sites, and are limited to early resection stages. Together, while these complementary methods comprise a toolbox for dissecting meiotic hotspot landscapes, a more robust and facile approach for routine detection of meiotic DSB hotspots across diverse species remains to be developed.