Transposase-assisted in situ capture of recombination DSB hotspots (TAID-seq) [CUT&Tag]

Genome-wide profiling of the meiotic recombination initiation sites – DNA double-strand break (DSB) hotspots – is essential for understanding the evolution of species of variable origins in sexually reproducing organisms, and to provide the mechanistic insights into recombination, genetic engineering, and plant or animal breeding. While current high-throughput sequencing approaches are powerful tools for detecting DSB hotspots, revealing remarkable mechanisms underlying meiotic recombination, they are often time-consuming, labor-intensive, and, in some occasions, practically impossible owing to large sample inputs. Herein, we present Transposase-assisted in situ capture of recombination DSB hotspots (TAID-seq), an approach that leverages both RNA:DNA hybrids and D-loop intermediates at DSB sites. TAID-seq enables the rapid and efficient genome-wide capture of meiotic DSB hotspots. Compared with existing approaches, the TAID-seq workflow requires as few as 50,000 testicular cells, sequencing depths as low as 8 million (M) reads, and can be completed in under 1.5 days. We show that TAID-seq can recapitulate the global recombination DSB landscape in mice and humans. TAID-seq is compatible with archived frozen tissues, and revealed significant difference in the DSB hotspot patterning in human individuals. Further extended applications of TAID-seq strategy will likely unravel the genome-wide recombination DSB landscapes between sexes, populations, and in more rare species, while also illuminating rules and mechanisms underlying spatiotemporal regulation of recombination in health and disease.