R-loop landscapes in yeast meiosis

Meiotic recombination is initiated by the Spo11-dependent programmed DNA double-strand breaks (DSBs) that are preferentially concentrated within genomic regions known as hotspots, but the factor(s) which specify the positions for meiotic DSB hotspots remain unclear. Here, we show that the frequency and distribution of R-loops, a type of functional chromatin structure comprising single-stranded DNA and a DNA:RNA hybrid, change dramatically throughout meiosis. We detected the formation of multiple de novo R-loops in the pachytene stage, and found they co-localize with meiotic DSB hotspots. We further show that transcription-replication head-on collisions could promote R-loop formation during meiosis, and apparently direct the initiation of meiotic DSB formation. Furthermore, the hotspots can be eliminated by reverse the direction of either transcription or replication, and reconstituted by reverse both of their direction. Our study reveals that R-loops may play dual roles in meiotic recombination. In addition to participation in meiotic DSB processing, some meiotic DSB hotspots may be originated from the transcription-replication head-on collisions during meiotic DNA replication. Overall design: Detection of R-loops by using ssDRIP-seq in yeast meiosis.