Genome-wide Map of R-loops Reveals its interplays with Transcription and Genome Integrity during Germ Cell Meiosis

R-loop is a naturally formed three-strand nucleic acid structure that was reported to take part in multiple biological processes. In our study, we firstly mapped R-loop genomic distribution in mammalian meiotic cells by genome-wide S9.6 CUT & Tag seq. R-loop mainly distributed at promoter-related regions, and combined with systematically transcriptome analysis showed R-loop was closely related to transcription in the meiotic process. Moreover, we verified the conclusion by constructing conditional knockout mice of Rnaseh1, which delete the R-loop endonuclease before meiosis entry. Lack of RNase H1 caused mice completely sterile with R-loop accumulation and abnormal DSB repairing in spermatocytes. Further analysis showed R-loop accumulation in leptotene/zygotene influenced transcriptional regulation in the pachytene stage. Thus, mutual regulation of R-loop and transcription plays an essential role in spermatogenesis. Overall design: Genome-wide R-loop profiling during spermatogenesis generated by S9.6 CUT&Tag deep sequencing