R-loops orchestrate the maternal-to-zygotic transition by harnessing RNA polymerase II pause release

R-loops, ubiquitous three-stranded nucleic acid structures abundant in the mammalian genome, play pivotal roles in diverse biological processes ^1–3 . However, the dynamics and functions of R-loops during mammalian preimplantation embryonic development remain poorly understood. Here we optimized an innovative, ultra-sensitive RIAN-seq method capable of mapping genome-wide R-loop landscape using ultra-low cell numbers to investigate R-loop dynamics in mouse gametes and early embryos. Our findings reveal the widespread presence of AT-rich R-loops during early mouse embryonic development and highlight their critical roles in orchestrating transcription machinery during zygotic genome activation (ZGA). We demonstrate that the stability and inheritance of R-loops through developmental stages are governed by their sequence composition, with GC-rich R-loops exhibiting greater stability. Notably, R-loops, particularly AT-rich R-loops, inhibit DDX21 helicase activity on the 7SK/HEXIM1 snRNP complex, thereby reducing CDK9 release. This, in turn, modulates the phosphorylation of Ser2 at C-terminal domain (CTD) of RNA polymerase II (RNAPIIS2p) at the promoters of major ZGA and maternal genes. Furthermore, R-loops promote RNAPII accumulation at major ZGA gene promoters, preventing RNAPII from premature release and ensuring timely activation of major ZGA genes. Conversely, R-loops enhance the retention of stalled RNAPII at maternal gene promoters, effectively repressing their expression and facilitating the maternal-to-zygotic transition. In summary, our study unveils a key role for R-loops in regulating the maternal-to-zygotic transcription transition and early embryonic development in mice.