%0 Journal Article
%T ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis.
%A Xu W
%A Liu X
%A Li J
%A Sun C
%A Chen L
%A Zhou J
%A Li K
%A Li Q
%A Meng A
%A Sun Q
%J Cell Insight
%V 3
%N 4
%D 2024 Aug
%M 38974143
暂无%R 10.1016/j.cellin.2024.100179
%X R-loop, a chromatin structure containing one RNA:DNA hybrid and one unpaired single-stranded DNA, plays multiple biological roles. However, due to technical limitations, the landscapes and potential functions of R-loops during embryogenesis remain elusive. Here, we developed a quantitative and high-resolution ultra-low input R-loop profiling method, named ULI-ssDRIP-seq, which can map global R-loops with as few as 1000 cells. By using ULI-ssDRIP-seq, we reveal the R-loop dynamics in the zebrafish from gametes to early embryos. In oocytes, the R-loop level is relatively low in most regions of the nuclear genome, except maternal-inherited rDNA and mitochondrial genome. The correlation between R-loop and CG methylation dynamics during early development is relatively weak. Furthermore, either up- or down-regulation of global R-loops by knockdown or overexpression of RNase H1 causes a delay of embryonic development with dramatic expression changes in zygotic and maternal genes. This study provides comprehensive R-loop landscapes during early vertebrate embryogenesis and demonstrates the implication of R-loops in embryonic development.