{Reference Type}: Journal Article
{Title}: ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis.
{Author}: Xu W;Liu X;Li J;Sun C;Chen L;Zhou J;Li K;Li Q;Meng A;Sun Q;
{Journal}: Cell Insight
{Volume}: 3
{Issue}: 4
{Year}: 2024 Aug
暂无{DOI}: 10.1016/j.cellin.2024.100179
{Abstract}: 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.