数字农科院2.0

ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis

文献类型： 外文期刊

作者： Wei Xu;Xin Liu;Jinjin Li;Changbin Sun;Luxi Chen;Jincong Zhou;Kuan Li;Qin Li;Anming Meng;Qianwen Sun

作者机构：

关键词： （1-0-2）Embryogenesis;Embryonic development;Next generation sequencing;R-loop;Zygotic genome activation

期刊名称： Cell Insight

ISSN： 2772-8927

年卷期： 2024 年 3 卷 4 期

页码：

收录情况： 无来源刊（2024版）

摘要： 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.

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