PDF(Pubmed)
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.
摘要：
R-loop,染色质结构包含一个RNA：DNA杂交体和一个未配对的单链DNA，发挥多种生物学作用。然而,由于技术限制,胚胎发育过程中R环的景观和潜在功能仍然难以捉摸。这里,我们开发了一种定量和高分辨率的超低输入R环分析方法，命名为ULI-ssDRIP-seq，它可以映射全球R循环与1000个细胞。通过使用ULI-ssDRIP-seq，我们揭示了斑马鱼从配子到早期胚胎的R环动态。在卵母细胞中，在核基因组的大多数区域，R环水平相对较低，除了母系遗传的rDNA和线粒体基因组。早期发育过程中R-loop和CG甲基化动力学之间的相关性相对较弱。此外，通过敲低或过表达RNaseH1来上调或下调全局R环，会导致胚胎发育延迟，合子和母本基因的表达发生巨大变化。这项研究提供了早期脊椎动物胚胎发生过程中全面的R环景观，并证明了R环在胚胎发育中的意义。
