Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
Center for Plant Biology, Tsinghua University, Beijing, 100084, China.
Nat Plants. 2017 Sep;3(9):704-714. doi: 10.1038/s41477-017-0004-x. Epub 2017 Aug 28.
R-loops are functional structures in chromatin comprising one single-stranded DNA and a DNA:RNA hybrid. Here, we report ssDRIP-seq, a single-strand DNA ligation-based library preparation technique for genome-wide identification of R-loops. When applied in Arabidopsis, ssDRIP-seq exhibits high efficiency, low bias and strand specificity. We found that Arabidopsis R-loops are enriched by both AT and GC skews, and are formed in the sense and antisense orientations. R-loops are strongly enriched in gene promoters and gene bodies, and are highly associated with noncoding RNA and repetitive genomic regions. Furthermore, R-loops are negatively correlated with CG DNA hypermethylation, and are prevalent in regions with multiple chromatin modifications, showing strong correlations with the activated and repressed gene loci. Our analyses indicate that R-loops are common features in the Arabidopsis genome and suggest that the R-loops play diverse roles in genome organization and gene regulation, thereby providing insights into plant nuclear genome formation and function.
R 环是染色质中的功能性结构，由一条单链 DNA 和一条 DNA:RNA 杂交体组成。在这里，我们报告了 ssDRIP-seq，这是一种基于单链 DNA 连接的文库制备技术，可用于全基因组鉴定 R 环。当应用于拟南芥时，ssDRIP-seq 表现出高效、低偏差和链特异性。我们发现，拟南芥 R 环富含 AT 和 GC 倾斜，并且以 sense 和 antisense 方向形成。R 环在基因启动子和基因体中高度富集，并与非编码 RNA 和重复基因组区域高度相关。此外，R 环与 CG DNA 超甲基化呈负相关，并且在具有多个染色质修饰的区域中普遍存在，与激活和抑制基因座表现出强烈的相关性。我们的分析表明，R 环是拟南芥基因组中的常见特征，并表明 R 环在基因组组织和基因调控中发挥着多种作用，从而为植物核基因组的形成和功能提供了新的见解。
