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.

中文翻译：

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R-环是拟南芥基因组的常见染色质特征。

R-环是染色质中的功能结构，包含一个单链DNA和一个DNA：RNA杂种。在这里，我们报告ssDRIP-seq，基于单链DNA连接的文库制备技术，用于R环的全基因组鉴定。当在拟南芥中使用时，ssDRIP-seq表现出高效率，低偏性和链特异性。我们发现拟南芥的R环被AT和GC偏斜所丰富，并以有义和反义方向形成。R环在基因启动子和基因体中高度富集，并且与非编码RNA和重复性基因组区域高度相关。此外，R环与CG DNA超甲基化负相关，并且在具有多个染色质修饰的区域中普遍存在，显示出与激活和抑制的基因位点有很强的相关性。