Arabidopsis thaliana Raw sequence reads. Arabidopsis thaliana

Inspired by the important roles of the special chromatin structure R-loops, here we report an efficient, unbiased, high-throughput, strand-specific method, ssDRIP-seq, for genome-wide identification of R-loops in Arabidopsis genome. We found that Arabidopsis R-loops are formed in both the sense and antisense orientations of genes, and prefer both AT and GC skews, especially high accumulated in regions having both AT- and GC skews. R-loops are prevalent in regions with multiple chromatin modifications, and negatively correlated with DNA methylation. R-loops are strongly enriched in gene promoters and gene bodies, highly associated with lncRNAs and repetitive loci, and correlated with both activated and repressed genes. In summary, our data showed that R-loops are a common feature, and probably the main components, of the Arabidopsis genome. Our further integrative analysis suggested the diverse roles of R-loops in genome organization and gene regulation, thereby providing novel insights into plant nuclear genome formation.