Extended Data Fig. 8: R-loop distribution and epigenetic features of ChRD-PET.
From: The landscape of promoter-centred RNA–DNA interactions in rice
a, Density distribution of H3K4me3 ChRD-PET DNA at H3K4me3 peak center. Three categories of H3K4me3 ChRD-PET DNA related to R-loop were analysed: H3K4me3 anchors overlapping with hybrid RNA: DNAs, H3K4me3 anchors overlapping with R-loop and associating with proximal RNA, and H3K4me3 anchors not overlapping with R-loop. b, Density distribution of H3K4me3 ChIP-seq at H3K4me3 peaks center in different categories as same as classification in a. c, Conservation analysis of ChRD-PET RNA in different categories of interacting DNA with same classification as a. d, Methylation ratios of peaks with H3K4me3 modification in different categories as same as classification in a. Random: regions on the genome randomly generated by BEDTools. e, Methylation ratios of ChRD-PET RNA in different categories of interacting DNA with same classification as a. Random: regions on the genome randomly generated by BEDTools. f, Density distribution and heatmap of H3K4me3 ChIP-seq and ATAC-seq for three types of peaks classified in Fig. 5c. g, DNA methylation level of three types of peaks classified in Fig. 5c.
