Extended Data Fig. 6: Characterization of H3K4me3 peaks overlapping with R-loops.
From: The landscape of promoter-centred RNA–DNA interactions in rice
a, Venn diagram showing the peak overlap between H3K4me3 ChIP-seq, H3K4me3 ChRD-PET DNA, and ssDRIP-seq. b, Density distribution of H3K4me3 ChIP-seq, H3K4me3 ChRD-PET DNA, and ssDRIP-seq at transcription start site. c, The percentage of S9.6 foci colocalized/non-colocalized with H3K4me3 foci in 29 rice nuclei. Averagely, 91% S9.6 foci were colocalized with H3K4me3 foci, 9% non-colocalized. Biological replicates, n=29. p value was calculated using two-sided Wilcoxon rank-sum test. Centre line represents the median, box extent ranges from 25th to 75th percentile, and whiskers extend at most to 1.5× the interquartile range (distance between the first and third quartiles). d, Number of ChRD-PET interactions for coding RNA, lncRNA, snRNA/snoRNA and, microRNA in the overlap and non-overlap portion of ChRD-PET DNA and ssDRIP-seq peaks. e, Histogram showing the number of R-loop derived RNA-DNA interactions related to ncRNAs in H3K4me3 ChRD-PET filtered by RNase H treated H3K4me3 ChRD-PET and 8-bp RNA-DNA complementary pairing test. f, Histogram showing the number of R-loops in different categories of RNA. g, Histogram showing the number of RNAs in different categories of R-loops.
