Extended Data Fig. 7: Analysis of RNase H treated H3K4me3 ChRD-PET interactions.
From: The landscape of promoter-centred RNA–DNA interactions in rice
a, Density distribution of RNase H treated H3K4me3 ChRD-PET DNAs around the H3K4me3 peak center. b, Density distribution of RNase H treated H3K4me3 ChRD-PET sense (red) and antisense (grey) RNA at the annotated genes region. c, Length distribution of RNase H treated H3K4me3 ChRD-PET DNA and RNA reads. d, Genomic distributions of uniquely mapped RNase H treated H3K4me3 ChRD-PET DNA (left) and RNA reads (right). e, Genome-wide contact heatmap at 1Mb resolution of RNase H treated H3K4me3 ChRD-PET. X-axis: RNase H treated H3K4me3 ChRD-PET RNA. Y-axis: RNase H treated H3K4me3 ChRD-PET DNA. f, Histogram showing the number fraction of R-loop derived RNA-DNA interactions and non R-loop derived RNA-DNA interactions in local, proximal, distal interactions. g, Screenshot showing osa-MIR2106 mediated R-loop formation in trans. Track 1: ChRD-PET RNA coverage signals. Arrows point out the trans location of RNA strand involved in R-loop. Track 2: ssDRIP-seq coverage signals and peak in the forward strand. Track 3: ssDRIP-seq coverage signals and peak in the reverse strand. Track 4: RNase H treated ssDRIP-seq. Track 5: ChRD-PET DNA coverage signals. Track 6: H3K4me3 ChIP-seq coverage signals and peak. Track 7: R-loop formation site. Track 8: annotation genes. Track 9: sequences and R-loop structure, RNA (red), DNA (blue).
