Extended Data Fig. 3: Features of RNA-DNA interactions in H3K4me3 ChRD-PET.
From: The landscape of promoter-centred RNA–DNA interactions in rice
a, Three types of ChRD-PET interactions of exon RNA and intron RNA. b, Screenshot showing introns of MH05g0031500 (chr5: 1,278,000-1292000) participating in local interactions, along with the epigenomic and transcriptomic features. Top: gene (track 1), ChRD-PET RNA (red, track 2), ChRD-PET DNA (blue, track 3). Bottom: local interactions, ChRD-PET DNA (blue), ChRD-PET intron RNA (green), linker (black). c, Three types of ChRD-PET interactions of RNAs from single- and multi-exon gene. Y-axis: average number of interacting DNA on each RNA. d, Gene Ontology of hub RNAs (top 5% RNAs) in ChRD-PET. p value was calculated using one-sided Fisher’s exact test. p values are corrected for multiple comparison using the Yekutieli_FDR correction. e, Network showing the targets of SNAC1 RNA (red). ChRD-PET DNAs: yellow and blue, blue: DNAs showed in Fig. 2h. Gene Ontology of SNAC1’s targets are shown on the Bottom. p value was calculated using one-sided hypergeometric distribution test. p value is corrected for multiple comparison using the Benjamini-Hochberg correction. f, The motifs of ATAC-seq related to SNAC1 RNA targets. g, Three types of ChRD-PET interactions of transcription factor RNA and non-transcription factor RNA. Y-axis: average number of interacting DNA on each RNA.
