Extended Data Fig. 4: Coding and non-coding RNA in H3K4me3 ChRD-PET.
From: The landscape of promoter-centred RNA–DNA interactions in rice
a, Number of interactions of coding RNA, lncRNA, snRNA/snoRNA, and microRNA in ChRD-PET. Total RNAs: coding RNAs were from coding genes, while lncRNA, snRNA/snoRNA, and microRNA were predicted. RNAs in ChRD-PET interactions: RNAs from total RNAs and involved in ChRD-PET interactions. ChRD-PET interactions: ChRD-PET interactions related to each type of RNAs. b, c, Scatter plots of RNA reads detected by ChRD-PET in comparison with RNA-seq (b) and total RNA-seq (c) Bin size: the transcribed region of a gene. d, Histogram showing the number of DNA/coding RNA numbers in each coding RNA/DNA category. Bottom left: histogram showing the number of DNA regions interacting with different number of coding RNAs. For the second pillar, there are 5496 DNA peaks, and each peak interacting with 2 coding RNAs. Upper right: histogram showing the number of RNAs in each DNA peak category. For the second pillar, there are 4956 RNAs, and each RNA interacted with 2 DNA peaks. e, Cluster analysis of the pairwise correlation between the associated DNA regions of 8 types of snoRNA in ChRD-PET. Bin size: 25kb. f, Top: genomic loci, ChIP-seq, ChRD-PET and transcriptome information for lncRNA MSTRG.20623. Bottom: circlet plot of H3K4me3 ChRD-PET interactions related to lncRNA MSTRG.20623. g, Top: genomic loci, ChIP-seq, ChRD-PET and transcriptome information for microRNA osa-MIR2106. Bottom: circlet plot of H3K4me3 ChRD-PET interactions related to osa-MIR2106. h, Top: genomic loci, ChIP-seq, ChRD-PET and transcriptome information for the cluster of snoRNAs. Bottom: circlet plot of H3K4me3 ChRD-PET interactions related to the cluster of snoRNAs. i, j, k, l, m, Circlet plot of ChRD-PET interactions in which 5 types of snRNA were involved. U1(i), U2 (j), U4 (k), U5 (l), U6atac (m).
