Fig. 6: R-loops distibution at pri-miRNA encoding loci.

a, Schematic representation of the region scaled for metagene analysis of R-loop formation over MIRNA loci. MIRNA loci were scaled either from the TSS to the nt before miRNA-5p (green) or from miRNA-5p to the end of miRNA-3p (red). Metagene analysis was then plotted in b and d adding 300 base pairs upstream or downstream from the windows, respectively. b, Metagene analysis of sense (red) and antisense (blue) R-loops over all MIRNA loci. Metagene plots are scaled from the TSS to the nt before the first nt of miRNA-5p (upper panel) or from the first nt of miRNA-5p to the last of miRNA-3p. c, Quantification of R-loops near the TSS of MIRNAs belonging to different categories of R-loop pattern (defined in d) as measures by DRIP–qPCR assays. Values of DRIP samples are normalized to the input and expressed as relative to the DRIP signal in sample IP after RNase H treatment (red line). Failure to detect R-loops is noted as non-detected (ND). A known R-loop over SEPALLATA3 (SEP3) was used as positive control (C+) Data are presented as mean values ± s.d.; n = 3 biologically independent samples. d, Metagene analysis of R-loop formation over MIRNA loci sorted by R-loop distribution. α-MIRNA loci without R-loops; β-MIRNA loci with R-loops over the ssRNA 5’-end of the pri-miRNAs; γ-MIRNA loci with bipartite R-loop signals at the beginning and end of the pri-miRNAs; δ-MIRNA loci with R-loops over the entire loci; ε-MIRNA loci with colliding sense (red) and antisense (blue) R-loops. e, Boxplot of co-transcriptional processing ratios of pri-miRNAs with R-loop profiles of categories α, β + γ or δ + ε. Equal processing type frequency (=1) is marked with a dashed line. Error bars show the maximum and minimum values. P value of a two-tailed unpaired t-test; n = 2 biologically independent datasets. The box represents the Q3 and Q1 borders, with the median (horizontal line) and mean (white dot). Whiskers show larger and smaller values while coloured dots note outliers.