a, The sensitivity, accuracy and resolution of existing methods for detecting the structure of pre-miRNA. Sensitivity, the number of detected pre-miRNAs; accuracy, the percentage of chimeric reads that support correct stem–loop structures; resolution, the mean distance of chimeric junctions from the apical loop. Notably, RNA proximity ligation (RPL) did not detect pre-miRNA. N.A., not available. b, U1 binding sites in MALAT1 detected by mapping RNA interactome in vivo (MARIO), ligation of interacting RNA followed by high-throughput sequencing (LIGR-seq), sequencing of psoralen crosslinked, ligated, and selected hybrids (SPLASH) and RPL methods. U1 motifs, purple lines; y axis, chimeric read number. c, Venn diagram showing overlapping duplexes detected by RIC-seq and PARIS methods in different cell lines. RNAs with fragments per kilobase of transcript per million mapped reads (FPKM) values ≥ 1 in both cell types are used for the analysis. d, The transcriptomic span distance of RIC-seq-specific (red, n = 69,351) and overlapped clusters (blue, n = 10,951). The transcriptomic span excludes introns. Two-sided Kolmogorov–Smirnov test was used to calculate the P value. e, Box plot showing the minimum free energy (MFE) of duplexes among RIC-seq-specific and overlapped groups. f, Venn diagram showing the proximal RNAs detected by RIC-seq and proximity RNA-seq in two different cell lines. Two-sided Fisher’s exact test was used to calculate the P value. g, Cartoon depicting the number of colocalized RNAs in four subcellular compartments revealed by APEX-seq. Dashed lines, in silico random contacts. h, The percentage of intracompartment RNA–RNA interactions observed by RIC-seq (n = 71) is higher than that of random contacts. The one-sided binomial test was used to calculate the P value. i, Box plot showing that the RIC-seq signal strength of intracompartment RNA–RNA interactions is stronger than for intercompartment interactions. Two-tailed unpaired t-test was used to calculate the P values in e and i. For the box plots in e and i, the centre line represents the median, the box borders represent the first (Q1) and third (Q3) quartiles, and the whiskers are the most extreme data points within 1.5× the interquartile range (from Q1 to Q3).