a, Schematic of RIC-seq technology. An RBP-mediated RNA–RNA contact is zoomed in. MNase, micrococcal nuclease. b, The percentages of cytosine around the junction of chimeric reads. c, Comparison of known structures (blue arcs) of pre-miR-296 to RIC-seq chimeric reads (grey boxes). Blue line, A>C mismatch; red line, pCp. d, pCp distribution around the apical loop of 280 pre-miRNAs in HeLa cells. Colour scale, normalized RIC-seq coverage. e, RIC-seq recapitulates known structures of TERC. The reads shown in boxes support P1, P2 or P2–P3 pseudoknot structures. f, RIC-seq identifies U1 binding sites in MALAT1. Light pink shading denotes regions detected by both RIC-seq and PARIS. Light-blue-shaded and light-green-shaded regions are revealed either by RIC-seq or by PARIS, respectively. Purple lines, U1 motif. Arrowheads mark fragments that were chosen for RAP–qPCR. Cons., conservation; NT, non-target region. g, RAP–qPCR validates U1-specific binding sites on MALAT1. Top, 5′-end biotin-labelled probes can pull-down U1 interacting sites (C1–C3 and S1–S3) on MALAT1. Bottom, the U1 biotin probes can pull-down MALAT1 upon formaldehyde treatment. Data are mean ± s.d.; n = 3 biological replicates. h, Comparing the RNA physical interaction map and in vivo RNA 3D interaction map of 28S rRNA. The dark grey marked regions are absent from the cryo-EM structure. Boxes 1, 2 and 3 illustrate different types of RNA–RNA interaction. i, ROC analysis showing the performance of RIC-seq (black line) in detecting the 3D structure of 28S rRNA. Dashed line, random classifier; blue line, ROC curve of PARIS.