a, The chimeric reads mapped to rRNA. b, The RNA–RNA interactions of 28S rRNA in pCp- samples. c, The RIC-seq and cryo-EM data of 28S rRNA are highly correlated. The RIC-seq signal markedly decreases with increased distance to known pairwise-interacting sites in 28S rRNA (x axis) and with the increased spatial distance (y axis). d, The true-positive and true-negative datasets are generated from the cryo-EM model of 28S rRNA. e, The boundaries of RNA duplexes in 28S rRNA tend to be occupied by RBPs. The spatial distance to the nearest amino acid is calculated from the cryo-EM model. Regions absent from the structure are shown in light grey. f, RIC-seq captures the G4000 duplex protruding from the RBP (in different colours) complex. The arrowhead represents MNase random cut and pCp–biotin labelling position. g, The intermolecular interactions between 5.8S, 18S and 28S rRNA. The histogram on the inner circle represents the number of chimeric reads at the given positions. The red arc lines marked interactions between 5.8S and 28S rRNA are shown on the right. h, The modelled structure of 28S rRNA (PDB ID 4V6X). i, The secondary structure deduced from RIC-seq data for two missing 28S rRNA regions (nt 2951–3246 and nt 3301–3561). The bases are marked by different colours based on in vivo click selective 2-hydroxyl acylation and profiling experiment (icSHAPE) scores, and the base pairs are denoted by different lines on the basis of the strength of the RIC-seq signal. j–l, The structural model, physical interaction map and RIC-seq interaction map of 7SK 5′-hairpin, SRP (7SL RNA) and RPPH1. Grey regions in the physical maps indicate no structural data available. m, RIC-seq showed comparable performance to PARIS in detecting the structure of 7SK, SRP RNA and RPPH1. Dashed line, random classifier.