a–c, RIC-seq recapitulates known structures of tRNA, U3 snoRNA and RPPH1 lncRNA. Known structural elements are marked above specific arc lines. For U3 snoRNA, only three clusters of chimeric reads that support stem–loops 1 to 3 are shown. Mismatches based on variation from the reference transcriptome sequence are marked as red dots in b (C>T), and green dots in c (G>A). d, RIC-seq recapitulates known intra- and intermolecular interactions of U4 and U6 snRNAs. Red dots, C>T mismatches. e, RIC-seq recapitulates snoRNA-interacting sites in 28S rRNA. The red arrow indicates known modification sites. The boxed region represents the D′ box. f–h, PARIS signal, RIC-seq signal and U1-motif density in three different groups of U1–MALAT1 contact sites. Common regions, n = 11; RIC-seq-specific regions, n = 8; PARIS-specific regions, n = 2. i, The genomic distribution of snoRNA-interacting sites detected by RIC-seq. j, The SNORD22 interacting sites in SPHK2 and BCL2L2 RNA. The D box is shown in blue. k, qPCR showing reduced mRNA levels of BCL2L2 and SPHK2 upon knockdown of SNORD22 with ASOs. LENG8 and PM20D2 served as negative controls. Data are mean ± s.d., n = 3 biological replicates. Two-tailed unpaired t-test was used to calculate the P values in f–h, k.