a, Intermolecular RNA–RNA interactions (n = 2,088,874) were plotted against the average pairwise interaction counts from 100,000 simulations. b, A single random dataset (n = 3,536,556) was taken for further 100,000 simulations and plotted as in a. c, The observed pairwise interactions were compared with simulated random counts to identify high-confidence interactions (P ≤ 0.05, red dots). d, Box plot showing how the P value distribution changed as the Monte Carlo simulation progressed using n = 2,088,874 intermolecular RNA–RNA interaction events. The 100,000 simulations were divided into 100 batches. e, RNA–RNA interaction types and their numbers of RIC-seq chimeric reads. f, The violin plot shows the expression levels of MALAT1- and NEAT1-targeting genes. g, The enriched motifs among MALAT1 or NEAT1 chimeric targets. h, Overlaps of MALAT1 and NEAT1 binding sites identified by RIC-seq and CHART-seq. Two-sided Fisher’s exact test was used to calculate the P value. i, Summary of NEAT1 foci and their overlap with MALAT1 in 15 cells. j, Structured illumination microscopy analysis showing the localization of MALAT1 with NEAT1 5′ region, NEAT1 middle region or NEAT1 3′ non-contact region. The regions marked by white boxes are magnified at the top right. The violin plot illustrates the distance from NEAT1 foci to the nearest MALAT1 puncta in 20 cells. 5′ end, n = 131; middle, n = 169; 3′ non-contact region, n = 166. Two-tailed unpaired t-test was used to calculate the P values in f and j. For the violin or box plots in d, f and j, the white centre point represents the median, the box limits represent the Q1 and Q3, the whiskers are the most extreme data points within 1.5 × the interquartile range (from Q1 to Q3), and the upper–lower limits represent the maximum–minimum values.