The icSHAPE reactivity scores128 were mapped from GRCh38 to GRCh37 human genome assembly by LiftOver129. The reactivity score of a CCR was calculated as the average reactivity of its base-paired nucleotides, for which the icSHAPE reactivity score was available. The background reactivity was calculated as the average reactivity of the same number of nucleotides chosen at random outside the CCR, but in the same CIR. Wilcoxon’s signed-rank test was applied to matched samples of reactivity score differences to test for departures from zero.

The coordinates of base-paired regions from PARIS experiments22 (15,036 pairs) were mapped from GRCh38 to GRCh37 by Liftover129. The coordinates of base-paired regions from LIGR-seq data (551,926 pairs) were used in the GRCh37 human genome assembly23. The coordinates of intramolecular base-paired regions from RIC-seq data24 (501,144 pairs) were kindly provided by Prof. Xue by request (Supplementary Data File 5). In all three datasets, we selected the interacting pairs that were located intramolecularly within CIR of protein-coding genes from 1 to 10,000 nts apart from each other. This resulted in 907 such pairs for PARIS, 586 for LIGR-seq, and 1804 for RIC-seq. In order to evaluate the precision and recall, we selected CIR with at least one nucleotide overlapping the experimentally validated structures and confined our analysis to PCCRs located in these regions. A CCR was classified as a true positive if it had at least one common nucleotide with an experimentally validated structure. A PCCR was classified as a true positive if both its CCRs intersected by at least one nucleotide with an experimentally validated such pair.

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