eCLIP peaks for 74 RBPs assayed in HepG2 human cell line were downloaded from the ENCODE data repository in bed format65,130,131 (Table S4). The peaks were filtered by the conditions log FC ≥ 3 and p value < 0.001. Since the agreement between two replicates was moderate, we use the pooled set of eCLIP peaks. To quantify the association between RBP binding and individual CCR, we calculated for each RBP the number of CCRs that intersected with its eCLIP peaks by at least 50% of the CCR length. This number was compared to the respective number of intersections obtained in the random shift control. To quantify the association of RBP binding with both CCRs in a PCCR, we constructed a contingency table for the number of PCCRs that had/did not have eCLIP peaks in left/right CCR for each RBP, and computed the respective OR. The 95% confidence interval for the OR was calculated by Fisher’s test.

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