Extended Data Fig. 4: Splicing regulatory activity of RBNS+ and RBNS− eCLIP peaks.

a, Density of 5mers in skipped exons and their flanking intronic up/downstream 100 nt in 24 changed versus control skipped exons upon PCBP2 knockdown in HepG2 cells. The ratio of changed and control frequency was computed for each 5mer with the ratio plotted as density on the y-axis, and 5mers were separated by C-rich (contain 4–5 Cs), G-rich (contain 4–5 Gs), or ‘other’. Significance determined by one-sided Kolmogorov–Smirnov test. Box, 25th to 75th percentiles; notch, median. b, Percentage of eCLIP peaks that contain a C- or G-rich motif (5mer with 4 or 5 of the respective base). PCBP2 eCLIP in HepG2 cells is noted (eCLIP with the third highest proportion of peaks with C-rich motifs; median for peaks containing G-rich motifs). Box, 25th to 75th percentiles; notch, median. c, Bottom left, distribution of change ΔΨ upon knockdown in each of the six eCLIP+ peak region–skipped exon splicing change types compared to that of eCLIP− skipped exons for KHSRP in HepG2 cells (significant if P < 0.05 by one-sided Wilcoxon rank-sum test). Right, regions of significance for eCLIP+ versus eCLIP− skipped exons for each eCLIP experiment and proportion of skipped exons in each of the six eCLIP+ types for each eCLIP experiment. d, Same set of RBPs and corresponding eCLIP+ peak region–skipped exon splicing change types as in Fig. 3c, but separating eCLIP peaks on whether they contain the top ‘eCLIP-only’ 5mer (based on the motifs from Extended Data Fig. 3f) instead of the top RBNS 5mer. Box, 25th to 75th percentiles; notch, median; line, outliers. Significance was determined by one-sided Wilcoxon rank-sum test and indicated if P < 0.05. e, As in Fig. 3c, but shown for RBP-activated skipped exons (decreased inclusion upon RBP knockdown). Box, 25th to 75th percentiles; notch, median; line, outliers. Significance was determined by one-sided Wilcoxon rank-sum test and indicated if P < 0.05.