Fig. 4

Position-dependent activation of pre-mRNA processing by CFIm. a The distributions of average terminal exon lengths (see “Methods”) computed from 5123 multi-PAS terminal exons quantified in CFIm 25, CFIm 68 knock-down, and control samples indicate significant shortening of 3′ UTRs upon CFIm depletion (asterisks indicate two-sided Wilcoxon signed-rank test p value < 0.0001). b Smoothened (± 5 nt) UGUA motif density around PAS of terminal exons with exactly two quantified poly(A) sites, grouped according to the log fold change of the proximal/distal ratio (p/d ratio) upon CFIm knock-down. The left panel shows the UGUA motif frequency around the proximal and distal PAS of the 750 exons with the largest change in p/d ratio, while the right panel shows similar profiles for the 750 exons with the smallest change in p/d ratio. c KAPAC analysis of CFIm knock-down and control samples uncovers the poly(A) signal and UGUA motif as most significantly associated with changes in PAS usage (n = 3727). d UGUA motif activity is similar when the PAS quantification is done by PAQR from RNA sequencing data of CFIm 25 knock-down and control cells (n = 4287) [11]