A Proportion of reads spanning exon–intron junctions determined by RNA-Seq analysis of HeLa cells treated with control (CTRL), UBL5, or SART1 siRNAs for 48 h [mean ± SEM (error bars); N = 2]. Supplementary Table shows full RNA-Seq results.
B Density of RNA-Seq reads (pink) mapping to exons (yellow) and introns (blue) in the FASN gene, representative of genes displaying intron retention.
C Frequency of intron retention (IR) among all classified alternative splicing events, obtained via spliceR from RefSeq, Gencode, and UBL5 transcriptomes. Asterisk (*) denotes statistically significant changes (P < 2.2 × 10−16, Fisher’s exact test).
D Significantly differentially expressed transcripts were extracted and divided into the four indicated, overlapping subsets. The distribution of IF values from each condition was plotted. Asterisk (*) denotes changes that are statistically significant between control and all other samples (P < 1 × 10−4, pairwise Mann–Whitney U-test).
E Significantly differentially expressed transcripts were extracted, and the frequency of NMD sensitivity was compared between transcripts with and without IR. Asterisk (*) denotes statistically significant changes (P < 2.2 × 10−16, Fisher’s exact test).
F Whole-cell extracts (WCE) of HeLa cells transfected with non-targeting (CTRL) or UBL5 siRNAs for 48 h were immunoblotted with indicated antibodies.