Fig. 5. Increased intron retention in mRNAs upon RNF113A deficiency, especially in Cisplatin-treated lung cancer cells.

a–d Analysis of alternative splicing (AS) at the level of individual splicing events with rMATS (replicate Multivariate Analysis of Transcript Splicing). a Schematic representation of the different types of AS events analyzed by rMATS. Inclusion and skipping forms are quantified using reads overlapping junctions and reads unique to the inclusion form. b Number of AS events found in RNF113A-depleted and control A549 cells treated or not with Cisplatin. Each entry in the table has three values: Total number of events evaluated in that comparison (Inclusion significantly lower in S2: Inclusion significantly higher in S2). Samples are as follow: C = control shRNA—no drug, Ccis = control shRNA + Cisplatin, D = RNF113A shRNA—no drug, Dcis = RNF113A shRNA + Cisplatin. Significant events are defined as FDR<5% and delta inclusion level (|ΔΨ|) of at least 20%. c Fraction of analyzed AS events with inclusion level significantly lower or higher upon treatment (four comparisons) for each category of AS events. d Comparison of fraction of transcripts with retained intron in RNF113A-depleted and control A549 cells treated or not with Cisplatin. Each dot represents an intron retention event. Events with statistically significant difference between conditions are represented in red. Black broken line: identity axis. e-f Analysis of Intron Retention at the level of individual genes. e Comparison, for each protein-coding gene, of the ratio of mRNAseq reads in intronic versus exonic regions (average of three replicates) between RNF113A-depleted and control A549 cells treated or not with Cisplatin. Black broken line: identity axis. Shift towards higher ratios upon RNF113A depletion are significant (p-value < 2.2 × 10⁻¹⁶; Wilcoxon signed rank tests (paired tests); see Supplementary Fig. 8c). f Total number of reads covering introns versus total number of reads restricted to annotated exons for both RNF113A-depleted and control A549 cells treated or not with Cisplatin. Data were obtained from three replicates for each experimental condition (mean ± SD, two-sided T-test, **p < 0.01, **p < 0.05).