Fig. 1. RBM39 controls the inclusion of a poison exon into its own mRNA.

a–c Volcano plots showing up- and downregulation of transcripts (a), alternative exons (b), and retained introns (c), upon RBM39 depletion. P values were computed using two-sided Wald test (a, c) or χ² likelihood-ratio test (b), and adjusted for multiple comparison using the procedure of Benjamini and Hochberg, n = 3. Statistically significant alterations (p_adj <0.05) are highlighted in colour. The bar plots indicate the fraction of rescued events (p_adj <0.05) and their directionality among the 1000 most significant changes. d Sashimi plot showing the reads observed for the beginning of the RBM39 gene upon control knock down (Ctrl KD), RBM39 knock down (RBM39 KD) and FLAG-RBM39 rescue. e Schematic representation of both RBM39 mRNA isoforms. In the longer isoform, the exon 2b is included and introduces a premature termination codon (PTC). f RT-PCR validation of the RBM39-dependency of exon 2b inclusion. Quantification and statistics are shown in Fig. 2g. g Boxplot showing the percent of exon 2b inclusion in transcriptomic data grouped according to cancer type. This plot was generated using RNA-Seq data from The Cancer Genome Atlas (TCGA). Within each box, horizontal black lines denote median values. Lower and upper hinges correspond to the 25th and the 75th percentile, respectively, whereas vertical lines extend to the most extreme values within 1.5 × interquartile range. For cancer type, n is indicated in the plot.