Fig. 4: De novo SF3B1 variants E722K, P780L and N829S alter RNA splicing.
From: De novo variants in the splicing factor gene SF3B1 are associated with neurodevelopmental disorders
A Schematic representation of the experimental strategy used to characterise the impact of SF3B1 variants on alternative splicing. B Total number of significant differentially spliced junctions associated with SF3B1 variants, in comparison to the wild type condition. Dark and white bars indicate known junctions and novel (i.e. not annotated) junctions, respectively. The number of differentially spliced junctions was 2244 (1396 novel) for E722K, 2691 (1767 novel) for P780L, 2042 (1261 novel) for N829S and 3573 (2468 novel) for K700E when using delta PSI > 0.1. C Type and number of splicing events significantly associated with each SF3B1 variant, in comparison to the wild type condition. D Proportion of novel splicing events associated with each SF3B1 variant. E Venn diagram and Upset Plots visualising the number of differentially spliced junctions that are in common between NDD-associated SF3B1 variants (Venn) and K700E (Upset Plots) for Skipping Exons (SE). Number of SE events in common with K700E: 259/1018 for E722K, 284/989 for P780L and 269/840 for N829S. Number of SE events that are variant-specific: 374/500 for P780L, 258/382 for E722K and 183/298 for N829S. F Dot-plot highlighting the top30 enriched REACTOME terms for differentially spliced genes (adjusted p value < 0.05) that were found in common between NDD-associated SF3B1 variants. Enrichment analysis was performed using a modified Fisher’s exact test to evaluate term overrepresentation. Only P780L data is shown. G Principal component analysis (PCA) performed on PSI values of significant SE events from short-term cultured lymphocytes. RNA-Seq were performed on P1 and P26 individuals, harbouring the variants p.N829S and p.P370L, respectively, and on 14 NDD individuals without SF3B1 variant. PCA were performed using the PSI values of significant events for alternative exon skipping (n = 37)(see Supplementary Fig. 8 for all splicing events). Blue: controls, yellow: SF3B1 individuals.
