Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage

• Published in: Nature communications Vol. 7; no. 1; pp. 10615 - 12
• Main Authors: Alsafadi, Samar, Houy, Alexandre, Battistella, Aude, Popova, Tatiana, Wassef, Michel, Henry, Emilie, Tirode, Franck, Constantinou, Angelos, Piperno-Neumann, Sophie, Roman-Roman, Sergio, Dutertre, Martin, Stern, Marc-Henri
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 04.02.2016; Nature Publishing Group; Nature Portfolio
• Subjects: 13/44; 38/77; 38/89; 631/208/737; 631/337/1645/1946; 631/67/68; Alternative Splicing - genetics; Cell Line, Tumor; Genetics; HEK293 Cells; Humanities and Social Sciences; Humans; Immunoblotting; Immunoprecipitation; Life Sciences; Melanoma; Melanoma - genetics; multidisciplinary; Mutation; Phosphoproteins - genetics; Ribonucleoprotein, U2 Small Nuclear - genetics; RNA Splice Sites - genetics; RNA Splicing Factors; Science; Science (multidisciplinary); Sequence Analysis, DNA; Sequence Analysis, RNA; Uveal Neoplasms - genetics
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms10615

Hotspot mutations in the spliceosome gene SF3B1 are reported in ∼20% of uveal melanomas. SF3B1 is involved in 3′-splice site (3′ss) recognition during RNA splicing; however, the molecular mechanisms of its mutation have remained unclear. Here we show, using RNA-Seq analyses of uveal melanoma, that the SF3B1 R625/K666 mutation results in deregulated splicing at a subset of junctions, mostly by the use of alternative 3′ss. Modelling the differential junctions in SF3B1 WT and SF3B1 R625/K666 cell lines demonstrates that the deregulated splice pattern strictly depends on SF3B1 status and on the 3’ss-sequence context. SF3B1 WT knockdown or overexpression do not reproduce the SF3B1 R625/K666 splice pattern, qualifying SF3B1 R625/K666 as change-of-function mutants. Mutagenesis of predicted branchpoints reveals that the SF3B1 R625/K666 -promoted splice pattern is a direct result of alternative branchpoint usage. Altogether, this study provides a better understanding of the mechanisms underlying splicing alterations induced by mutant SF3B1 in cancer, and reveals a role for alternative branchpoints in disease. Mutations in the splicing factor SF3B1 are found in uveal melanoma. Here, Alsafadi et al . use RNA-sequencing data from these cancers and experimental models, and show that mutant SF3B1 promotes alternative branchpoints in a specific gene subset and that the mutant protein gains a new function.