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

Nat Commun. 2016 Feb 4;7:10615. doi: 10.1038/ncomms10615.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing / genetics*
  • Cell Line, Tumor
  • HEK293 Cells
  • Humans
  • Immunoblotting
  • Immunoprecipitation
  • Melanoma / genetics*
  • Mutation
  • Phosphoproteins / genetics*
  • RNA Splice Sites / genetics*
  • RNA Splicing Factors
  • Ribonucleoprotein, U2 Small Nuclear / genetics*
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA
  • Uveal Neoplasms / genetics*

Substances

  • Phosphoproteins
  • RNA Splice Sites
  • RNA Splicing Factors
  • Ribonucleoprotein, U2 Small Nuclear
  • SF3B1 protein, human

Supplementary concepts

  • Uveal melanoma