Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis

Nat Commun. 2018 Aug 17;9(1):3315. doi: 10.1038/s41467-018-05748-7.

Abstract

Mutations causing aberrant splicing are frequently implicated in human diseases including cancer. Here, we establish a high-throughput screen of randomly mutated minigenes to decode the cis-regulatory landscape that determines alternative splicing of exon 11 in the proto-oncogene MST1R (RON). Mathematical modelling of splicing kinetics enables us to identify more than 1000 mutations affecting RON exon 11 skipping, which corresponds to the pathological isoform RON∆165. Importantly, the effects correlate with RON alternative splicing in cancer patients bearing the same mutations. Moreover, we highlight heterogeneous nuclear ribonucleoprotein H (HNRNPH) as a key regulator of RON splicing in healthy tissues and cancer. Using iCLIP and synergy analysis, we pinpoint the functionally most relevant HNRNPH binding sites and demonstrate how cooperative HNRNPH binding facilitates a splicing switch of RON exon 11. Our results thereby offer insights into splicing regulation and the impact of mutations on alternative splicing in cancer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing / genetics*
  • Base Sequence
  • Binding Sites
  • Exons / genetics
  • HEK293 Cells
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H / metabolism
  • Humans
  • Introns / genetics
  • Linear Models
  • MCF-7 Cells
  • Mutagenesis / genetics*
  • Mutation / genetics
  • Neoplasms / genetics*
  • RNA-Binding Proteins / metabolism
  • Receptor Protein-Tyrosine Kinases / genetics*
  • Regulatory Sequences, Nucleic Acid / genetics
  • Sequence Analysis, RNA

Substances

  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H
  • RNA-Binding Proteins
  • RON protein
  • Receptor Protein-Tyrosine Kinases