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

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

Author information

1
Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
2
Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.
3
Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.
4
Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus Gambelas, 8005-139, Faro, Portugal.
5
Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany. s.legewie@imb-mainz.de.
6
Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany. j.koenig@imb-mainz.de.
7
Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany. kathi.zarnack@bmls.de.

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.

PMID:
30120239
PMCID:
PMC6098099
DOI:
10.1038/s41467-018-05748-7
[Indexed for MEDLINE]
Free PMC Article

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