Title

Poison Exon Splicing Regulates a Coordinated Network of SR Protein Expression during Differentiation and Tumorigenesis.

Document Type

Article

Publication Date

11-19-2020

Keywords

JGM

JAX Source

Mol Cell Nov 19; 80(4):648-665.e9

PMID

33176162

DOI

https://doi.org/10.1016/j.molcel.2020.10.019

Grant

CA178206; GM138541; HG009900; EB028898; CA034196

Abstract

The RNA isoform repertoire is regulated by splicing factor (SF) expression, and alterations in SF levels are associated with disease. SFs contain ultraconserved poison exon (PE) sequences that exhibit greater identity across species than nearby coding exons, but their physiological role and molecular regulation is incompletely understood. We show that PEs in serine-arginine-rich (SR) proteins, a family of 14 essential SFs, are differentially spliced during induced pluripotent stem cell (iPSC) differentiation and in tumors versus normal tissues. We uncover an extensive cross-regulatory network of SR proteins controlling their expression via alternative splicing coupled to nonsense-mediated decay. We define sequences that regulate PE inclusion and protein expression of the oncogenic SF TRA2β using an RNA-targeting CRISPR screen. We demonstrate location dependency of RS domain activity on regulation of TRA2β-PE using CRISPR artificial SFs. Finally, we develop splice-switching antisense oligonucleotides to reverse the increased skipping of TRA2β-PE detected in breast tumors, altering breast cancer cell viability, proliferation, and migration.

Comments

We thank T. Helenius and G. Carmichael for comments on the manuscript; E. Guccione for discussions and help with 20OMe ASO work; D. Wee, R. Lee, and Tom Tabaglio from TechNOA for assistance with 20OMe ASO design; the Ethier lab for the gift of SUM159PT; the Krainer lab for HeLa, HEK293, and HS578T; and the Pathania lab for AR7-HMEC.

We acknowledge assistance from Microscopy, Single Cell Biology Laboratory, and Genome Technologies Sequencing Services at The Jackson Laboratory (JAX).

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