MTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control.

Jae-Woong Chang,Rui Kuang,Naima Ahmed Fahmi,Luke Erber,Jeongsik Yong,Sze Cheng,Yue Chen,Alexander M Bui,Meeyeon Park,Ryan Nasti,Jiao Sun,Wei Zhang,Hsin-Sung Yeh

doi:10.1093/nar/gkz761

Jae-Woong Chang, Rui Kuang + Show 11 more

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https://doi.org/10.1093/nar/gkz761

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Abstract

U2 auxiliary factor 1 (U2AF1) functions in 3′-splice site selection during pre-mRNA processing. Alternative usage of duplicated tandem exons in U2AF1 produces two isoforms, U2AF1a and U2AF1b, but their functional differences are unappreciated due to their homology. Through integrative approaches of genome editing, customized-transcriptome profiling and crosslinking-mediated interactome analyses, we discovered that the expression of U2AF1 isoforms is controlled by mTOR and they exhibit a distinctive molecular profile for the splice site and protein interactomes. Mechanistic dissection of mutually exclusive alternative splicing events revealed that U2AF1 isoforms’ inherent differential preferences of nucleotide sequences and their stoichiometry determine the 3′-splice site. Importantly, U2AF1a-driven transcriptomes feature alternative splicing events in the 5′-untranslated region (5′-UTR) that are favorable for translation. These findings unveil distinct roles of duplicated tandem exon-derived U2AF1 isoforms in the regulation of the transcriptome and suggest U2AF1a-driven 5′-UTR alternative splicing as a molecular mechanism of mTOR-regulated translational control.

Highlights

Eukaryotic pre-mRNA is spliced to mRNA by the spliceosome which is composed of small nuclear ribonucleoprotein complexes
Among the RNA-binding proteins (RBPs) whose transcript levels changed upon mammalian target of rapamycin (mTOR) activation, U2af1 was interesting: one of the two U2af1 isoforms, U2af1a, shows a ∼2-fold expression difference in Tsc1−/− MEFs while the U2af1b expression remained unchanged between WT and Tsc1−/− MEFs (Figure 1A and B, Supplementary Figure S1A–D)
U2 auxiliary factor 1 (U2AF1) has been extensively studied for its crucial role in pre-mRNA splicing and the pathogenesis of myelodysplasia syndrome (MDS) [1,6,9,14,27,28,29,30,31,32,34,35,36,48,49,50]

Summary

Introduction

Eukaryotic pre-mRNA is spliced to mRNA by the spliceosome which is composed of small nuclear ribonucleoprotein complexes (snRNPs). The U2AF1 gene contains duplicated tandem exons between exon 2 and exon 4 These two duplicated tandem exons (3a and 3b (formerly designated as exon Ab)) are mutually exclusive in splicing and yield two highly similar isoforms, U2AF1a and U2AF1b. They are evolutionary conserved and only differ by seven amino acids in the final protein products (97.1% identity) [7,8]. Examples of PKM and FGFR2 genes provide evidence that tandem exon-derived isoforms function differently and distinctively affect cells [10,11,12,13]

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