mTOR-driven widespread exon skipping renders multifaceted gene regulation and proteome complexity

Abstract

<jats:title>Abstract</jats:title><jats:p>The mammalian target of rapamycin (mTOR) pathway is crucial in cell proliferation. Previously, we reported transcriptome-wide 3’-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon-skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: alternative splicing (AS) in the 5’-UTR controls translation efficiency while AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.</jats:p>

Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes

“…Previous work revealed a handful of splicing factors that can independently mediate post-splicing activities, such as mRNA translation (Chen et al, 2019; Maslon et al, 2014; Kim et al, 2014). Instead, alternative splicing mediated by splicing factors can cause downstream effects on the translation of the spliced target genes depending on the qualitative decision of which mRNA isoforms are being produced (Lim et al, 2018; Wang et al, 2020; Leppek et al, 2018; Pelletier & Sonenberg, 1985; Mauger et al, 2019; Cheng et al, 2020; Katahira, 2015; Drummond & Wilke, 2008; Qian et al, 2012; Nott et al, 2004; Lewis et al, 2003). Remarkably, the high fraction of splicing factors that we find to influence translation suggests previously unanticipated roles for many more splicing regulators in this process.…”

“…In the nucleus, RBPs can coordinate the process of splicing and translation by modulating different structural and sequence properties of the mRNAs that are exported to the cytoplasm. For instance, highly structured regions in 5’ UTRs can decrease the efficiency of translation initiation at the cost of an overall lower translational output (Lim et al, 2018; Wang et al, 2020; Leppek et al, 2018; Pelletier & Sonenberg, 1985), whereas increased RNA structures in CDS or 3’UTR regions may also enhance transcript stability and hence mRNA half-life, in turn yielding higher protein output over time (Mauger et al, 2019; Cheng et al, 2020). Additionally, alternative UTR usage can expose translated uORFs or miRNA binding sites affecting mRNA translation and/or stability.…”

Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes

“…activities, such as mRNA translation [55][56][57]. Instead, alternative splicing mediated by splicing factors can cause downstream effects on the translation of spliced target genes, depending on the qualitative decision of which mRNA isoforms are being produced [19][20][21][22][23][24][25][26][27][28][29]. Remarkably, the high fraction of splicing factors that we find to influence translation would suggests previously unanticipated roles for many more splicing regulators in this process.…”

“…In the nucleus, RBPs can coordinate the process of splicing and translation by modulating different structural and sequence properties of the mRNAs that are exported to the cytoplasm. For instance, highly structured regions in 5' UTRs can decrease the efficiency of translation initiation at the cost of an overall lower translational output [19][20][21][22], whereas increased RNA structures in CDS or 3' UTR regions may also enhance transcript stability and hence mRNA half-life, in turn yielding higher protein output over time [23,24]. Additionally, alternative UTR usage can expose translated upstream ORFs (uORFs) or miRNA binding sites affecting mRNA translation and/or stability.…”