Perspective in Alternative Splicing Coupled to Nonsense-Mediated mRNA Decay

Abstract

Alternative splicing (AS) of precursor mRNA (pre-mRNA) is a cellular post-transcriptional process that generates protein isoform diversity. Nonsense-mediated RNA decay (NMD) is an mRNA surveillance pathway that recognizes and selectively degrades transcripts containing premature translation-termination codons (PTCs), thereby preventing the production of truncated proteins. Nevertheless, NMD also fine-tunes the gene expression of physiological mRNAs encoding full-length proteins. Interestingly, around one third of all AS events results in PTC-containing transcripts that undergo NMD. Numerous studies have reported a coordinated action between AS and NMD, in order to regulate the expression of several genes, especially those coding for RNA-binding proteins (RBPs). This coupling of AS to NMD (AS-NMD) is considered a gene expression tool that controls the ratio of productive to unproductive mRNA isoforms, ultimately degrading PTC-containing non-functional mRNAs. In this review, we focus on the mechanisms underlying AS-NMD, and how this regulatory process is able to control the homeostatic expression of numerous RBPs, including splicing factors, through auto- and cross-regulatory feedback loops. Furthermore, we discuss the importance of AS-NMD in the regulation of biological processes, such as cell differentiation. Finally, we analyze interesting recent data on the relevance of AS-NMD to human health, covering its potential roles in cancer and other disorders.

Keywords: AS-NMD; alternative splicing (AS); gene expression regulation; nonsense-mediated RNA decay (NMD).

Figure 1

Representation of the exon junction complex (EJC)-dependent and EJC-independent nonsense-mediated RNA decay (NMD) pathway, targeting a transcript generated by alternative splicing (AS). Introns are represented as black lines and exons as blue boxes. A gene is transcribed into a pre-mRNA and AS gives rise to two different mRNA isoforms. The left one represents a productive isoform that encodes a functional protein, and the two isoforms on the right include a premature stop codon (PTC)-containing exon that triggers NMD. The EJC-dependent model: During the first round of translation, the ribosome encounters a stop codon located more than 50-55 nucleotides upstream of an exon-exon junction, and eRF1/3 interact with UPF1 and SMG1, resulting in the SURF complex. Then, UPF1 interacts with UPF2 at the EJC, which ends in the DECID complex formation and activation of UPF1 through phosphorylation by SMG1. The EJC-independent model: If the interaction between PABPC1 and eRF3 is inhibited when the ribosome reaches a PTC, eRF3 can interact with UPF1 originating the SURF complex. Then, UPF2 and UPF3B diffused in the cytoplasm interact with UPF1, triggering UPF1 phosphorylation by SMG1 and the DECID complex assembly. The next steps are common to both models: The active UPF1 leads to its helicase function, rearranging the transcript to allow the recruitment of SMG5, SMG6, and SMG7. SMG6 cleaves the mRNA near the PTC, which results in unprotected ends. Meanwhile, SMG5 and SMG7 bind as a heterodimer to recruit the DCP1 and DCP2 decapping enzymes and the CCR4-NOT deadenylation complex. These RNA modifications allow 5′-3′ and 3′-5′ degradation by XRN1 and the exosome, respectively. TSS: Transcription start site.

Figure 2

Alternative splicing (AS) patterns inducing inclusion of a premature termination codon (PTC). Introns are represented as black lines and exons as blue boxes. The first splicing pattern listed in the image creates a full-length productive isoform that encodes a functional protein. The other represented transcripts contain a PTC that commits the isoform to nonsense-mediated mRNA decay (NMD). Cassette exon events, such as poison exon inclusion, induce retention of a PTC-containing exon, as shown for SRSF3 [78]. Exon skipping, another cassette exon event, may result in a frameshift leading to a PTC-positive isoform, as reported for PTBP1 [79]. Usage of an alternative 5′ or 3′ splice site, as well as intron retention, can include a segment of RNA with an in-frame PTC, turning the transcript into an NMD target, as represented above for RPS3, SRSF5, and LMNB1, respectively [71,80,81,82]. Splicing in the 3′ untranslated region (UTR) of hnRNPA2B1 can recruit an exon junction complex to a position located more than 55 nucleotides downstream of the stop codon, creating a premature context that triggers NMD [72]. The last example represents the inclusion of two exons in FGFR2, which are mutually exclusive, but if both exons are included or neither exon are in the splice variant, they introduce a frameshift that creates a PTC [83].