Post-transcriptional Regulation of Gene Expression via Unproductive Splicing

Abstract

Unproductive splicing is a mechanism of post-transcriptional gene expression control in which premature stop codons are inserted into protein-coding transcripts as a result of regulated alternative splicing, leading to their degradation via the nonsense-mediated decay pathway. This mechanism is especially characteristic of RNA-binding proteins, which regulate each other's expression levels and those of other genes in multiple auto- and cross-regulatory loops. Deregulation of unproductive splicing is a cause of serious human diseases, including cancers, and is increasingly being considered as a prominent therapeutic target. This review discusses the types of unproductive splicing events, the mechanisms of auto- and cross-regulation, nonsense-mediated decay escape, and problems in identifying unproductive splice isoforms. It also provides examples of deregulation of unproductive splicing in human diseases and discusses therapeutic strategies for its correction using antisense oligonucleotides and small molecules.

Keywords: antisense oligonucleotides; nonsense-mediated decay; regulation; splicing; unproductive splicing.

Fig. 1

The EEJ-dependent mechanism of NMD. (A) EEJ complexes (orange circles) are displaced from the mRNA by the ribosome during the first round of translation. (B) The EEJ complexes that remain bound to mRNA outside of the reading frame serve as a signal that a PTC has appeared

Fig. 2

Types of unproductive splicing events. Protein-coding isoforms are shown in blue. Unproductive isoforms are shown in red. PTCs are indicated with bright vertical red lines. (A) A poison exon carrying a PTC. (B) A poison exon inducing a PTC via frameshift. (C) An essential exon inducing a PTC via frameshift. (D) An essential exon inducing a PTC on the EEJ. (E) An alternative 5’-splice site inducing a PTC via intron retention. (F) An alternative 5’-splice site inducing a PTC via frameshift. (G) A pair of mutually exclusive exons

Fig. 3

Regulation of unproductive splicing. ‘R’ denotes a splicing repressor. ‘A’ denotes a splicing activator. ‘G’ denotes the target gene. Exon colors are as in Fig. 2. (A) An increase in R or a decrease in A leads to poison exon skipping, and expression of G increases. (B) A decrease in R or an increase in A suppresses essential exon skipping, and expression of G also increases

Fig. 4

Alternative polyadenylation promotes NMD escape by cutting off a part of the UTR that contains EEJ. This converts a PTC into a normal stop codon (bright vertical blue line)