Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes

Abstract

We have recently shown that a third of reliably-inferred alternative mRNA isoforms are candidates for nonsense-mediated mRNA decay (NMD), an mRNA surveillance system (Lewis et al., 2003; PROC: Natl Acad. Sci. USA, 100, 189-192). Rather than being translated to yield protein, these transcripts are expected to be degraded and may be subject to regulated unproductive splicing and translation (RUST). Our initial experimental studies are consistent with these predictions and suggest an unappreciated role for NMD in several human diseases.

The Coupling of Alternative Splicing and Nonsense-Mediated mRNA Decay

“…45 Further experiments showed that the PTC + isoforms increased in abundance relative to the PTC -isoforms when cells were treated with cycloheximide, which blocks translation and thereby inactivates the NMD pathway. 46 This result confirmed that all eight mRNA isoforms are produced but that the four PTC + isoforms are degraded by NMD. Other experimentally confirmed examples in the literature reflect apparent constitutive unproductive splicing (Table 1a).…”

Molecular characterization of three novel splicing mutations causing factor V deficiency and analysis of the F5 gene splicing pattern

“…Furthermore, the identification of the first F5 alternative splicing event associated with NMD suggests that F5 gene expression could be regulated post-transcriptionally by a mechanism coupling alternative splicing and NMD. 27,28 To analyze the F5 splicing pattern further, RT-PCR assays covering almost the whole F5 coding sequence were performed. This analysis revealed the occurrence of multiple alternative splicing events; among the various fragments produced, we further characterized the major ones, which, on the basis of their electrophoretic mobility, showed in-frame exon skipping (i.e.…”

“…24,25 Likewise, comparison of expression profiles of human cells with normal or reduced NMD activity revealed that NMD targets hundreds of genes. 26 In this frame, it was suggested that coupling of unproductive alternative splicing and NMD might be a way to regulate gene expression post-transcriptionally, 27 even if it is not clear to what extent this mechanism is common within the cell. 28 In this paper, we report the identification of three novel splicing mutations causing FV deficiency.…”

Global analysis of mRNA splicing

“…Several studies have probed connections between AS and nonsense-mediated decay (AS-NMD) in light of estimates that some 35% of annotated alternative splicing events introduce premature termination codons (PTCs) (Green et al 2003). Surprisingly, blocking NMD identified few changes in splice isoform levels in junction array profiles, suggesting that AS-NMD is confined to a small subset of AS events (Pan et al 2006;Ni et al 2007).…”