Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans

By Benjamin P. Lewis, R. Green, Steven E. Brenner. Proceedings of the National Academy of Sciences of the United States of America, 2002

1,105 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4bc2f7b19c8edbada6644530d6500e36ede3db44

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Citations in the corpus

Genome-wide mapping of alternative splicing in Arabidopsis thaliana. (2010, background): “It has been estimated that up to 72% of alter- native splicing events in human spliceosomal factors introduce inframe PTCs (Saltzman et al. 2008), while more than one-third of PTC+ splicing isoforms could be targeted for NMD (Lewis et al. 2003).”
Circular RNA Expression: Its Potential Regulation and Function (2016, background): “The existence of intron retention in circRNAs would not be surprising, considering that linear intron-retained transcripts are known to be generated by metazoan splicing machinery [38].”
Learning the sequence determinants of alternative splicing from millions of random sequences. (2015, result): “This is consistent with previous studies on nonsense-mediated decay that suggest the premature stop codon must occur >50 nt upstream of the last exon junction (Lewis et al., 2003).”
Splicing in disease: disruption of the splicing code and the decoding machinery (2007, background): “Furthermore, one-third of alternative splicing events introduce premature termination codons (PTCs), which cause mRNA degradation by nonsense-mediated decay (NMD”
Understanding alternative splicing: towards a cellular code (2005, background): “and a third apparently leading to NONSENSE-MEDIATED DECAY (NMD) of the RNA produc”
Nonsense-mediated decay approaches the clinic (2004, background): “Approximately 75% of these alternative transcripts would be expected to undergo NMD due to the position of the PT”
The Sequence Ontology: a tool for the unification of genome annotations (2005, background): “First, regardless of exon class, most entirely untranslated exons are 5-prime exons; the lower frequency of 3prime untranslated exons is perhaps due to nonsense-mediated decay [31], as the presence of splice junctions in a processed transcript downstream of its stop codon are believed to target that”
Opportunities and challenges Genome-wide analyses of alternative splicing in plants: (2008, positive): “Lewis et al. (2003) determined that 35% of a set of >3000 alternatively spliced human genes have predicted isoforms that result in PTCs, concluded that ∼75% of these are apparent targets for NMD, and proposed that coupled AS and NMD plays a functional role in regulating protein expression levels.”
Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. (2007, background): “…nonsense-containing transposon or retroviral sequences within their coding regions (Mendell et al. 2004; Wittmann et al. 2006; Chan et al. 2007); and (3) alternatively spliced mRNAs, an estimated one-third of which in humans are thought to be slated for NMD (Lewis et al. 2003; Lareau et al. 2004).”
Function of alternative splicing. (2005, positive): “Since approximately 75% of these exons are predicted to be subject to nonsensemediated decay, an estimated 18–25% of transcripts will be switched off by stop codons caused by alternative splicing and nonsense-mediated decay (Lewis et al., 2003).”
Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise (2004, background): “Bioinformatic analyses have suggested that introduction of PTCs through alternative splicing is a relatively common feature of the human transcriptom”
GENCODE: producing a reference annotation for ENCODE (2006, background): “The latter often results in unusual structures, with multi-exon 5’ and/or 3’ UTRs that are at odds with rules governing re-initiation [24] and nonsense mediated decay (NMD) [25] (for example, Pairagon at the AC008937.”