Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression

Banting and Best Department of Medical Research, University of Toronto, Ontario, M5G 1L6, Canada.
Genes & Development (Impact Factor: 12.64). 02/2006; 20(2):153-8. DOI: 10.1101/gad.1382806
Source: PubMed

ABSTRACT Sequence-based analyses have predicted that approximately 35% of mammalian alternative splicing (AS) events produce premature termination codon (PTC)-containing splice variants that are targeted by the process of nonsense-mediated mRNA decay (NMD). This led to speculation that AS may often regulate gene expression by activating NMD. Using AS microarrays, we show that PTC-containing splice variants are generally produced at uniformly low levels across diverse mammalian cells and tissues, independently of the action of NMD. Our results suggest that most PTC-introducing AS events are not under positive selection pressure and therefore may not contribute important functional roles.

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    • ") . Taken to - gether , these estimates correlate well with those reported for flies , worms , and human ( Rehwinkel et al . , 2005 ; Pan et al . , 2006 ; Ramani et al . , 2009 ; Weischenfeldt et al . , 2012 ) . Importantly , Kalyna et al . ( 2012 ) identified AS transcripts that contained NMD features but were immune to NMD . Unexpectedly , the majority of IR transcripts were not sensitive to NMD despite containing PTCs , downstream splice junctions , and long 39UTRs . By contrast , tr"
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    ABSTRACT: Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
    The Plant Cell 10/2013; 25(10). DOI:10.1105/tpc.113.117523 · 9.58 Impact Factor
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    • "Most predicted PTC-introducing alternative splicing events [5] appear as cellular noises produced at low level by inefficient splicing during the post-transcriptional processing independently of NMD [13] [14]. There is evidence that only a relatively small proportion of PTC containing AS gene transcripts are subjected to NMD disruption [14]. It has, in fact, been found that absence of the NMD SMG1 factor induces expression changes of only 9% of the predicted PTC-containing AS products, and only 2% of these show level changes of more than 20% [15]. "
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    ABSTRACT: In this study the impact of hUPF1 and hUPF2 knockdown on alternative splicing (AS) isoforms of different genes encoding subunits of respiratory chain complex I and complex IV is described. As expected, loss of both hUPF1 and hUPF2 led to impairment of nonsense-mediated mRNA decay (NMD) and accumulation of PTC-containing NMD substrates generated by both complex I and complex IV genes. The levels of some complex I splice variants, which did not contain PTC as well as the level of some complex I canonical transcripts were, however, affected only by hUPF1 knockdown. This finding confirms that NMD plays a role in the maintenance of the transcriptome integrity and reveals a specific impact of hUPF1 on the regulation of complex I genes.
    Biochimie 08/2012; 94(12). DOI:10.1016/j.biochi.2012.07.022 · 3.12 Impact Factor
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    • "Nonetheless, our identification of conserved NMD is interesting, although not unprecedented. It has been reported that most mammalian NMD transcripts are not under selective pressure and therefore likely to be noise (Pan et al. 2006). However, members of the SR (serine–arginine) family of splicing factors use NMD isoforms to downregulate their own translation in a homeostatic manner, and it is speculated that this strategy (regulated unproductive splicing and translation or ''RUST'') may be common to splicing factors generally (Sureau et al. 2001; Lareau et al. 2007). "
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    ABSTRACT: Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the contribution of AS to the generation of phenotypic complexity and to study the evolution of splicing patterns. We have compared the AS of 309 protein-coding genes in the human ENCODE pilot regions against their mouse orthologs in unprecedented detail, utilizing traditional transcriptomic and RNAseq data. The conservation status of every transcript has been investigated, and each functionally categorized as coding (separated into coding sequence [CDS] or nonsense-mediated decay [NMD] linked) or noncoding. In total, 36.7% of human and 19.3% of mouse coding transcripts are species specific, and we observe a 3.6 times excess of human NMD transcripts compared with mouse; in contrast to previous studies, the majority of species-specific AS is unlinked to transposable elements. We observe one conserved CDS variant and one conserved NMD variant per 2.3 and 11.4 genes, respectively. Subsequently, we identify and characterize equivalent AS patterns for 22.9% of these CDS or NMD-linked events in nonmammalian vertebrate genomes, and our data indicate that functional NMD-linked AS is more widespread and ancient than previously thought. Furthermore, although we observe an association between conserved AS and elevated sequence conservation, as previously reported, we emphasize that 30% of conserved AS exons display sequence conservation below the average score for constitutive exons. In conclusion, we demonstrate the value of detailed comparative annotation in generating a comprehensive set of AS transcripts, increasing our understanding of AS evolution in vertebrates. Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution.
    Molecular Biology and Evolution 05/2011; 28(10):2949-59. DOI:10.1093/molbev/msr127 · 14.31 Impact Factor
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