Pan, Q. et al. Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev. 20, 153-158

Banting and Best Department of Medical Research, University of Toronto, Ontario, M5G 1L6, Canada.
Genes & Development (Impact Factor: 10.8). 02/2006; 20(2):153-8. DOI: 10.1101/gad.1382806
Source: PubMed


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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Available from: Benjamin J Blencowe, Oct 29, 2015
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    • "One important challenge in the study of all alternative splice events is to define the relative biological impact of the gain of the alternative splice form versus the loss of the constitutive form. While the induction of alternative splice variants often have important biological effects, in extreme cases alternative splicing serves only to dampen gene expression, as is the case when these events are coupled to the nonsense-mediated decay pathway [19], [20]. To shed light on the mechanism controlling the TAF6δ pathway of apoptosis, here we have compared the transcriptome impacts of loss of function of the major TAF6α splice variant via siRNA depletion versus those resulting from the induction of the pro-apoptotic TAF6δ splice variant. "
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    ABSTRACT: The TAF6δ pathway of apoptosis can dictate life versus death decisions independently of the status of p53 tumor suppressor. TAF6δ is an inducible pro-apoptotic subunit of the general RNA polymerase II (Pol II) transcription factor TFIID. Alternative splice site choice of TAF6δ has been shown to be a pivotal event in triggering death via the TAF6δ pathway, yet nothing is currently known about the mechanisms that promote TAF6δ splicing. Furthermore the transcriptome impact of the gain of function of TAF6δ versus the loss of function of the major TAF6α splice form remains undefined. Here we employ comparative microarray analysis to show that TAF6δ drives a transcriptome profile distinct from that resulting from depletion of TAF6α. To define the cis-acting RNA elements responsible for TAF6δ alternative splicing we performed a mutational analysis of a TAF6 minigene system. The data point to several new RNA elements that can modulate TAF6δ and also reveal a role for RNA secondary structure in the selection of TAF6δ.
    PLoS ONE 07/2014; 9(7):e102399. DOI:10.1371/journal.pone.0102399 · 3.23 Impact Factor
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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 · 9.34 Impact Factor
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    • "Recently it was discovered that NMD also regulates normal gene expression [55], together suggesting that NMD manipulations could potentially cause both loss-and gain- of -function changes and be of clinical benefit. AS/NMD coupling was suggested before [56] and was termed ‘regulated unproductive splicing and translation’ (RUST) [11,50,57]. Correspondingly, the identified NMD/AS changes reflect DBS-inducible enhancement of cellular response to stress and alternative splicing, both were rapidly modified by stimulation cessation to NMD-induced functional changes in immune and inflammation properties. "
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    ABSTRACT: Nonsense-Mediated decay (NMD) selectively degrades mRNA transcripts that carry premature stop codons. NMD is often triggered by alternative splicing (AS) modifications introducing such codons. NMD plays an important regulatory role in brain neurons, but the in vivo dynamics of AS and NMD changes in neurological diseases and under treatment were scarcely explored. Here, we report exon arrays analysis of leukocyte mRNA AS events prior to and following Deep Brain Stimulation (DBS) neurosurgery, which efficiently improves the motor symptoms of Parkinson's disease (PD), the leading movement disorder, and is increasingly applied to treat other diseases. We also analyzed publicly available exon array dataset of whole blood cells from mixed early and advanced PD patients. Our in-house exon array dataset of leukocyte transcripts was derived from advanced PD patients' pre- and post-DBS stimulation and matched healthy control volunteers. The mixed cohort exhibited 146 AS changes in 136 transcripts compared to controls, including 9 NMD protein-level assessed events. In comparison, PD patients from our advanced cohort differed from healthy controls by 319 AS events in 280 transcripts, assessed as inducing 27 protein-level NMD events. DBS stimulation induced 254 AS events in 229 genes as compared to the pre-DBS state including 44 NMD inductions. A short, one hour electrical stimulus cessation caused 234 AS changes in 125 genes compared to ON-stimulus state, 22 of these were assessed for NMD. Functional analysis highlighted disease-induced DNA damage and inflammatory control and its reversal under ON and OFF stimulus as well as alternative splicing in all the tested states. The study findings indicate a potential role for NMD both in PD and following electrical brain stimulation. Furthermore, our current observations entail future implications for developing therapies for PD, and for interfering with the impaired molecular mechanisms that underlie PD and other neurodegenerative and neurological disorders, as well as DBS-treatable conditions in general.
    BMC Genomics 07/2013; 14(1):478. DOI:10.1186/1471-2164-14-478 · 3.99 Impact Factor
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