Effects of Nonsense Mutations on Nuclear and Cytoplasmic Adenine Phosphoribosyltransferase RNA

Kessler, Ofra; Chasin, Lawrence A.

doi:10.1128/mcb.16.8.4426

Cited by 64 publications

(54 citation statements)

References 64 publications

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“…Moreover, there was no difference in the densities of in-frame and out-of-frame stop codons in either set. We believe our approach, leading to the opposite conclusion, represents a more direct test of the hypothesis in question.These conclusions are in agreement with several genetic studies in which nonsense mutations that did not affect splicing were described, for example, in the genes for dhfr (Urlaub et al 1989), aprt (Kessler andChasin 1996), or hprt (Valentine 1998). Similarly, no nonsense mutations were found among 70 mutants of a three-exon dhfr minigene selected for skipping of the central exon (Chen and Chasin 1993).…”

supporting

confidence: 79%

The effect of nonsense codons on splicing: A genomic analysis: FIGURE 1.

Zhang¹,

Lee²,

Chasin³

2003

RNA

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The phenomenon of nonsense-associated altered splicing raises the possibility that the recognition of in-frame nonsense codons is used generally for exon identification during pre-mRNA splicing. However, nonsense codon frequencies in pseudo exons and in regions flanking 5 splice sites are no greater than that expected by chance, arguing against the widespread use of this strategy as a means of rejecting potential splice sites.Keywords: NAS; nonsense; pre-mRNA splicing; exon definition; latent splice sites; pseudo exons; exon skipping Two recent papers have bolstered the idea that the translatability of an exon can influence its splicing. Wang et al. (2002) have shown that an exon in the T-cell receptor transcript is not only excluded when it contains a nonsense codon, but that this event is accompanied by the inclusion of an overlapping cryptic alternative exon. The new exon restores an open reading frame. Independently, Li et al. (2002) have shown that a latent 5Ј splice site downstream of an exon can be activated if all in-frame nonsense codons are removed from the region between it and the upstream exon. In these mutated pre-mRNA molecules, a new enlarged exon is chosen for splicing, based on its newfound extended translatability. Explanations offered for these two results include nuclear recognition of the translatability of an exon before it is spliced.The recognition of exons or introns during the splicing process cannot rest on the splice site sequences alone, because similar sequences abound in large pre-mRNA molecules (Senapathy et al. 1990). There is considerable evidence that it is the exon that is the initial element of recognition, providing a size constraint for choosing real splice sites. However, if we define "pseudo exons" as intronic regions of typical exon size (50-250 nt) bounded by sequences that closely match the consensuses for 3Ј and 5Ј splice sites, their abundance still outweighs that of real exons by an order of magnitude (Sun and Chasin 2000). Splicing enhancers, assayed mostly in the context of alternatively spliced exons, are also quite varied and degenerate, and candidate sequences are easily found in pseudo exons (data not shown). How then does the cell distinguish real exons from pseudo exons? Exon translatability could be providing the missing information.To test this idea, we examined the predicted translatability of pseudo exons. If pseudo exons are being generally discriminated against because they contain nonsense codons, then each should contain at least one in-frame nonsense codon. If, on the other hand, nonsense codons play no such role, then nonsense codons should occur at a frequency dictated simply by chance. We culled pseudo exons from a human intron-exon database (Saxonov et al. 2000) after eliminating redundant and predicted genes. We defined these pseudo exons as intronic sequences that have at the upstream end a pseudo splice site with a consensus 3Ј matrix score of 78 and at the downstream end a pseudo splice site with a consensus 5Ј matrix score of 75; u...

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supporting

confidence: 79%

The effect of nonsense codons on splicing: A genomic analysis: FIGURE 1.

Zhang¹,

Lee²,

Chasin³

2003

RNA

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“…Given that bulk translation is cytoplasmic in all eukaryotic systems, an unexpected finding was that mammalian NMD occurs in association with nuclei Kessler and Chasin 1996;Wilkinson and Shyu 2002). In addition, other observations in mammalian systems have shown that a PTC can affect specific nuclear events, such as alternative splicing and 3 end formation (Brogna 1999;Wang et al 2002).…”

Section: Introductionmentioning

confidence: 99%

“…The first invokes a nuclear scanning model, which requires nuclear translation (Kessler and Chasin 1996). The second suggests that cytoplasmic translation begins during export of RNA from the nucleus to the cytoplasm.…”

Section: Introductionmentioning

confidence: 99%

Nonsense-mediated decay does not occur within the yeast nucleus

Kuperwasser

Brogna²,

Dower³

et al. 2004

RNA

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Nonsense-mediated decay (NMD) is a eukaryotic regulatory process that degrades mRNAs with premature termination codons (PTCs). Although NMD is a translation-dependent process, there is evidence from mammalian systems that PTC recognition and mRNA degradation takes place in association with nuclei. Consistent with this notion, degradation of mammalian PTC-containing mRNAs occurs when they are bound by the cap binding complex (CBC) during a "pioneer" round of translation. Moreover, there are reports indicating that a PTC can trigger other nuclear events such as alternative splicing, abnormal 3 end processing, and accumulation of pre-mRNA at transcription sites. To examine whether a PTC can elicit similar nuclear events in yeast, we used RNA export-defective mutants to sequester mRNAs within nuclei. The results indicate that nuclear PTCcontaining yeast RNAs are NMD insensitive. We also observed by fluorescent in situ hybridization that there was no PTC effect on mRNA accumulated at the site of transcription. Finally, we show that yeast NMD occurs minimally if at all on CBC-bound transcripts, arguing against a CBC-mediated pioneer round of translation in yeast. The data taken together indicate that there are no direct consequences of a PTC within the yeast nucleus.

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“…46,47 Here, we studied the role of UPF1 by examining the changes in abundance and decay rates of transcripts that respond to depletion of UPF1, using a recently developed inhibitor-free genomewide method for measuring RNA stability: 5'-bromo-uridine immunoprecipitation chase-deep sequencing analysis (BRICseq). 48 BRIC-seq involves pulse-labeling endogenous RNAs with 5'-bromo-uridine (BrU) and measuring the ongoing decrease in RNA levels over time by deep sequencing, without the use of transcriptional inhibitors.…”

Section: Identification Of Hundreds Of Novel Upf1 Targetmentioning

confidence: 99%