Regulation of splicing: The importance of being translatable: FIGURE 1.

Miriami, Elana; Sperling, Ruth; Sperling, Joseph; Motro, Uzi

doi:10.1261/rna.5112704

Cited by 18 publications

(20 citation statements)

References 9 publications

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“…We found no evidence for an increased frequency of stop codons upstream of such LSs, arguing against this model (Zhang et al 2003). Miriami et al (2003), in their response to that report, claim that we erred in plotting our data. We see no errors in our graph, and believe these authors misconstrued what was plotted.…”

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confidence: 66%

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Latent splice sites and stop codons revisited: FIGURE 1.

Zhang

Chasin²

2003

RNA

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The accuracy of the data we reported in an RNA Letter to the Editor earlier this year on the possible relationship between stop codons and splicing is questioned by Miriami et al. (this issue). We reply here that we see no inaccuracy in our data presentation and offer a possible explanation for their interpretation.We recently reported a genomic analysis testing the model of Li et al. (2002) that in-frame stop codons (SCs) upstream of false or "latent" 5Ј splice sites (LSs) were a determining factor in distinguishing false sites from true sites (Zhang et al 2003). We found no evidence for an increased frequency of stop codons upstream of such LSs, arguing against this model (Zhang et al. 2003). Miriami et al. (2003), in their response to that report, claim that we erred in plotting our data. We see no errors in our graph, and believe these authors misconstrued what was plotted. We reproduce the graph here and more fully explain what was plotted (Fig. 1).We reasoned that if in-frame stop codons acted as general signals to ignore a downstream LS, then they should always be found between the real 5Ј splice site and the LS. If this model is not correct, then the frequency of in-frame SCs should be not greater than that expected by chance. We chose to plot these data as a function of the position that the LS occupies downstream of the exon boundary, because both predictions approach the same frequency of one at distances greater than ∼ 100 nt.The X-axis in the figure represents introns grouped by the distance at which their most 5Ј LS is found (in windows of five). The number of introns in each class ranged from 21 to 82. The Y-axis represents the proportion of each intron class that have at least one in-frame SC upstream of the LS.The solid line represents the expected proportion of introns in each class that have at least one SC upstream of the LS if this occurrence happened by chance. To make this calculation, we divided the 100-nt region into two components. The first 6 nt of all introns comprise part of the splice site itself, which has a high probability of harboring an SC because of the URA embedded in its consensus sequence AG/GURAGU. Based on the matrix of bases underlying this consensus sequence, we calculated that the probability of an SC sequence occurring by chance is 0.74. We divided this number by 3 for the three possible reading frames to obtain this probability for an in-frame occurrence (0.247). Based on a Poisson distribution, the expected frequency of introns having an in-frame SC within the splice site is 1 − P 0 , where P 0 = e −0.247 . The second component represents the probability of a stop codon occurring within the remaining 94 nt of this 100-nt flank. We used the Poisson distribution to calculate the fraction of introns in different distance classes expected to contain at least one in-frame SC. We calculated P 0 based on the mean SC frequency per triplet (m) in the regions 100 nt downstream of all real introns, regardless of the presence of an LS. For this calculation, the 92 tripl...

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contrasting

confidence: 66%

“…The confusion may have arisen from the fact that we based our estimation of the probability of SCs occurring within the splice site by chance on the weight matrix (as stated in our paper), whereas Miriami et al (2003) apparently assumed that we used the actual frequency of in-frame SCs, as they did in a related but different type of analysis.…”

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confidence: 99%

Latent splice sites and stop codons revisited: FIGURE 1.

Zhang

Chasin²

2003

RNA

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“…We previously demonstrated the occurrence of SOS in two gene systems, CAD and IDUA, by eliciting splicing at latent 5Ј splice sites in minigenes in which in-frame stop codons upstream of the latent 5Ј splice sites were eliminated (Li et al 2002). These results were further supported by compu- Nonsense-mediated suppression of splicing www.rnajournal.org tational analyses, thereby making a strong case for the generality of the SOS phenomenon (Miriami et al , 2004. The occurrence of SOS invokes a mechanism that can recognize the mRNA reading frame at the level of pre-mRNA and suppress splicing events that would lead to the production of nonsense mRNAs.…”

Section: Discussionmentioning

confidence: 80%

“…Under normal growth conditions, splicing events involving latent 5Ј splice sites have not been reported, although such latent sites are highly abundant in introns (Miriami et al , 2004. We previously employed a highly sensitive RT-PCR procedure to show that splicing involving a latent 5Ј splice site in the wild-type CAD and IDUA genes ( Fig.…”

Section: Latent Splicing Is Not Activated By Chx-an Inhibitor Of Tranmentioning

confidence: 99%

“…We first noticed this phenomenon upon the discovery that a latent 5Ј splice site in the CAD gene is activated after heat shock (Miriami et al 1994). We also conducted a survey of a database consisting of 2311 introns from 446 human protein-coding-genes, in which we identified 10,490 latent 5Ј splice sites (Miriami et al , 2004. In most cases, the lack of splicing at the latent sites could be correlated with the occurrence of upstream in-frame stop codons, indicating a general role for SOS in maintaining the translatability of mRNAs.…”

Section: Introductionmentioning

confidence: 99%

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Stop codon-mediated suppression of splicing is a novel nuclear scanning mechanism not affected by elements of protein synthesis and NMD

Wachtel¹,

Li²,

Sperling³

et al. 2004

RNA

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The pre-mRNA splicing machine must frequently discriminate between normal and many potential 5 splice sites that match the consensus sequence but remain latent. Suppression of splicing (SOS) at such latent 5 splice sites is required for the maintenance of an open reading frame, and to ensure that only RNAs that encode for functional proteins will be formed. In this study we show that SOS is a novel mechanism distinct from the known RNA surveillance mechanisms. First, SOS is distinct from nonsensemediated mRNA decay (NMD) because it is not dependent on translation and is not affected by RNAi-mediated down-regulation of hUpf1 and hUpf2-two key components of the NMD pathway. Second, SOS is distinct from nonsense-associated alternative splicing (NAS), because a mutant of hUpf1, which was shown to abrogate NAS, does not activate latent splicing. Elucidating the mechanism of SOS is pertinent to human disease in view of the large number of human genes that harbor latent splice sites.

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Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing

et al. 2007

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Although single base-pair substitutions in splice junctions constitute at least 10% of all mutations causing human inherited disease, the factors that determine their phenotypic consequences at the RNA level remain to be fully elucidated. Employing a neural network for splice-site recognition, we performed a meta-analysis of 478 disease-associated splicing mutations, in 38 different genes, for which detailed laboratory-based mRNA phenotype assessment had been performed. Inspection of the +/-50-bp DNA sequence context of the mutations revealed that exon skipping was the preferred phenotype when the immediate vicinity of the affected exon-intron junctions was devoid of alternative splice-sites. By contrast, in the presence of at least one such motif, cryptic splice-site utilization, became more prevalent. This association was, however, confined to donor splice-sites. Outside the obligate dinucleotide, the spatial distribution of pathological mutations was found to differ significantly from that of SNPs. Whereas disease-associated lesions clustered at positions -1 and +3 to +6 for donor sites and -3 for acceptor sites, SNPs were found to be almost evenly distributed over all sequence positions considered. When all putative missense mutations in the vicinity of splice-sites were extracted from the Human Gene Mutation Database for the 38 studied genes, a significantly higher proportion of changes at donor sites (37/152; 24.3%) than at acceptor splice-sites (1/142; 0.7%) was found to reduce the neural network signal emitted by the respective splice-site. Based upon these findings, we estimate that some 1.6% of disease-causing missense substitutions in human genes are likely to affect the mRNA splicing phenotype. Taken together, our results are consistent with correct donor splice-site recognition being a key step in exon recognition.

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Regulation of splicing: The importance of being translatable: FIGURE 1.

Cited by 18 publications

References 9 publications

Latent splice sites and stop codons revisited: FIGURE 1.

Latent splice sites and stop codons revisited: FIGURE 1.

Stop codon-mediated suppression of splicing is a novel nuclear scanning mechanism not affected by elements of protein synthesis and NMD

Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing

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