ArticleNucleic acids research2004
Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
46 citing papers in PubMed, 87 citations in OpenAlex.
- Glutamine codon-driven translational readthrough reveals context-dependent stop codon decoding fidelity.bioRxiv : the preprint server for biology · 2026Article
- Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity.Cell reports · 2025Article
- Mechanisms and Delivery of tRNA Therapeutics.Chemical reviews · 2024Review
- Shiga toxin-producing Escherichia coli O157:H7 among diarrheic patients and their cattle in Amhara National Regional State, Ethiopia.PloS one · 2023Article
- Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor.Nucleic acids research · 2022Article
- Therapeutic promise of engineered nonsense suppressor tRNAs.Wiley interdisciplinary reviews. RNA · 2021Review
- Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells.Nucleic acids research · 2021Article
- Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors.Molecular biology and evolution · 2021Article
- Discovery of a previously unknown biosynthetic capacity of naringenin chalcone synthase by heterologous expression of a tomato gene cluster in yeast.Science advances · 2020Article
- Readthrough Errors Purge Deleterious Cryptic Sequences, Facilitating the Birth of Coding Sequences.Molecular biology and evolution · 2020Article
- Translational recoding: canonical translation mechanisms reinterpreted.Nucleic acids research · 2020Review
- Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides.eLife · 2020Article
- Mutant GNLY is linked to Stevens-Johnson syndrome and toxic epidermal necrolysis.Human genetics · 2019Article
- Article
- Eukaryotic translational termination efficiency is influenced by the 3' nucleotides within the ribosomal mRNA channel.Nucleic acids research · 2018Article
- Phylogenetically Conserved Sequences Around Myelin P0 Stop Codon are Essential for Translational Readthrough to Produce L-MPZ.Neurochemical research · 2018Article
- Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli.Journal of proteome research · 2017Article
- The [PSIScientific reports · 2017Article
- The non-stop decay mRNA surveillance pathway is required for oxidative stress tolerance.Nucleic acids research · 2017Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
In-frame stop codons normally signal termination during mRNA translation, but they can be read as 'sense' (readthrough) depending on their context, comprising the 6 nt preceding and following the stop codon. To identify novel contexts directing readthrough, under-represented 5' and 3' stop codon contexts from Saccharomyces cerevisiae were identified by genome-wide survey in silico. In contrast with the nucleotide bias 3' of the stop codon, codon bias in the two codon positions 5' of the termination codon showed no correlation with known effects on stop codon readthrough. However, individually, poor 5' and 3' context elements were equally as effective in promoting stop codon readthrough in vivo, readthrough which in both cases responded identically to changes in release factor concentration. A novel method analysing specific nucleotide combinations in the 3' context region revealed positions +1,2,3,5 and +1,2,3,6 after the stop codon were most predictive of termination efficiency. Downstream of yeast open reading frames (ORFs), further in-frame stop codons were significantly over-represented at the +1, +2 and +3 codon positions after the ORF, acting to limit readthrough. Thus selection against stop codon readthrough is a dominant force acting on 3', but not on 5', nucleotides, with detectable selection on nucleotides as far downstream as +6 nucleotides. The approaches described can be employed to define potential readthrough contexts for any genome.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.