ArticleBMC genomics2016
Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 1 of them a synthesis that pooled it.
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Who cites it
42 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- Nuclear effects play an important role in determining codon usage-dependent human gene expression.Nature communications · 2025Article
- Hypoxia-mediated regulation of mRNA metabolism: from transcription to stability.Cell communication and signaling : CCS · 2025Review
- Ubiquitin-dependent translation control mechanisms: Degradation and beyond.Cell reports · 2024Review
- Modeling of mRNA deadenylation rates reveal a complex relationship between mRNA deadenylation and decay.The EMBO journal · 2024Article
- Unveiling RNA structure-mediated regulations of RNA stability in wheat.Nature communications · 2024Article
- Codon optimality influences homeostatic gene expression in zebrafish.G3 (Bethesda, Md.) · 2024Article
- UPF1 regulates mRNA stability by sensing poorly translated coding sequences.Cell reports · 2024Article
- Review
- Synonymous codon usage regulates translation initiation.Cell reports · 2023Article
- Specific recognition and ubiquitination of translating ribosomes by mammalian CCR4-NOT.Nature structural & molecular biology · 2023Article
- mRNA stability and mMolecular cell · 2023Article
- Proteome effects of genome-wide single gene perturbations.Nature communications · 2022Article
- Mitotic checkpoint gene expression is tuned by codon usage bias.The EMBO journal · 2022Article
- iCodon customizes gene expression based on the codon composition.Scientific reports · 2022Article
- Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown.Nucleic acids research · 2022Article
- Codon optimality-mediated mRNA degradation: Linking translational elongation to mRNA stability.Molecular cell · 2022Review
- Ribosome slowdown triggers codon-mediated mRNA decay independently of ribosome quality control.The EMBO journal · 2022Article
- Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression.Nature reviews. Molecular cell biology · 2022Review
- Reply to Qian and Zhang: Demonstration of the effect of codon usage on transcription by multiple approaches from fungi to animal cells.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
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2 authors.
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Abstract
backgroundRecent experiments have shown that codon optimality is a major determinant of mRNA stability in Saccharomyces cerevisiae and that this phenomenon may be conserved in Escherichia coli and some metazoans, although work in Neurospora crassa is not consistent with this model.
resultsWe examined the association between codon optimality and mRNA stability in the fission yeast Schizosaccharomyces pombe. Our analysis revealed the following points. First, we observe a genome-wide association between codon optimality and mRNA stability also in S. pombe, suggesting evolutionary conservation of the phenomenon. Second, in both S. pombe and S. cerevisiae, mRNA synthesis rates are also correlated at the genome-wide analysis with codon optimality, suggesting that the long-appreciated association between codon optimality and mRNA abundance is due to regulation of both mRNA synthesis and degradation. However, when we examined correlation of codon optimality and either mRNA half-lives or synthesis rates controlling for mRNA abundance, codon optimality was still positively correlated with mRNA half-lives in S. cerevisiae, but the association was no longer significant for mRNA half-lives in S. pombe or for synthesis rates in either organism. This illustrates how only the pairwise analysis of multiple correlating variables may limit these types of analyses. Finally, in S. pombe, codon optimality is associated with known DNA/RNA sequence motifs that are associated with mRNA production/stability, suggesting these two features have been under similar selective pressures for optimal gene expression.
conclusionsConsistent with the emerging body of studies, this study suggests that the association between codon optimality and mRNA stability may be a broadly conserved phenomenon. It also suggests that the association can be explained at least in part by independent adaptations of codon optimality and other transcript features for elevated expression during evolution.
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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.