ArticleNucleic acids research2019
Codon stabilization coefficient as a metric to gain insights into mRNA stability and codon bias and their relationships with translation.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
- Tandem Repeat Gene Strategy for High-Yield Production and Functional Evaluation of Bioactive Wheat Oligopeptides.Applied biochemistry and biotechnology · 2026Article
- Accelerate the Highly Efficient Development of mRNA Vaccines Through Advanced Computational Methods.MedComm · 2026Review
- Life at the extremes: maximally divergent microbes with similar genomic signatures linked to extreme environments.NAR genomics and bioinformatics · 2025Article
- Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances.bioRxiv : the preprint server for biology · 2025Article
- Codon Composition in Human Oocytes Reveals Age-Associated Defects in mRNA Decay.International journal of molecular sciences · 2025Article
- Ageing-related decline of translation as a consequence of transcription dysregulation.Journal of the Royal Society, Interface · 2025Article
- Cytoplasmic mRNA decay and quality control machineries in eukaryotes.Nature reviews. Genetics · 2025Review
- Assessment of mRNA Decay and Calculation of Codon Occurrence to mRNA Stability Correlation Coefficients after 5-EU Metabolic Labeling.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Production of Complement Inhibitor Proteins in Mammalian Cell Lines-Light at the End of the Tunnel?Biomedicines · 2024Review
- Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability.Science advances · 2023Article
- Optimization of ribosome utilization inPNAS nexus · 2023Article
- Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation.Nature communications · 2023Article
- Implications of tRNA abundance on translation elongation across bovine tissues.Frontiers in genetics · 2023Article
- Oligodendrocyte differentiation alters tRNA modifications and codon optimality-mediated mRNA decay.Nature communications · 2022Article
- Mitotic checkpoint gene expression is tuned by codon usage bias.The EMBO journal · 2022Article
- Codon optimality-mediated mRNA degradation: Linking translational elongation to mRNA stability.Molecular cell · 2022Review
- Determinants of the temperature adaptation of mRNA degradation.Nucleic acids research · 2022Article
- Relative specificity as an important consideration in the big data era.Frontiers in genetics · 2022Article
- Downregulation of METTL6 mitigates cell progression, migration, invasion and adhesion in hepatocellular carcinoma by inhibiting cell adhesion molecules.International journal of oncology · 2022Article
- Codon optimality in cancer.Oncogene · 2021Review
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5 authors.
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Abstract
The codon stabilization coefficient (CSC) is derived from the correlation between each codon frequency in transcripts and mRNA half-life experimental data. In this work, we used this metric as a reference to compare previously published Saccharomyces cerevisiae mRNA half-life datasets and investigate how codon composition related to protein levels. We generated CSCs derived from nine studies. Four datasets produced similar CSCs, which also correlated with other independent parameters that reflected codon optimality, such as the tRNA abundance and ribosome residence time. By calculating the average CSC for each gene, we found that most mRNAs tended to have more non-optimal codons. Conversely, a high proportion of optimal codons was found for genes coding highly abundant proteins, including proteins that were only transiently overexpressed in response to stress conditions. We also used CSCs to identify and locate mRNA regions enriched in non-optimal codons. We found that these stretches were usually located close to the initiation codon and were sufficient to slow ribosome movement. However, in contrast to observations from reporter systems, we found no position-dependent effect on the mRNA half-life. These analyses underscore the value of CSCs in studies of mRNA stability and codon bias and their relationships with protein expression.
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