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Codon Optimality Is a Major Determinant of mRNA Stability
Open accessAbstract
mRNA degradation represents a critical regulated step in gene expression. Although the major pathways in turnover have been identified, accounting for disparate half-lives has been elusive. We show that codon optimality is one feature that contributes greatly to mRNA stability. Genome-wide RNA decay analysis revealed that stable mRNAs are enriched in codons designated optimal, whereas unstable mRNAs contain predominately non-optimal codons. Substitution of optimal codons with synonymous, non-optimal codons results in dramatic mRNA destabilization, whereas the converse substitution significantly increases stability. Further, we demonstrate that codon optimality impacts ribosome translocation, connecting the processes of translation elongation and decay through codon optimality. Finally, we show that optimal codon content accounts for the similar stabilities observed in mRNAs encoding proteins with coordinated physiological function. This work demonstrates that codon optimization exists as a mechanism to finely tune levels of mRNAs and, ultimately, proteins.
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“These strategies have yielded modest improvements in RNA stability10, 13–16, and thus alternative approaches to RNA stabilization, such as circularization, are desirable.”
From Engineering circular RNA for potent and stable translation in eukaryotic cells (2018) · cites this paper as [15]
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“Furthermore, the rate of codon-dependent translation elongation has been a primary factor of mRNA stability, codon modification is critical for mRNA stability (Presnyak et al. 2015).”
From Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency (2022) · cites this paper as Presnyak et al. 2015
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“Furthermore, the rate of codon-dependent translation elongation has been a primary factor of mRNA stability, codon modification is critical for mRNA stability (Presnyak et al. 2015).”
From Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency (2022) · cites this paper as Presnyak et al. 2015
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“To improve the safety, efficacy, and stability of mRNA vaccines, researchers usually performed codon optimization172,239–243 on the antigen-coding sequence to enhance translation efficiency.”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [240]
In the citing paper
“Codon optimization in the mRNA sequence to e.g., match host transfer (t)RNA abundances, or as a determinant of introducing secondary structures, can drastically impact the protein synthesis rate and ribosome dwell time (i.e. mRNA functional half-life) [33,34]”
From The dawn of mRNA vaccines: the COVID-19 case (2021) · cites this paper as [33]
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“Critically, optimal codons are postulated to be decoded faster and more accurately by the ribosome than non-optimal codons (Akashi, 1994; Drummond and Wilke, 2008), which are hypothesized to slow translation elongation (Novoa and Ribas de Pouplana, 2012; Tuller et al., 2010).”
BackgroundAn evolutionarily conserved mechanism for controlling the efficiency of protein translation
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“Other surveillance routes, such as no-go decay, nonstop decay and codon optimality-mediated decay, coordinate decay with translation kinetics and messenger RNP structure 78–80 .”
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“25,26 Codon optimization involves replacing rare codons with synonymous codons that are more frequently used in the host, thereby increasing the utilization of cognate tRNAs and accelerating translation elongation.”
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“In addition, codon optimality and thus elongation rate has also been suggested to be positively associated with mRNA stability ( Presnyak et al., 2015 ).”
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“Despite the degeneracy of the genetic code, synonymous codons can influence mRNA half-life and protein expression in yeast [15].”
Ribosome demand links transcriptional bursts to protein expression noisePreprint
Pal, S., Ray, U., & Dhar, R. (2025) · eLife · doi:10.7554/elife.99322.2 · Cited by 1
Protein language models reveal evolutionary constraints on synonymous codon choicePreprint
Sakharova, H., & Lareau, L. F. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.05.668603 · Cited by 2
“Fast translation elongation generally leads to higher protein output, while slow translation elongation decreases output by triggering mRNA degradation and limiting translation initiation (Presnyak et al. , 2015; Barrington et al. , 2023; Lyons et al. , 2024).”
Du, S., Kaynar, G., Li, J., You, Z., Tang, S., & Kingsford, C. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.12.705465 · Cited by 1
“Recent advances in RNA biology have revealed that mRNA secondary structure stability, quantified by minimum free energy (MFE), plays a role in determining expression levels [Presnyak et al., 2015, Hanson and Coller, 2018].”
Variation of Human Transfer RNA Demand and SupplyPreprint
Külp, M., Wiegand, A.-S., Bonig, H. B., & Rieger, M. A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.26.708130 · Cited by 1
Splice-Aware Optimization Prevents Pervasive Missplicing of Natural and Synthetic cDNAsPreprint
Ahmad, M., Molías, F. B., Cano-Aroca, L., Mordstein, C., Watson, S., Bhuiyan, N., Clarke, M. J., Kimchi‐Sarfaty, C., Katneni, U., Gaunt, E. R., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.25.727620 · Cited by 2
Homeostasis in the Central Dogma of Molecular Biology: the importance of mRNA instability
Pérez-Ortín, J. E., Tordera, V., & Chávez, S. (2019) · doi:10.1101/599050 · Cited by 1
Mechanisms of Post-transcriptional Gene Regulation
Arvola, R. M., Abshire, E. T., Bohn, J. A., & Goldstrohm, A. C. (2015) · Springer eBooks · doi:10.1007/978-3-319-25124-0_1
REGULATORY ROLES OF G-QUADRUPLEX IN microRNA PROCESSING AND mRNA TRANSLATION
Arachchilage, G. M., & Gayan, S. (2016) · OhioLink ETD Center (Ohio Library and Information Network)
Modulation of Translation Efficiency in S. cerevisiae by Codon Pairs and mRNA Structure
Gamble, C. E. (2016) · ResearchWorks at the University of Washington (University of Washington)
Bailey, K. (2016) · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)
Ribosome Processivity and Co-translational Protein Folding
Thommen, M. (2017) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-6242
DRUID: A pipeline for reproducible transcriptome-wide measurements of mRNA stabilityPreprint
Lugowski, A., Nicholson, B. L., & Rissland, O. S. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/149195
“…, these experiments typically involve using a temperature-sensitive mutant of RNA polymerase II (Herrick et al. 1990; Grigull et al. 2004; Presnyak et al. 2015), and work in mammalian cell lines has predominantly relied upon drugs that target RNA polymerases, such as actinomycin D and α…”
Investigating tRNA abundance as a determinant of decoding speed in Saccharomyces cerevisiae.
Pain, C. (2016) · Kent Academic Repository (University of Kent)
Regulation of Local Translation, Synaptic Plasticity, and Cognitive Function by CNOT7
McFleder, R. L. (2017) · The Journal of the American Medical Association (JAMA) Network (American Medical Association) · doi:10.13028/m2km3r
mRNA stability in soma and neurites of cultured neuronal cells
Srinath, C. (2017) · DSpace@MIT (Massachusetts Institute of Technology)
Optimizing gene expression by adapting splicingPreprint
Frumkin, I., Yofe, I., Bar‐Ziv, R., Voichek, Y., & Pilpel, Y. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/220228
Combinations of slow translating codon clusters can increase mRNA half-lifePreprint
Sharma, A. K., & O’Brien, E. P. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/490995
“(6) against coding sequence length does not exhibit this behavior (Fig.”
BackgroundInfluentialSplicing buffers suboptimal codon usage in human cellsPreprint
Mordstein, C., Savisaar, R., Young, R. S., Bazile, J., Talmane, L., Luft, J., Liss, M. A., Taylor, M. S., Hurst, L. D., & Kudla, G. R. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/527440
“Recent studies also highlight patterns of codon usage as major determinants of RNA stability in yeast (Presnyak et al., 2015), zebrafish (Mishima and Tomari, 2016) and other species (Bazzini et al., 2016).”
BackgroundMake or break: the ribosome as a regulator of mRNA decay
Veltri, A. J., D’Orazio, K. N., & Green, R. (2020) · Cell Research · doi:10.1038/s41422-019-0271-3
Genome-scale conserved molecular principles of mRNA half-life regulationPreprint
Basu, S., Mallik, S., Hait, S., & Kundu, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.17.952267
Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosaPreprint
Callens, M., Scornavacca, C., & Bedhomme, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.11.198432
Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiaePreprint
Mangkalaphiban, K., He, F., Ganesan, R., Wu, C., Baker, R., & Jacobson, A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.15.422930
Zare, N. (2020) · Carleton University's Institutional Repository (MacOdrum Library, Carleton University) · doi:10.22215/etd/2020-14316
Tomecki, R., & Drążkowska, K. (2021) · FEBS Journal · doi:10.1111/febs.15742
Visualizing mRNA quality control
Hoek, T. A. (2021) · doi:10.33540/625
iCodon: ideal codon design for customized gene expressionPreprint
Bazzini, A. (2021) · Research Square · doi:10.21203/rs.3.rs-598844/v1
Zhao, F., & Liu, Y. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2104896118
The role of the coding sequence in regulating human mRNA stability
Narula, A. (2018) · TSpace (University of Toronto)
Metadata
- Authors
- Presnyak, V., Alhusaini, N., Chen, Y.-H., Martin, S., Morris, N., Kline, N., Olson, S., Weinberg, D., Baker, K. E., Graveley, B. R., & Coller, J.
- Affiliations
- Case Western Reserve University (US)
- UConn Health (US)
- University of California, San Francisco (US)
- Corresponding author
- Coller, Jeff
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2015-03
- Volume
- 160
- Issue
- 6
- Pages
- 1111-1124
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC4359748
- OpenAlex
- W2013321787
- Cited by
- 1,078
- References
- 43
- Citations by year
- 2026: 94 · 2025: 139 · 2024: 122 · 2023: 115 · 2022: 77 · 2021: 127 · 2020: 93 · 2019: 70 · 2018: 96 · 2017: 68 · 2016: 57 · 2015: 20
- FWCI
- 34.90
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (GM080465, GM095621)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Keywords
- codon optimality, mRNA stability, mRNA degradation, codon usage bias, synonymous codons, ribosome translocation, translation elongation, gene expression regulation, mRNA half-life
- MeSH terms
- Codon, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae, Protein Biosynthesis, RNA Stability
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