The DOI matches its Crossref record; 143 of the 143 references it cites were found in a registry or an index.
Codon optimality, bias and usage in translation and mRNA decay
Open accessAbstract
The advent of ribosome profiling and other tools to probe mRNA translation has revealed that codon bias - the uneven use of synonymous codons in the transcriptome - serves as a secondary genetic code: a code that guides the efficiency of protein production, the fidelity of translation and the metabolism of mRNAs. Recent advancements in our understanding of mRNA decay have revealed a tight coupling between ribosome dynamics and the stability of mRNA transcripts; this coupling integrates codon bias into the concept of codon optimality, or the effects that specific codons and tRNA concentrations have on the efficiency and fidelity of the translation machinery. In this Review, we first discuss the evidence for codon-dependent effects on translation, beginning with the basic mechanisms through which translation perturbation can affect translation efficiency, protein folding and transcript stability. We then discuss how codon effects are leveraged by the cell to tailor the proteome to maintain homeostasis, execute specific gene expression programmes of growth or differentiation and optimize the efficiency of protein production.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“elements including the relative frequencies of codon use for each amino acid, local and global GC composition, mRNA secondary structure stability, and the presence of cryptic termination signals or splice sites are significant factors impacting the degree of protein expression”
From Codon optimization is an essential parameter for the efficient allotopic expression of mtDNA genes (2020) · cites this paper as [61]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“The translation elongation rate is controlled by the accessibility of cognate tRNA species and the codon usage modification to prevent the match rare tRNA sequence of species and integrate sequences that match more common tRNA species (Hanson and Coller 2018).”
From Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency (2022) · cites this paper as Hanson and Coller 2018
In the citing paper
“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 [239]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853
Global analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750
Regulation of mRNA Translation and Stability by microRNAs
Fabian, M. R., Sonenberg, N., & Filipowicz, W. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060308-103103 · Cited by 3,214
Synonymous but not the same: the causes and consequences of codon bias
Plotkin, J. B., & Kudla, G. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2899 · Cited by 1,722
Coding-Sequence Determinants of Gene Expression in Escherichia coli
Kudla, G., Murray, A. W., Tollervey, D., & Plotkin, J. B. (2009) · Science · doi:10.1126/science.1170160 · Cited by 1,458
Ikemura, T. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90003-6 · Cited by 1,423
Codon bias and heterologous protein expression
Gustafsson, C., Govindarajan, S., & Minshull, J. (2004) · Trends in Biotechnology · doi:10.1016/j.tibtech.2004.04.006 · Cited by 1,330
The translational landscape of mTOR signalling steers cancer initiation and metastasis
Hsieh, A. C., Liu, Y., Edlind, M. P., Ingolia, N. T., Janes, M. R., Sher, A., Shi, E. Y., Stumpf, C. R., Christensen, C., Bonham, M. J., et al. (2012) · Nature · doi:10.1038/nature10912 · Cited by 1,313
Li, G., Burkhardt, D. H., Gross, C. A., & Weissman, J. S. (2014) · Cell · doi:10.1016/j.cell.2014.02.033 · Cited by 1,259
Lu, P., Vogel, C., Wang, R., Yao, X., & Marcotte, E. M. (2007) · Nature Biotechnology · doi:10.1038/nbt1270 · Cited by 1,139
Cited by
Sorted by citations
On the origin and continuing evolution of SARS-CoV-2
Tang, X., Wu, C., Li, X., Song, Y., Yao, X., Wu, X., Duan, Y., Zhang, H., Wang, Y., Qian, Z., et al. (2020) · National Science Review · doi:10.1093/nsr/nwaa036 · Cited by 1,627
“Synonymous substitutions may serve as another layer of genetic regulation, guiding the efficiency of mRNA translation by changing codon usage [23].”
RNA modifications modulate gene expression during development
Frye, M., Harada, B. T., Behm, M., & He, C. (2018) · Science · doi:10.1126/science.aau1646 · Cited by 1,263
“1B) ( 15, 16 ).”
Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction
Koblan, L. W., Doman, J. L., Wilson, C., Levy, J. M., Tay, T., Newby, G. A., Maianti, J. P., Raguram, A., & Liu, D. R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4172 · Cited by 944
Acetylation of Cytidine in mRNA Promotes Translation Efficiency
Arango, D., Sturgill, D., Alhusaini, N., Dillman, A. A., Sweet, T. J., Hanson, G., Hosogane, M., Sinclair, W. R., Nanan, K. K., Mandler, M. D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.030 · Cited by 862
Self-citationThe expanding world of tRNA modifications and their disease relevance
Suzuki, T. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00342-0 · Cited by 733
Metadata
- Authors
- Hanson, G., & Coller, J.
- Affiliations
- Case Western Reserve University (US)
- Corresponding author
- Hanson, Gavin
- Coller, Jeff
- Venue
- Nature Reviews Molecular Cell Biology
- Published
- 2017-10-11
- Volume
- 19
- Issue
- 1
- Pages
- 20-30
- ISSN
- 1471-0072 (ISSN-L)
- 1471-0080
- PMC
- PMC6594389
- OpenAlex
- W2762868004
- Cited by
- 825
- References
- 143
- Citations by year
- 2026: 92 · 2025: 114 · 2024: 108 · 2023: 113 · 2022: 93 · 2021: 122 · 2020: 78 · 2019: 58 · 2018: 46
- FWCI
- 4.66
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Molecular Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM118018, R01GM125086, T32GM007250)
- 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 modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- codon usage bias, codon optimality, synonymous codons, tRNA abundance, translation efficiency, translation fidelity, ribosome profiling, mRNA degradation, transcript stability, protein folding, ribosome dynamics, gene expression regulation
- MeSH terms
- Animals, Codon, Homeostasis, Humans, Proteins, Ribosomes, RNA, Messenger, Protein Biosynthesis, Protein Folding, RNA Stability
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
