ArticleMolecular biology and evolution2014
Quantifying position-dependent codon usage bias.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- The PAXT connection is a modifier of rare codon-enriched protein expression.Nature communications · 2026Article
- Position-dependent codon occurrence is associated with patterns of translational efficiency and ribosomal occupancy in the human transcriptome.PLoS computational biology · 2026Article
- Codon Usage Bias Analysis of Citrus Leaf Blotch Virus.Viruses · 2025Article
- Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Quality control of protein synthesis in the early elongation stage.Nature communications · 2023Article
- Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference.Interdisciplinary sciences, computational life sciences · 2022Article
- Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.PLoS genetics · 2022Article
- Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach.BMC genomics · 2022Article
- Generating dynamic gene expression patterns without the need for regulatory circuits.PloS one · 2022Article
- Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5' End of ORFeomes.mSystems · 2020Article
- Translation at first sight: the influence of leading codons.Nucleic acids research · 2020Article
- Codon usage pattern and predicted gene expression inGene: X · 2019Article
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- Review
- Article
- A novel framework for evaluating the performance of codon usage bias metrics.Journal of the Royal Society, Interface · 2018Article
- Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes.Genomics & informatics · 2017Article
- Leveraging genome-wide datasets to quantify the functional role of the anti-Shine-Dalgarno sequence in regulating translation efficiency.Open biology · 2017Article
- The Need for Integrated Approaches in Metabolic Engineering.Cold Spring Harbor perspectives in biology · 2016Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Although the mapping of codon to amino acid is conserved across nearly all species, the frequency at which synonymous codons are used varies both between organisms and between genes from the same organism. This variation affects diverse cellular processes including protein expression, regulation, and folding. Here, we mathematically model an additional layer of complexity and show that individual codon usage biases follow a position-dependent exponential decay model with unique parameter fits for each codon. We use this methodology to perform an in-depth analysis on codon usage bias in the model organism Escherichia coli. Our methodology shows that lowly and highly expressed genes are more similar in their codon usage patterns in the 5'-gene regions, but that these preferences diverge at distal sites resulting in greater positional dependency (pD, which we mathematically define later) for highly expressed genes. We show that position-dependent codon usage bias is partially explained by the structural requirements of mRNAs that results in increased usage of A/T rich codons shortly after the gene start. However, we also show that the pD of 4- and 6-fold degenerate codons is partially related to the gene copy number of cognate-tRNAs supporting existing hypotheses that posit benefits to a region of slow translation in the beginning of coding sequences. Lastly, we demonstrate that viewing codon usage bias through a position-dependent framework has practical utility by improving accuracy of gene expression prediction when incorporating positional dependencies into the Codon Adaptation Index model.
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