ReviewHuman molecular genetics2016
The Yin and Yang of codon usage.
Review in Human molecular genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
85 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives.Frontiers in genetics · 2019Pooled it
- Codon-dependent translation of N1-ethylpseudouridine-modified mRNA reduces innate immunity while preserving vaccine immunogenicity.Molecular therapy. Nucleic acids · 2026Article
- Comparative study on morphological traits and mitogenomes of the genus Echinolaelaps.Experimental & applied acarology · 2026Article
- Mapping the inter- and intra-genic codon-usage landscape inNAR genomics and bioinformatics · 2026Article
- Mapping evolutionary paradigm of Oropouche virus driven by dinucleotide bias and context-dependent codon bias.Virulence · 2025Article
- Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation in E. coli.Nucleic acids research · 2025Article
- tRNA Modifications: A Tale of Two Viruses-SARS-CoV-2 and ZIKV.International journal of molecular sciences · 2025Article
- OPT: Codon optimize gene sequences for E. coli protein overexpression.Journal of molecular biology · 2025Article
- Article
- Uncovering codon usage patterns during murine embryogenesis and tissue-specific developmental diseases.Frontiers in genetics · 2025Article
- Comprehensive analysis of the first complete mitogenome and plastome of a traditional Chinese medicine Viola diffusa.BMC genomics · 2024Article
- Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages.BMC bioinformatics · 2024Article
- Unleashing the potential of mRNA therapeutics for inherited neurological diseases.Brain : a journal of neurology · 2024Review
- Article
- Translation Rates and Protein Folding.Journal of molecular biology · 2024Review
- Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation.Nature communications · 2024Article
- Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae.BMC plant biology · 2024Article
- Genotype sampling for deep-learning assisted experimental mapping of a combinatorially complete fitness landscape.Bioinformatics (Oxford, England) · 2024Article
- Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity.Microorganisms · 2024Article
- Identification of a novel and plant height-independent QTL for coleoptile length in barley and validation of its effect using near isogenic lines.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
The genetic code is degenerate. With the exception of two amino acids (Met and Trp), all other amino acid residues are each encoded by multiple, so-called synonymous codons. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in genes/genomes suggested that codon choice might have functional implications beyond amino acid coding. The pattern of non-uniform codon use (known as codon usage bias) varies between organisms and represents a unique feature of an organism. Organism-specific codon choice is related to organism-specific differences in populations of cognate tRNAs. This implies that, in a given organism, frequently used codons will be translated more rapidly than infrequently used ones and vice versa A theory of codon-tRNA co-evolution (necessary to balance accurate and efficient protein production) was put forward to explain the existence of codon usage bias. This model suggests that selection favours preferred (frequent) over un-preferred (rare) codons in order to sustain efficient protein production in cells and that a given un-preferred codon will have the same effect on an organism's fitness regardless of its position within an mRNA's open reading frame. However, many recent studies refute this prediction. Un-preferred codons have been found to have important functional roles and their effects appeared to be position-dependent. Synonymous codon usage affects the efficiency/stringency of mRNA decoding, mRNA biogenesis/stability, and protein secretion and folding. This review summarizes recent developments in the field that have identified novel functions of synonymous codons and their usage.
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Registered trials
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.