ArticleMolecular biology and evolution2017
Codon-Resolution Analysis Reveals a Direct and Context-Dependent Impact of Individual Synonymous Mutations on mRNA Level.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 83 citations in OpenAlex.
- Comparative Chloroplast Genomics, Codon Usage Bias, and Phylogenetic Placement ofCurrent issues in molecular biology · 2026Article
- Multilayered nucleotide organization reveals purifying selection and host-driven adaptation in CPV and FPV.BMC veterinary research · 2026Article
- A naturally synonymous mutation modulates an ERK-centered regulatory network to mediate thermotolerance divergence in Crassostrea oysters.Communications biology · 2026Article
- Advancing codon language modeling with synonymous codon constrained masking.Nucleic acids research · 2026Article
- A slight mismatch between a gene's codon usage and the cellular tRNA supply is beneficial.Nature communications · 2026Article
- Functional synonymous mutations and their evolutionary consequences.Nature reviews. Genetics · 2025Review
- Ciprofloxacin-driven purifying selection on viral genomes accelerates soil NProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Translation of the downstream ORF from bicistronic mRNAs by human cells: Impact of codon usage and splicing in the upstream ORF.Protein science : a publication of the Protein Society · 2025Article
- Complete mitochondrial genome sequencing and phylogenetic analysis of Phellinus igniarius.Scientific reports · 2024Article
- Further Evidence for Strong Nonneutrality of Yeast Synonymous Mutations.Molecular biology and evolution · 2024Article
- A Suite of Foundation Models Captures the Contextual Interplay Between Codons.bioRxiv : the preprint server for biology · 2024Article
- Evolutionary trade-off and mutational bias could favor transcriptional over translational divergence within paralog pairs.PLoS genetics · 2023Article
- Using protein-per-mRNA differences among human tissues in codon optimization.Genome biology · 2023Article
- The DuckAnimals : an open access journal from MDPI · 2023Article
- Codon usage bias and genetic diversity in chloroplast genomes ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2023Article
- Genome-wide sequencing identifies a thermal-tolerance related synonymous mutation in the mussel, Mytilisepta virgata.Communications biology · 2023Article
- Multi-Omics Analysis and Verification of the Oncogenic Value of CCT8 in Pan-Cancers.Journal of inflammation research · 2023Article
- Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process of ribosome scanning.Genome biology · 2022Article
- Chicken Protein S Gene Regulates Adipogenesis and Affects Abdominal Fat Deposition.Animals : an open access journal from MDPI · 2022Article
- Preferred synonymous codons are translated more accurately: Proteomic evidence, among-species variation, and mechanistic basis.Science advances · 2022Article
Corrections and comments
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Authors and funding
9 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon usage bias (CUB) refers to the observation that synonymous codons are not used equally frequently in a genome. CUB is stronger in more highly expressed genes, a phenomenon commonly explained by stronger natural selection on translational accuracy and/or efficiency among these genes. Nevertheless, this phenomenon could also occur if CUB regulates gene expression at the mRNA level, a hypothesis that has not been tested until recently. Here, we attempt to quantify the impact of synonymous mutations on mRNA level in yeast using 3,556 synonymous variants of a heterologous gene encoding green fluorescent protein (GFP) and 523 synonymous variants of an endogenous gene TDH3. We found that mRNA level was positively correlated with CUB among these synonymous variants, demonstrating a direct role of CUB in regulating transcript concentration, likely via regulating mRNA degradation rate, as our additional experiments suggested. More importantly, we quantified the effects of individual synonymous mutations on mRNA level and found them dependent on 1) CUB and 2) mRNA secondary structure, both in proximal sequence contexts. Our study reveals the pleiotropic effects of synonymous codon usage and provides an additional explanation for the well-known correlation between CUB and gene expression level.
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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.