ArticleGenetics2012
The relation of codon bias to tissue-specific gene expression in Arabidopsis thaliana.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- A Suite of Foundation Models Captures the Contextual Interplay Between Codons.bioRxiv : the preprint server for biology · 2024Article
- Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation.Nature communications · 2024Article
- Synthetic biology approach revealed enhancement in haeme oxygenase-1 gene expression by codon pair optimization while reduction by codon deoptimization.Annals of medicine and surgery (2012) · 2024Article
- Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts.Pathogens (Basel, Switzerland) · 2023Article
- An investigation of codon usage pattern analysis in pancreatitis associated genes.BMC genomic data · 2022Article
- The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.NAR genomics and bioinformatics · 2022Article
- Distinct responses to rare codons in selecteLife · 2022Article
- Mapping rRNA 2'-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants.RNA biology · 2021Article
- Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes.BMC genomics · 2021Article
- LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3'-CCA end for high-throughput sequencing.RNA biology · 2020Article
- Evidence of multifaceted functions of codon usage in translation within the model beetle Tribolium castaneum.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster.Genome biology and evolution · 2019Article
- Article
- Codon optimality, bias and usage in translation and mRNA decay.Nature reviews. Molecular cell biology · 2018Review
- Differential evolutionary patterns and expression levels between sex-specific and somatic tissue-specific genes in peanut.Scientific reports · 2017Article
- Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome.Genetica · 2017Article
- Bicodon bias can determine the role of synonymous SNPs in human diseases.BMC genomics · 2017Article
- Article
- Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections.Scientific reports · 2016Article
- The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function.Journal of molecular evolution · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The codon composition of coding sequences plays an important role in the regulation of gene expression. Herein, we report systematic differences in the usage of synonymous codons among Arabidopsis thaliana genes that are expressed specifically in distinct tissues. Although we observed that both regionally and transcriptionally associated mutational biases were associated significantly with codon bias, they could not explain the observed differences fully. Similarly, given that transcript abundances did not account for the differences in codon usage, it is unlikely that selection for translational efficiency can account exclusively for the observed codon bias. Thus, we considered the possible evolution of codon bias as an adaptive response to the different abundances of tRNAs in different tissues. Our analysis demonstrated that in some cases, codon usage in genes that were expressed in a broad range of tissues was influenced primarily by the tissue in which the gene was expressed maximally. On the basis of this finding we propose that genes that are expressed in certain tissues might show a tissue-specific compositional signature in relation to codon usage. These findings might have implications for the design of transgenes in relation to optimizing their expression.
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Registered trials
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