ArticleeLife2018
Codon choice directs constitutive mRNA levels in trypanosomes.
Article in eLife, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- From RNA design to delivery: Computational strategies for functional RNA therapeutics.Bioactive materials · 2027Review
- Transcripts enriched in codons that trigger P-site tRNA-mediated mRNA decay possess stable mRNA.FEBS open bio · 2026Article
- Kozak sequences regulate gene expression in Trypanosoma brucei.Nucleic acids research · 2026Article
- CRISPR-Cas9 precision editing of kinetochore protein phosphosite codons inFrontiers in cellular and infection microbiology · 2026Article
- DeepCodon: A deep learning codon-optimization model to enhance protein expression.Biodesign research · 2025Article
- Article
- Article
- Precision-edited histone tails disrupt polycistronic gene expression controls in trypanosomes.Nature communications · 2025Article
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Less is more: slow-codon windows enhance eGFP mRNA resilience against RNA interference.Journal of the Royal Society, Interface · 2025Article
- SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes.Nucleic acids research · 2025Article
- Molecular Markers for the Phylogenetic Reconstruction ofPathogens (Basel, Switzerland) · 2025Review
- Trypanosoma cruzi eIF4E3- and eIF4E4-containing complexes bind different mRNAs and may sequester inactive mRNAs during nutritional stress.Nucleic acids research · 2025Article
- Article
- Decoding post-transcriptional gene expression controls in trypanosomatids using machine learning.Wellcome open research · 2025Article
- Knocking out histidine ammonia-lyase by using CRISPR-Cas9 abolishes histidine role in the bioenergetics and the life cycle ofMicrobial cell (Graz, Austria) · 2025Article
- Article
- mRNA vaccine sequence and structure design and optimization: Advances and challenges.The Journal of biological chemistry · 2025Review
- Codon optimality influences homeostatic gene expression in zebrafish.G3 (Bethesda, Md.) · 2024Article
- Eukaryotic mRNA decapping factors: molecular mechanisms and activity.The FEBS journal · 2023Review
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4 authors.
Funding
Abstract
Selective transcription of individual protein coding genes does not occur in trypanosomes and the cellular copy number of each mRNA must be determined post-transcriptionally. Here, we provide evidence that codon choice directs the levels of constitutively expressed mRNAs. First, a novel codon usage metric, the gene expression codon adaptation index (geCAI), was developed that maximised the relationship between codon choice and the measured abundance for a transcriptome. Second, geCAI predictions of mRNA levels were tested using differently coded GFP transgenes and were successful over a 25-fold range, similar to the variation in endogenous mRNAs. Third, translation was necessary for the accelerated mRNA turnover resulting from codon choice. Thus, in trypanosomes, the information determining the levels of most mRNAs resides in the open reading frame and translation is required to access this information.
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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 Socratic graph.