ArticleBMC genomics2017
The link between adjacent codon pairs and mRNA stability.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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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.
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Who cites it
22 citing papers in PubMed, 49 citations in OpenAlex.
- The Tor pathway, ribosome concentration, and wobble decoding mediate inhibitory effects of the Leu-Pro CUC-CCG codon pair inRNA (New York, N.Y.) · 2026Article
- The patterns of alternative TSS usage explain the highly heterogeneous landscape of 5'UTR lengths in eukaryotes.NAR genomics and bioinformatics · 2025Article
- Suboptimal codon pairs trigger ribosome collisions and cellular quality control responses in tRNA modification mutants.Nucleic acids research · 2025Article
- Interrogating nucleotide sequences with AI to understand codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Predicting gene sequences with AI to study codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Diverse intrinsic properties shape transcript stability and stabilization inNAR genomics and bioinformatics · 2024Article
- Article
- Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning.Nucleic acids research · 2023Article
- Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria.bioRxiv : the preprint server for biology · 2023Article
- Codon optimality in cancer.Oncogene · 2021Review
- Ribosome dynamics and mRNA turnover, a complex relationship under constant cellular scrutiny.Wiley interdisciplinary reviews. RNA · 2021Review
- Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization.Genome biology · 2021Article
- PlncRNA-HDeep: plant long noncoding RNA prediction using hybrid deep learning based on two encoding styles.BMC bioinformatics · 2021Article
- Genome-wide analysis of lncRNA stability in human.PLoS computational biology · 2021Article
- Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs).RNA (New York, N.Y.) · 2021Article
- Review
- Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- GCN sensitive protein translation in yeast.PloS one · 2020Article
- Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection.Nucleic acids research · 2019Article
- The Interplay between the RNA Decay and Translation Machinery in Eukaryotes.Cold Spring Harbor perspectives in biology · 2018Review
Corrections and comments
- Erratum issued
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundEvidence in diverse organisms suggests that codon optimality is a major determinant of mRNA translation and degradation. Codon optimality is thought to act by modulating the efficiency of ribosome elongation. In Saccharomyces cerevisiae, a recent study has identified 17 adjacent codon pairs that mediate strong inhibition of translation elongation. However, relationships between the inhibitory codon pairs and other aspects of gene expression are unknown.
resultsTo gain insights into how the inhibitory codon pairs may affect aspects of gene expression, we utilized existing datasets to conduct genome-scale analyses in S. cerevisiae. Our analysis revealed the following points. First, the inhibitory codon pairs are significantly associated with faster mRNA decay. The association is not solely due to the content of nucleotides, individual codons, or dipeptides encoded by the inhibitory codon pairs. Second, the inhibitory codon pairs cannot fully explain the previously known relationship of codon optimality with mRNA stability, suggesting that optimality of individual codons and properties of adjacent codon pairs both contribute to gene regulation. Finally, although the inhibitory codon pairs are associated with slower mRNA synthesis and protein instability, the associations can be attributed to usage bias in individual codons.
conclusionsThis study suggests an association of inhibitory codon pairs with mRNA stability and thus another layer of complexity in the codon-mediated gene regulation.
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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.