ArticleeLife2016
Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea.
Article in eLife, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Genomic indicators of gene function: a systematic assessment of the human genome.G3 (Bethesda, Md.) · 2026Article
- Maintaining transcriptome solubility constrains mRNA sequence composition.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.Molecular cell · 2026Article
- How Binding Affinity and Binding Specificity Map to Sequence Space.Journal of molecular evolution · 2026Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.bioRxiv : the preprint server for biology · 2025Article
- Mutability and hypermutation antagonize immunoglobulin codon optimality.Molecular cell · 2025Article
- Cas9-independent tracrRNA cytotoxicity inmicroLife · 2025Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites.PLoS computational biology · 2021Article
- TISIGNER.com: web services for improving recombinant protein production.Nucleic acids research · 2021Article
- Fitness landscape of a dynamic RNA structure.PLoS genetics · 2021Article
- Pervasive Selection against MicroRNA Target Sites in Human Populations.Molecular biology and evolution · 2020Article
- Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis.BMC molecular and cell biology · 2020Article
- RNA⁻Protein Interactions Prevent Long RNA Duplex Formation: Implications for the Design of RNA-Based Therapeutics.Molecules (Basel, Switzerland) · 2018Article
- Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function.Molecular biology and evolution · 2018Article
- Article
- Manifold Routes to a Nucleus.Frontiers in microbiology · 2018Article
- In vivo selection of sfGFP variants with improved and reliable functionality in industrially important thermophilic bacteria.Biotechnology for biofuels · 2018Article
- RNA search engines empower the bacterial intranet.Biochemical Society transactions · 2017Review
- A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.Bioinformatics (Oxford, England) · 2017Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A critical assumption of gene expression analysis is that mRNA abundances broadly correlate with protein abundance, but these two are often imperfectly correlated. Some of the discrepancy can be accounted for by two important mRNA features: codon usage and mRNA secondary structure. We present a new global factor, called mRNA:ncRNA avoidance, and provide evidence that avoidance increases translational efficiency. We also demonstrate a strong selection for the avoidance of stochastic mRNA:ncRNA interactions across prokaryotes, and that these have a greater impact on protein abundance than mRNA structure or codon usage. By generating synonymously variant green fluorescent protein (GFP) mRNAs with different potential for mRNA:ncRNA interactions, we demonstrate that GFP levels correlate well with interaction avoidance. Therefore, taking stochastic mRNA:ncRNA interactions into account enables precise modulation of protein abundance.
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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.