ArticleGenome biology2020
High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 40 citations in OpenAlex.
- Position-dependent codon occurrence is associated with patterns of translational efficiency and ribosomal occupancy in the human transcriptome.PLoS computational biology · 2026Article
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Silent mutations in coding regions of Hepatitis C virus affect patterns of HCV RNA structures and attenuate viral replication and pathogenesis.Genome biology · 2025Article
- AI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits.Science advances · 2025Article
- Why AGG is associated with high transgene output: passenger effects and their implications for transgene design.NAR genomics and bioinformatics · 2025Article
- Comparative Analysis of Codon Optimization Tools: Advancing toward a Multi-Criteria Framework for Synthetic Gene Design.Journal of microbiology and biotechnology · 2025Article
- Synthetic rational design of live-attenuated Zika viruses based on a computational model.Nucleic acids research · 2025Article
- Yeast-derived low-purity FGF2 supports bovine ESC and MSC aggregates in suspension.Frontiers in nutrition · 2025Article
- DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via mNature communications · 2024Article
- The impact of host microRNAs on the development of conserved mutations of SARS-CoV-2.Scientific reports · 2024Article
- Synonymous and non-synonymous codon substitutions can alleviate dependence on GroEL for folding.Protein science : a publication of the Protein Society · 2024Article
- The Causes for Genomic Instability and How to Try and Reduce Them Through Rational Design of Synthetic DNA.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Differential Synonymous Codon Selection in the B56 Gene Family of PP2A Regulatory Subunits.International journal of molecular sciences · 2023Article
- Lipid carriers for mRNA delivery.Acta pharmaceutica Sinica. B · 2023Review
- Article
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach.BMC genomics · 2022Article
- Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data.Nucleic acids research · 2022Article
- Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts.Computational and structural biotechnology journal · 2022Article
- Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts.RNA biology · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundmRNA can form local secondary structure within the protein-coding sequence, and the strength of this structure is thought to influence gene expression regulation. Previous studies suggest that secondary structure strength may be maintained under selection, but the details of this phenomenon are not well understood.
resultsWe perform a comprehensive study of the selection on local mRNA folding strengths considering variation between species across the tree of life. We show for the first time that local folding strength selection tends to follow a conserved characteristic profile in most phyla, with selection for weak folding at the two ends of the coding region and for strong folding elsewhere in the coding sequence, with an additional peak of selection for strong folding located downstream of the start codon. The strength of this pattern varies between species and organism groups, and we highlight contradicting cases. To better understand the underlying evolutionary process, we show that selection strengths in the different regions are strongly correlated, and report four factors which have a clear predictive effect on local mRNA folding selection within the coding sequence in different species.
conclusionsThe correlations observed between selection for local secondary structure strength in the different regions and with the four genomic and environmental factors suggest that they are shaped by the same evolutionary process throughout the coding sequence, and might be maintained under direct selection related to optimization of gene expression and specifically translation regulation.
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