ArticleGenome research2003
Widespread selection for local RNA secondary structure in coding regions of bacterial genes.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 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
118 citing papers in PubMed, 206 citations in OpenAlex.
- Genomic indicators of gene function: a systematic assessment of the human genome.G3 (Bethesda, Md.) · 2026Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.Molecular cell · 2026Article
- Mapping Patterns of G-Quadruplex-Forming Sequence Conservation in Primates.Journal of molecular evolution · 2026Article
- Screening metatranscriptomes for ultrastable RNA secondary structures reveals hidden bacteriophages and novel capsid nanomaterials.bioRxiv : the preprint server for biology · 2026Article
- Hierarchical evolution of the proteobacterial essential chaperone SecB reveals non-neutral synonymous evolution under extreme purifying selection.Molecular genetics and genomics : MGG · 2026Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.bioRxiv : the preprint server for 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
- Measuring the selective packaging of RNA molecules by viral coat proteins in cells.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences.Nucleic acids research · 2025Article
- Increasing recombinant protein production in E. coli via FACS-based selection of N-terminal coding DNA libraries.The FEBS journal · 2025Article
- Article
- Application of Modified mRNA in Somatic Reprogramming to Pluripotency and Directed Conversion of Cell Fate.International journal of molecular sciences · 2021Review
- Article
- Weak selection on synonymous codons substantially inflatesProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population.GigaScience · 2021Article
- Autoregulation of yeast ribosomal proteins discovered by efficient search for feedback regulation.Communications biology · 2020Article
- Signals of selection in the mitogenome provide insights into adaptation mechanisms in heterogeneous habitats in a widely distributed pelagic fish.Scientific reports · 2020Article
- High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life.Genome biology · 2020Article
- Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples.mSystems · 2019Article
- Passenger Hotspot Mutations in Cancer.Cancer cell · 2019Article
58 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Redundancy of the genetic code dictates that a given protein can be encoded by a large collection of distinct mRNA species, potentially allowing mRNAs to simultaneously optimize desirable RNA structural features in addition to their protein-coding function. To determine whether natural mRNAs exhibit biases related to local RNA secondary structure, a new randomization procedure was developed, DicodonShuffle, which randomizes mRNA sequences while preserving the same encoded protein sequence, the same codon usage, and the same dinucleotide composition as the native message. Genes from 10 of 14 eubacterial species studied and one eukaryote, the yeast Saccharomyces cerevisiae, exhibited statistically significant biases in favor of local RNA structure as measured by folding free energy. Several significant associations suggest functional roles for mRNA structure, including stronger secondary structure bias in the coding regions of intron-containing yeast genes than in intronless genes, and significantly higher folding potential in polycistronic messages than in monocistronic messages in Escherichia coli. Potential secondary structure generally increased in genes from the 5' to the 3' end of E. coli operons, and secondary structure potential was conserved in homologous Salmonella typhi operons. These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control.
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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.