ArticleJournal of bacteriology2011
Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions.
Article in Journal of bacteriology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Codon bias shapes bacterial small RNA binding sites within protein-coding sequences.RNA (New York, N.Y.) · 2026Article
- Origin and adaptive evolutionary trajectory of the 3' UTR-derived sRNA UhpU in Enterobacteriaceae.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions.BMC bioinformatics · 2025Article
- ChimericFragments: computation, analysis and visualization of global RNA networks.NAR genomics and bioinformatics · 2024Article
- A 3' UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria.Nucleic acids research · 2022Article
- Meta-omics approaches reveal unique small RNAs exhibited by the uncultured microorganisms dwelling deep-sea hydrothermal sediment in Guaymas Basin.Archives of microbiology · 2022Article
- Prokaryotic ncRNAs: Master regulators of gene expression.Current research in pharmacology and drug discovery · 2022Article
- Bioinformatic prediction reveals posttranscriptional regulation of the chromosomal replication initiator geneRNA biology · 2021Article
- Article
- Tandem Repeats inInternational journal of molecular sciences · 2021Article
- Synthetic small regulatory RNAs in microbial metabolic engineering.Applied microbiology and biotechnology · 2021Review
- A Novel Noncoding RNABiomolecules · 2019Article
- Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology.FEMS microbiology reviews · 2019Review
- High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites.Nature communications · 2018Article
- Origin, Evolution, and Loss of Bacterial Small RNAs.Microbiology spectrum · 2018Review
- Identification of a Novel Small RNAFrontiers in microbiology · 2018Article
- Probing the sRNA regulatory landscape of P. aeruginosa: post-transcriptional control of determinants of pathogenicity and antibiotic susceptibility.Molecular microbiology · 2017Article
- Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria.BMC genomics · 2017Article
- A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.Bioinformatics (Oxford, England) · 2017Article
- Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution.Journal of molecular evolution · 2017Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial small noncoding RNAs have attracted much interest in recent years as posttranscriptional regulators of genes involved in diverse pathways. Small RNAs (sRNAs) are 50 to 400 nucleotides long and exert their regulatory function by directly base pairing with mRNA targets to alter their stability and/or affect their translation. This base pairing is achieved through a region of about 10 to 25 nucleotides, which may be located at various positions along different sRNAs. By compiling a data set of experimentally determined target-binding regions of sRNAs and systematically analyzing their properties, we reveal that they are both more evolutionarily conserved and more accessible than random regions. We demonstrate the use of these properties for computational identification of sRNA target-binding regions with high specificity and sensitivity. Our results show that these predicted regions are likely to base pair with known targets of an sRNA, suggesting that pointing out these regions in a specific sRNA can help in searching for its targets.
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