ArticleRNA biology2012
Accessibility and conservation: general features of bacterial small RNA-mRNA interactions?
Article in RNA biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 69 citations in OpenAlex.
- Distribution of prophage-encoded Pas sRNAs across pathogenicbioRxiv : the preprint server for biology · 2026Article
- Codon bias shapes bacterial small RNA binding sites within protein-coding sequences.RNA (New York, N.Y.) · 2026Article
- Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes.Briefings in functional genomics · 2024Review
- Unveiling the orchestration: mycobacterial small RNAs as key mediators in host-pathogen interactions.Frontiers in microbiology · 2024Review
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- 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
- Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production inAntibiotics (Basel, Switzerland) · 2021Article
- tRFtarget: a database for transfer RNA-derived fragment targets.Nucleic acids research · 2021Article
- RNA-Dependent Regulation of Virulence in Pathogenic Bacteria.Frontiers in cellular and infection microbiology · 2019Review
- Small RNA profiling inProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Origin, Evolution, and Loss of Bacterial Small RNAs.Microbiology spectrum · 2018Review
- Structure and Interaction Prediction in Prokaryotic RNA Biology.Microbiology spectrum · 2018Review
- Translational regulation by bacterial small RNAs via an unusual Hfq-dependent mechanism.Nucleic acids research · 2018Article
- Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria.BMC genomics · 2017Article
- sRNARNA biology · 2017Article
- RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach.Bioinformatics (Oxford, England) · 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
- Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.Current protocols in bioinformatics · 2016Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial small RNAs (sRNAs) are a class of structural RNAs that often regulate mRNA targets via post-transcriptional base pair interactions. We determined features that discriminate functional from non-functional interactions and assessed the influence of these features on genome-wide target predictions. For this purpose, we compiled a set of 71 experimentally verified sRNA-target pairs from Escherichia coli and Salmonella enterica. Furthermore, we collected full-length 5' untranslated regions by using genome-wide experimentally verified transcription start sites. Only interaction sites in sRNAs, but not in targets, show significant sequence conservation. In addition to this observation, we found that the base pairing between sRNAs and their targets is not conserved in general across more distantly related species. A closer inspection of RybB and RyhB sRNAs and their targets revealed that the base pairing complementarity is only conserved in a small subset of the targets. In contrast to conservation, accessibility of functional interaction sites is significantly higher in both sRNAs and targets in comparison to non-functional sites. Based on the above observations, we successfully used the following constraints to improve the specificity of genome-wide target predictions: the region of interaction initiation must be located in (1) highly accessible regions in both interaction partners and (2) unstructured conserved sRNA regions derived from reliability profiles of multiple sRNA alignments. Aligned sequences of homologous sRNAs, functional and non-functional targets, and a supplementary document with supplementary tables, figures and references are available at http://www. bioinf.uni-freiburg.de/Supplements/srna-interact-feat.
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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.