ArticleProceedings of the National Academy of Sciences of the United States of America2013
Comparative genomics boosts target prediction for bacterial small RNAs.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 papers.
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Who cites it
144 citing papers in PubMed, 252 citations in OpenAlex.
- Small RNA Transcriptome of the Oral Microbiome during Periodontitis Progression.Applied and environmental microbiology · 2015Trial
- Bacterial small RNAs and extracellular vesicles in inflammatory and osteoimmune diseases: regulatory mechanisms and host-microbe communication.Archives of microbiology · 2026Review
- Distribution of prophage-encoded Pas sRNAs across pathogenicbioRxiv : the preprint server for biology · 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
- Coordination of the Fe-S cluster biogenesis network by the sRNA RyhB inRNA biology · 2025Article
- An RNA sponge directs the transition from feast to famine in Caulobacter crescentus.Nature communications · 2025Article
- Assessing the conservation and targets of putative sRNAs inMicrobiology spectrum · 2025Article
- Linking Virulence and Iron Limitation Response inJournal of proteome research · 2025Article
- What makes a small RNA work?Nucleic acids research · 2025Review
- Benchmarking the methods for predicting base pairs in RNA-RNA interactions.Bioinformatics (Oxford, England) · 2025Article
- The Power Duo: How the Interplay Between Nucleoid-Associated Proteins and Small Noncoding RNAs Orchestrates the Cellular Regulatory Symphony.Molecular microbiology · 2025Review
- Improving prediction of bacterial sRNA regulatory targets with expression data.NAR genomics and bioinformatics · 2025Article
- Extracellular Vesicles From Xylella fastidiosa Carry sRNAs and Genomic Islands, Suggesting Roles in Recipient Cells.Journal of extracellular vesicles · 2025Article
- GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions.BMC bioinformatics · 2025Article
- The RNA Chaperone Hfq and Small Non-Coding RNAs Modulate the Biofilm Formation of the Fish PathogenInternational journal of molecular sciences · 2025Article
- Article
- Two temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX.Nucleic acids research · 2025Article
- An RNase III-processed sRNA coordinates sialic acid metabolism ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Investigating the role of theFEMS microbes · 2025Article
- Prediction of Circular RNA Secondary Structures and Their Targets.Advances in experimental medicine and biology · 2025Review
84 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 5 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small RNAs (sRNAs) constitute a large and heterogeneous class of bacterial gene expression regulators. Much like eukaryotic microRNAs, these sRNAs typically target multiple mRNAs through short seed pairing, thereby acting as global posttranscriptional regulators. In some bacteria, evidence for hundreds to possibly more than 1,000 different sRNAs has been obtained by transcriptome sequencing. However, the experimental identification of possible targets and, therefore, their confirmation as functional regulators of gene expression has remained laborious. Here, we present a strategy that integrates phylogenetic information to predict sRNA targets at the genomic scale and reconstructs regulatory networks upon functional enrichment and network analysis (CopraRNA, for Comparative Prediction Algorithm for sRNA Targets). Furthermore, CopraRNA precisely predicts the sRNA domains for target recognition and interaction. When applied to several model sRNAs, CopraRNA revealed additional targets and functions for the sRNAs CyaR, FnrS, RybB, RyhB, SgrS, and Spot42. Moreover, the mRNAs gdhA, lrp, marA, nagZ, ptsI, sdhA, and yobF-cspC were suggested as regulatory hubs targeted by up to seven different sRNAs. The verification of many previously undetected targets by CopraRNA, even for extensively investigated sRNAs, demonstrates its advantages and shows that CopraRNA-based analyses can compete with experimental target prediction approaches. A Web interface allows high-confidence target prediction and efficient classification of bacterial sRNAs.
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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.