ArticleBMC microbiology2019
Genome-wide discovery of structured noncoding RNAs in bacteria.
Article in BMC microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
34 citing papers in PubMed, 60 citations in OpenAlex.
- The Gut Commensal Butyricimonas Virosa Modulates Gut Microbiota-Dependent Thiamine Metabolism and Attenuates Mouse Steatotic Liver Disease.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Cryo-EM structure of a natural RNA nanocage.Nature · 2025Article
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- Regulatory orchestration of FK506 biosynthesis iniScience · 2025Article
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- The discovery of novel noncoding RNAs in 50 bacterial genomes.Nucleic acids research · 2024Article
- Genome-Wide Computational Prediction and Analysis of Noncoding RNAs inMicroorganisms · 2024Article
- Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology.Biodesign research · 2024Article
- A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine.Cell reports · 2023Article
- 8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A conserved uORF in theMicrobial genomics · 2023Article
- Discovering riboswitches: the past and the future.Trends in biochemical sciences · 2023Review
- The Promising Role of Non-Coding RNAs as Biomarkers and Therapeutic Targets for Leukemia.Genes · 2023Review
- Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms-An Insightful Perspective on Ecoepigenetics.Epigenomes · 2022Review
- BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria.Briefings in bioinformatics · 2022Article
- Key players in regulatory RNA realm of bacteria.Biochemistry and biophysics reports · 2022Review
- The Biochemical Landscape of Riboswitch Ligands.Biochemistry · 2022Article
- RNA Sequencing Unveils Very Small RNAs With Potential Regulatory Functions in Bacteria.Frontiers in molecular biosciences · 2022Article
- Architectures and complex functions of tandem riboswitches.RNA biology · 2022Article
- Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.RNA biology · 2021Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundStructured noncoding RNAs (ncRNAs) play essential roles in many biological processes such as gene regulation, signaling, RNA processing, and protein synthesis. Among the most common groups of ncRNAs in bacteria are riboswitches. These cis-regulatory, metabolite-binding RNAs are present in many species where they regulate various metabolic and signaling pathways. Collectively, there are likely to be hundreds of novel riboswitch classes that remain hidden in the bacterial genomes that have already been sequenced, and potentially thousands of classes distributed among various other species in the biosphere. The vast majority of these undiscovered classes are proposed to be exceedingly rare, and so current bioinformatics search techniques are reaching their limits for differentiating between true riboswitch candidates and false positives.
resultsHerein, we exploit a computational search pipeline that can efficiently identify intergenic regions most likely to encode structured ncRNAs. Application of this method to five bacterial genomes yielded nearly 70 novel genetic elements including 30 novel candidate ncRNA motifs. Among the riboswitch candidates identified is an RNA motif involved in the regulation of thiamin biosynthesis.
conclusionsAnalysis of other genomes will undoubtedly lead to the discovery of many additional novel structured ncRNAs, and provide insight into the range of riboswitches and other kinds of ncRNAs remaining to be discovered in bacteria and archaea.
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Registered trials
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.