ArticleRNA biology2021
Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.
Article in RNA biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 18 citations in OpenAlex.
- Mammalian therapeutic riboswitches: Engineering and custom ligands.Molecular therapy. Nucleic acids · 2026Review
- TheRNA (New York, N.Y.) · 2024Article
- The discovery of novel noncoding RNAs in 50 bacterial genomes.Nucleic acids research · 2024Article
- Decoding semiotic minimal genome: a non-genocentric approach.Frontiers in microbiology · 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
- Structure-based investigations of the NAD+-II riboswitch.Nucleic acids research · 2023Article
- Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The Biochemical Landscape of Riboswitch Ligands.Biochemistry · 2022Article
- Architectures and complex functions of tandem riboswitches.RNA biology · 2022Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives from individual bacterial genomes. This search process exploits the fact that genomic regions serving as templates for the transcription of structured RNAs tend to be present in longer than average noncoding 'intergenic regions' (IGRs) that are enriched in G and C nucleotides compared to the remainder of the genome. In the present study, we apply this computational pipeline to identify structured ncRNA candidates from 26 diverse bacterial species. Numerous novel structured ncRNA motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. Our findings support recent predictions that hundreds of novel ribo-switch classes and other ncRNAs remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.
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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.