ArticleNucleic acids research2009
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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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.
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Who cites it
91 citing papers in PubMed, 171 citations in OpenAlex.
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- Modular small RNA drives the emergence of virulence traits and environmental trade-offs in Vibrio cholerae.Nature communications · 2026Article
- Small RNAs beyond Model Organisms: Have We Only Scratched the Surface?International journal of molecular sciences · 2022Article
- Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.Scientific reports · 2022Article
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- Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions.BMC genomics · 2020Article
- Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.The Journal of biological chemistry · 2020Article
- Switching fatty acid metabolism by an RNA-controlled feed forward loop.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The Vc2 Cyclic di-GMP-Dependent Riboswitch of Vibrio cholerae Regulates Expression of an Upstream Putative Small RNA by Controlling RNA Stability.Journal of bacteriology · 2019Article
- Transcription ofJournal of bacteriology · 2019Article
- σJournal of bacteriology · 2019Article
- In silico 'fishing' using known small regulatory RNA (sRNA) candidates as the decoy from Escherichia coli, Salmonella typhi and Salmonella typhimurium manifested 14 novel sRNA candidates in the orthologous region of Proteus mirabilis.Molecular biology reports · 2018Article
- Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.BMC genomics · 2018Article
- MtlR negatively regulates mannitol utilization byMicrobiology (Reading, England) · 2017Article
- Genome-Wide Detection of Small Regulatory RNAs in Deep-Sea BacteriumFrontiers in microbiology · 2017Article
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- Small Antisense RNA RblR Positively Regulates RuBisCo inFrontiers in microbiology · 2017Article
- Bacterial antisense RNAs are mainly the product of transcriptional noise.Science advances · 2016Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Direct cloning and parallel sequencing, an extremely powerful method for microRNA (miRNA) discovery, has not yet been applied to bacterial transcriptomes. Here we present sRNA-Seq, an unbiased method that allows for interrogation of the entire small, non-coding RNA (sRNA) repertoire in any prokaryotic or eukaryotic organism. This method includes a novel treatment that depletes total RNA fractions of highly abundant tRNAs and small subunit rRNA, thereby enriching the starting pool for sRNA transcripts with novel functionality. As a proof-of-principle, we applied sRNA-Seq to the human pathogen Vibrio cholerae. Our results provide information, at unprecedented depth, on the complexity of the sRNA component of a bacterial transcriptome. From 407 039 sequence reads, all 20 known V. cholerae sRNAs, 500 new, putative intergenic sRNAs and 127 putative antisense sRNAs were identified in a limited number of growth conditions examined. In addition, characterization of a subset of the newly identified transcripts led to the identification of a novel sRNA regulator of carbon metabolism. Collectively, these results strongly suggest that the number of sRNAs in bacteria has been greatly underestimated and that future efforts to analyze bacterial transcriptomes will benefit from direct cloning and parallel sequencing experiments aided by 5S/tRNA depletion.
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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.