ArticleBMC genomics2011
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 52 citations in OpenAlex.
- Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets.Microbial genomics · 2024Article
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- Small regulatory RNAs of oral streptococci and periodontal bacteria.The Japanese dental science review · 2021Review
- Natural Selection Shapes Maintenance of Orthologous sRNAs in Divergent Host-Restricted Bacterial Genomes.Molecular biology and evolution · 2021Article
- Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs inInternational journal of molecular sciences · 2021Article
- Divergently Transcribed ncRNAs inFrontiers in molecular biosciences · 2021Article
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- Cross-Regulation between Bacteria and Phages at a Posttranscriptional Level.Microbiology spectrum · 2018Review
- Small RNA repertoires and their intraspecies variation in Aggregatibacter actinomycetemcomitans.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Global role of the bacterial post-transcriptional regulator CsrA revealed by integrated transcriptomics.Nature communications · 2017Article
- Article
- Landscape of RNA polyadenylation in E. coli.Nucleic acids research · 2017Article
- Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth.RNA biology · 2017Article
- An automated approach for global identification of sRNA-encoding regions in RNA-Seq data from Mycobacterium tuberculosis.Acta biochimica et biophysica Sinica · 2016Article
- Overcoming Challenges in Engineering the Genetic Code.Journal of molecular biology · 2016Review
- Bacterial small RNAs in the Genus Rickettsia.BMC genomics · 2015Article
- Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli.BMC genomics · 2015Article
- Acidic Residues in the Hfq Chaperone Increase the Selectivity of sRNA Binding and Annealing.Journal of molecular biology · 2015Article
- Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks.Briefings in bioinformatics · 2015Article
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn Escherichia coli, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. To provide a comprehensive overview of sRNAs, we analysed the low-molecular-weight RNAs (< 200 nt) of E. coli with deep sequencing, because the regulatory RNAs in bacteria are usually 50-200 nt in length.
resultsWe discovered 229 novel candidate sRNAs (≥ 50 nt) with computational or experimental evidence of transcription initiation. Among them, the expression of seven intergenic sRNAs and three cis-antisense sRNAs was detected by northern blot analysis. Interestingly, five novel sRNAs are expressed from prophage regions and we note that these sRNAs have several specific characteristics. Furthermore, we conducted an evolutionary conservation analysis of the candidate sRNAs and summarised the data among closely related bacterial strains.
conclusionsThis comprehensive screen for E. coli sRNAs using a deep sequencing approach has shown that many as-yet-undiscovered sRNAs are potentially encoded in the E. coli genome. We constructed the Escherichia coli Small RNA Browser (ECSBrowser; http://rna.iab.keio.ac.jp/), which integrates the data for previously identified sRNAs and the novel sRNAs found in this study.
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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.