ArticleNucleic acids research2012
An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 42 citations in OpenAlex.
- Role of Metabolic Adaptation ofPathogens (Basel, Switzerland) · 2023Review
- The stationary phase-specific sRNA FimR2 is a multifunctional regulator of bacterial motility, biofilm formation and virulence.Nucleic acids research · 2022Article
- Biofilm Formation in Streptococcus agalactiae Is Inhibited by a Small Regulatory RNA Regulated by the Two-Component System CiaRH.Microbiology spectrum · 2022Article
- An Inventory of CiaR-Dependent Small Regulatory RNAs inFrontiers in microbiology · 2021Review
- Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection.Genes · 2020Review
- Small RNA Regulation of Virulence in PathogenicFrontiers in cellular and infection microbiology · 2020Review
- The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence.PLoS pathogens · 2018Article
- Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes.BMC genomics · 2018Article
- Cross-Regulation between Bacteria and Phages at a Posttranscriptional Level.Microbiology spectrum · 2018Review
- Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing.Cell · 2018Article
- Article
- Fimbrial phase variation: stochastic or cooperative?Current genetics · 2016Review
- Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum.BMC genomics · 2016Article
- Regulatory RNAs in the Less Studied Streptococcal Species: From Nomenclature to Identification.Frontiers in microbiology · 2016Review
- Editorial: Small Non-coding RNAs inFrontiers in genetics · 2016Article
- RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.RNA biology · 2016Article
- sRNA-Mediated Regulation of P-Fimbriae Phase Variation in Uropathogenic Escherichia coli.PLoS pathogens · 2015Article
- Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae.BMC genomics · 2015Article
- Genome-wide analyses in bacteria show small-RNA enrichment for long and conserved intergenic regions.Journal of bacteriology · 2015Article
- Genome-wide analyses of small non-coding RNAs in streptococci.Frontiers in genetics · 2015Review
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Characterization of small non-coding ribonucleic acids (sRNA) among the large volume of data generated by high-throughput RNA-seq or tiling microarray analyses remains a challenge. Thus, there is still a need for accurate in silico prediction methods to identify sRNAs within a given bacterial species. After years of effort, dedicated software were developed based on comparative genomic analyses or mathematical/statistical models. Although these genomic analyses enabled sRNAs in intergenic regions to be efficiently identified, they all failed to predict antisense sRNA genes (asRNA), i.e. RNA genes located on the DNA strand complementary to that which encodes the protein. The statistical models enabled any genomic region to be analyzed theorically but not efficiently. We present a new model for in silico identification of sRNA and asRNA candidates within an entire bacterial genome. This model was successfully used to analyze the Gram-negative Escherichia coli and Gram-positive Streptococcus agalactiae. In both bacteria, numerous asRNAs are transcribed from the complementary strand of genes located in pathogenicity islands, strongly suggesting that these asRNAs are regulators of the virulence expression. In particular, we characterized an asRNA that acted as an enhancer-like regulator of the type 1 fimbriae production involved in the virulence of extra-intestinal pathogenic E. coli.
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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.