title: Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles.
abstract: Identification and characterization of functional elements in the noncoding regions of genomes is an elusive and time-consuming activity whose output does not keep up with the pace of genome sequencing. Hundreds of bacterial genomes lay unexploited in terms of noncoding sequence analysis, although they may conceal a wide diversity of novel RNA genes, riboswitches, or other regulatory elements. We describe a strategy that exploits the entirety of available bacterial genomes to classify all noncoding elements of a selected reference species in a single pass. This method clusters noncoding elements based on their profile of presence among species. Most noncoding RNAs (ncRNAs) display specific signatures that enable their grouping in distinct clusters, away from sequence conservation noise and other elements such as promoters. We submitted 24 ncRNA candidates from Staphylococcus aureus to experimental validation and confirmed the presence of seven novel small RNAs or riboswitches. Besides offering a powerful method for de novo ncRNA identification, the analysis of phylogenetic profiles opens a new path toward the identification of functional relationships between co-evolving coding and noncoding elements.
authors.affiliation: Université Paris-Sud 11, CNRS, UMR8621, Institut de Génétique et Microbiologie, F-91405 Orsay Cedex, France.
authors.forename: Antonin
authors.initials: A
authors.lastname: Marchais
authors.forename: Magali
authors.initials: M
authors.lastname: Naville
authors.forename: Chantal
authors.initials: C
authors.lastname: Bohn
authors.forename: Philippe
authors.initials: P
authors.lastname: Bouloc
authors.forename: Daniel
authors.initials: D
authors.lastname: Gautheret
mesh_terms: D000465:Algorithms; D001412:Bacillus subtilis / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D010802:Phylogeny; D012329:RNA, Bacterial / Q000145:classification / Q000235:genetics*; D022661:RNA, Untranslated / Q000145:classification / Q000235:genetics*; D015203:Reproducibility of Results; D013211:Staphylococcus aureus / Q000235:genetics; D014734:Vibrio cholerae / Q000235:genetics
chemical_list: D012329:RNA, Bacterial; D022661:RNA, Untranslated