title: Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae.
abstract: BACKGROUND
  Streptococcus agalactiae, or Group B Streptococcus, is a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. In an effort to reconstruct the transcriptional networks involved in S. agalactiae physiology and pathogenesis, we performed an extensive and robust characterization of its transcriptome through a combination of differential RNA-sequencing in eight different growth conditions or genetic backgrounds and strand-specific RNA-sequencing.
  
  
  RESULTS
  Our study identified 1,210 transcription start sites (TSSs) and 655 transcript ends as well as 39 riboswitches and cis-regulatory regions, 39 cis-antisense non-coding RNAs and 47 small RNAs potentially acting in trans. Among these putative regulatory RNAs, ten were differentially expressed in response to an acid stress and two riboswitches sensed directly or indirectly the pH modification. Strikingly, 15% of the TSSs identified were associated with the incorporation of pseudo-templated nucleotides, showing that reiterative transcription is a pervasive process in S. agalactiae. In particular, 40% of the TSSs upstream genes involved in nucleotide metabolism show reiterative transcription potentially regulating gene expression, as exemplified for pyrG and thyA encoding the CTP synthase and the thymidylate synthase respectively.
  
  
  CONCLUSIONS
  This comprehensive map of the transcriptome at the single nucleotide resolution led to the discovery of new regulatory mechanisms in S. agalactiae. It also provides the basis for in depth analyses of transcriptional networks in S. agalactiae and of the regulatory role of reiterative transcription following variations of intra-cellular nucleotide pools.
authors.affiliation: Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram Positif, 28 rue du Docteur Roux, 75724,, Paris Cedex 15, France. ichupin@pasteur.fr.|CNRS UMR 3525, Paris, France. ichupin@pasteur.fr.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Rosinski-Chupin
authors.affiliation: Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram Positif, 28 rue du Docteur Roux, 75724,, Paris Cedex 15, France. esauvage@pasteur.fr.|CNRS UMR 3525, Paris, France. esauvage@pasteur.fr.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Sauvage
authors.affiliation: Institut Pasteur, Transcriptome and Epigenome Platform, 28 rue du Docteur Roux, 75724,, Paris Cedex 15, France. osisme@pasteur.fr.
authors.forename: Odile
authors.initials: O
authors.lastname: Sismeiro
authors.affiliation: Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram Positif, 28 rue du Docteur Roux, 75724,, Paris Cedex 15, France. avillain@pasteur.fr.|CNRS UMR 3525, Paris, France. avillain@pasteur.fr.
authors.forename: Adrien
authors.initials: A
authors.lastname: Villain
authors.affiliation: Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram Positif, 28 rue du Docteur Roux, 75724,, Paris Cedex 15, France. violette.da-cunha@pasteur.fr.|CNRS UMR 3525, Paris, France. violette.da-cunha@pasteur.fr.
authors.forename: Violette
authors.initials: V
authors.lastname: Da Cunha
authors.affiliation: Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram Positif, 28 rue du Docteur Roux, 75724,, Paris Cedex 15, France. marie-elise.caliot@pasteur.fr.
authors.forename: Marie-Elise
authors.initials: ME
authors.lastname: Caliot
authors.affiliation: Institut Pasteur, Transcriptome and Epigenome Platform, 28 rue du Docteur Roux, 75724,, Paris Cedex 15, France. marie-agnes.dillies@pasteur.fr.
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Dillies
authors.affiliation: Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram Positif, 28 rue du Docteur Roux, 75724,, Paris Cedex 15, France. patrick.trieu-cuot@pasteur.fr.
authors.forename: Patrick
authors.initials: P
authors.lastname: Trieu-Cuot
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, bâtiment 400, 91405, Orsay, France. philippe.bouloc@u-psud.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Bouloc
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, bâtiment 400, 91405, Orsay, France. marie-frederique.lartigue@univ-tours.fr.|Université de Tours, UMR1282 Infectiologie et Santé Publique, F-37000, Tours, France. marie-frederique.lartigue@univ-tours.fr.|CHRU de Tours, F-37044, Tours, France. marie-frederique.lartigue@univ-tours.fr.|INRA, UMR1282 Infectiologie et Santé Publique, F-37380, Nouzilly, France. marie-frederique.lartigue@univ-tours.fr.
authors.forename: Marie-Frédérique
authors.initials: MF
authors.lastname: Lartigue
authors.affiliation: Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram Positif, 28 rue du Docteur Roux, 75724,, Paris Cedex 15, France. philippe.glaser@pasteur.fr.|CNRS UMR 3525, Paris, France. philippe.glaser@pasteur.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Glaser
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D009711:Nucleotides / Q000032:analysis*; D012329:RNA, Bacterial / Q000032:analysis; D012333:RNA, Messenger / Q000032:analysis*; D017423:Sequence Analysis, RNA / Q000379:methods; D013292:Streptococcus agalactiae / Q000235:genetics* / Q000254:growth & development
chemical_list: D009711:Nucleotides; D012329:RNA, Bacterial; D012333:RNA, Messenger