title: Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315.
abstract: BACKGROUND
  Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale.
  
  
  METHODS
  RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes.
  
  
  RESULTS
  Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered.
  
  
  CONCLUSIONS
  Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.
authors.affiliation: Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium. Andrea.Sass@UGent.be.
authors.forename: Andrea M
authors.initials: AM
authors.lastname: Sass
authors.affiliation: Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium. Heleen.VanAcker@UGent.be.
authors.forename: Heleen
authors.initials: H
authors.lastname: Van Acker
authors.affiliation: Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany. konrad.foerstner@uni-wuerzburg.de.
authors.forename: Konrad U
authors.initials: KU
authors.lastname: Förstner
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium. Filip.VanNieuwerburgh@UGent.be.
authors.forename: Filip
authors.initials: F
authors.lastname: Van Nieuwerburgh
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium. Dieter.Deforce@UGent.be.
authors.forename: Dieter
authors.initials: D
authors.lastname: Deforce
authors.affiliation: Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany. joerg.vogel@uni-wuerzburg.de.
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
authors.affiliation: Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium. Tom.Coenye@UGent.be.
authors.forename: Tom
authors.initials: T
authors.lastname: Coenye
mesh_terms: D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D018441:Biofilms / Q000254:growth & development; D057508:Burkholderia cenocepacia / Q000235:genetics* / Q000472:pathogenicity; D004352:Drug Resistance, Microbial / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D024363:Transcription Initiation Site
chemical_list: D000900:Anti-Bacterial Agents