title: The primary transcriptome of the major human pathogen Helicobacter pylori.
abstract: Genome sequencing of Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and noncoding RNA output. Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing global transcriptomic analysis. Here, using a novel differential approach (dRNA-seq) selective for the 5' end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. We discovered hundreds of transcriptional start sites within operons, and opposite to annotated genes, indicating that complexity of gene expression from the small H. pylori genome is increased by uncoupling of polycistrons and by genome-wide antisense transcription. We also discovered an unexpected number of approximately 60 small RNAs including the epsilon-subdivision counterpart of the regulatory 6S RNA and associated RNA products, and potential regulators of cis- and trans-encoded target messenger RNAs. Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species.
authors.affiliation: Max Planck Institute for Infection Biology, RNA Biology Group, D-10117 Berlin, Germany.
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Sharma
authors.forename: Steve
authors.initials: S
authors.lastname: Hoffmann
authors.forename: Fabien
authors.initials: F
authors.lastname: Darfeuille
authors.forename: Jérémy
authors.initials: J
authors.lastname: Reignier
authors.forename: Sven
authors.initials: S
authors.lastname: Findeiss
authors.forename: Alexandra
authors.initials: A
authors.lastname: Sittka
authors.forename: Sandrine
authors.initials: S
authors.lastname: Chabas
authors.forename: Kristin
authors.initials: K
authors.lastname: Reiche
authors.forename: Jörg
authors.initials: J
authors.lastname: Hackermüller
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D000595:Amino Acid Sequence; D001483:Base Sequence; D002478:Cells, Cultured; D020869:Gene Expression Profiling; D016680:Genome, Bacterial / Q000235:genetics*; D016481:Helicobacter Infections / Q000382:microbiology*; D016480:Helicobacter pylori / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009876:Operon / Q000235:genetics; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics; D022661:RNA, Untranslated; D016415:Sequence Alignment; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; C411065:6S RNA; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated