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          Institute: MPI für molekulare Genetik     Collection: Sequencing Group     Display Documents

ID: 536197.0, MPI für molekulare Genetik / Sequencing Group
The primary transcriptome of the major human pathogen Helicobacter pylori
Authors:Sharma, Cynthia M.; Hoffmann, Steve; Darfeuille, Fabien; Reignier, Jérémy; Findeiß, Sven; Sittka, Alexandra; Chabas, Sandrine; Reiche, Kristin; Hackermüller, Jörg; Reinhardt, Richard; Stadler, Peter F.; Vogel, Jörg
Date of Publication (YYYY-MM-DD):2010-03-11
Title of Journal:Nature
Journal Abbrev.:Nature
Issue / Number:7286
Start Page:250
End Page:255
Copyright:© 2010 Nature Publishing Group
Review Status:Peer-review
Audience:Experts Only
Abstract / Description: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 ~60 small RNAs including the ϵ-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.
Comment of the Author/Creator:E-mail: joerg.vogel@uni-wuerzburg.de
We thank F. Seifert; H. Hamoutene and B. Timmermann for technical support; M. Schmid for mass spectrometry analysis; H. De Reuse, A. van Vliet and M. K. Waldor for discussions; F. Thümmler for library preparation; M. Droege for pyrosequencing support. J.V. and R.R. are supported by NGFN+ grants (BMBF, Germany), and J.V. and P.F.S. by DFG Priority Program SPP1258 Sensory and Regulatory RNAs in Prokaryotes (Grants VO8751/2, VO8751/4; STA850/7-1). S.H. was supported by a formel.1 grant of the University of Leipzig, the Freistaat Sachsen (LIFE project), the German Research Foundation IZBI (BIZ6/1-4) and Volkswagen Stiftung (I/82 720). F.D. is supported by the French Agence Nationale de la Recherche (ANR-07-JCJC-0104-01), the French Association de la Recherche contre le Cancer (ARC) and La Ligue Nationale contre le Cancer (LNCC). We thank D. Rose for his supporting work and S. Washietl for a pre-release of the RNAcode software.
External Publication Status:published
Document Type:Article
Communicated by:Richard Reinhardt
Affiliations:MPI für molekulare Genetik
MPI für Infektionsbiologie
MPI für Mathematik in den Naturwissenschaften
External Affiliations:Univ Leipzig, Dept Comp Sci, D-04107 Leipzig, Germany
Univ Leipzig, Interdisciplinary Ctr Bioinformat, D-04107 Leipzig, Germany.
INSERM, U869, F-33076 Bordeaux, France.
Univ Bordeaux, F-33076 Bordeaux, France.
Fraunhofer Inst Cell Therapy & Immunol, RNom Grp, D-04103 Leipzig, Germany.
Univ Vienna, Inst Theoret Chem, A-1090 Vienna, Austria. Santa Fe Inst, Santa Fe, NM 87501 USA.
Univ Wurzburg, Inst Mol Infect Biol, D-97080 Wurzburg, Germany
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