The primary transcriptome of the major human pathogen Helicobacter pylori

Cynthia M. Sharma, Steve Hoffmann, Fabien Darfeuille, Jérémy Reignier, Sven Findeiß, Alexandra Sittka, Sandrine Chabas, Kristin Reiche, Jörg Hackermüller, Richard Reinhardt, Peter F. Stadler and Jörg Vogel ()
Additional contact information
Cynthia M. Sharma: Max Planck Institute for Infection Biology, RNA Biology Group, D-10117 Berlin, Germany
Steve Hoffmann: University of Leipzig
Fabien Darfeuille: INSERM U869 and,
Jérémy Reignier: INSERM U869 and,
Sven Findeiß: University of Leipzig
Alexandra Sittka: Max Planck Institute for Infection Biology, RNA Biology Group, D-10117 Berlin, Germany
Sandrine Chabas: INSERM U869 and,
Kristin Reiche: Fraunhofer Institute for Cell Therapy and Immunology, RNomics Group, D-04103 Leipzig, Germany
Jörg Hackermüller: Fraunhofer Institute for Cell Therapy and Immunology, RNomics Group, D-04103 Leipzig, Germany
Richard Reinhardt: Max Planck Institute for Molecular Genetics
Peter F. Stadler: University of Leipzig
Jörg Vogel: Max Planck Institute for Infection Biology, RNA Biology Group, D-10117 Berlin, Germany

Nature, 2010, vol. 464, issue 7286, 250-255

Abstract: 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 ∼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.

Date: 2010
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DOI: 10.1038/nature08756

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