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The primary transcriptome of the major human pathogen Helicobacter pylori

Author

Listed:
  • 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,
    Université de Bordeaux, F-33076 Bordeaux Cedex, France)

  • Jérémy Reignier

    (INSERM U869 and,
    Université de Bordeaux, F-33076 Bordeaux Cedex, France)

  • 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,
    Université de Bordeaux, F-33076 Bordeaux Cedex, France)

  • 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
    Fraunhofer Institute for Cell Therapy and Immunology, RNomics Group, D-04103 Leipzig, Germany
    Max Planck Institute for the Mathematics in Sciences
    University of Vienna, Institute for Theoretical Chemistry)

  • Jörg Vogel

    (Max Planck Institute for Infection Biology, RNA Biology Group, D-10117 Berlin, Germany
    University of Würzburg, Institute for Molecular Infection Biology)

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.

Suggested Citation

  • Cynthia M. Sharma & Steve Hoffmann & Fabien Darfeuille & Jérémy Reignier & Sven Findeiß & Alexandra Sittka & Sandrine Chabas & Kristin Reiche & Jörg Hackermüller & Richard Reinhardt & Peter F. Stadler, 2010. "The primary transcriptome of the major human pathogen Helicobacter pylori," Nature, Nature, vol. 464(7286), pages 250-255, March.
    • Handle: RePEc:nat:nature:v:464:y:2010:i:7286:d:10.1038_nature08756
    DOI: 10.1038/nature08756
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    Citations

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    Cited by:

    1. Daniel G. Mediati & Julia L. Wong & Wei Gao & Stuart McKellar & Chi Nam Ignatius Pang & Sylvania Wu & Winton Wu & Brandon Sy & Ian R. Monk & Joanna M. Biazik & Marc R. Wilkins & Benjamin P. Howden & T, 2022. "RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Mateusz Noszka & Agnieszka Strzałka & Jakub Muraszko & Rafał Kolenda & Chen Meng & Christina Ludwig & Kerstin Stingl & Anna Zawilak-Pawlik, 2023. "Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Amir Bar & Liron Argaman & Michal Eldar & Hanah Margalit, 2023. "TRS: a method for determining transcript termini from RNAtag-seq sequencing data," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Fabian König & Sarah L. Svensson & Cynthia M. Sharma, 2024. "Interplay of two small RNAs fine-tunes hierarchical flagella gene expression in Campylobacter jejuni," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    5. Alejandro Tejada-Arranz & Aleksei Lulla & Maxime Bouilloux-Lafont & Evelyne Turlin & Xue-Yuan Pei & Thibaut Douché & Mariette Matondo & Allison H. Williams & Bertrand Raynal & Ben F. Luisi & Hilde Reu, 2023. "Acetylation regulates the oligomerization state and activity of RNase J, the Helicobacter pylori major ribonuclease," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    6. Emily Petroni & Caroline Esnault & Daniel Tetreault & Ryan K. Dale & Gisela Storz & Philip P. Adams, 2023. "Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi," Nature Communications, Nature, vol. 14(1), pages 1-23, December.

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