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Integrative functional genomics decodes herpes simplex virus 1

Author

Listed:
  • Adam W. Whisnant

    (Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7)

  • Christopher S. Jürges

    (Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7)

  • Thomas Hennig

    (Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7)

  • Emanuel Wyler

    (Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine)

  • Bhupesh Prusty

    (Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7)

  • Andrzej J. Rutkowski

    (Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital)

  • Anne L’hernault

    (Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital)

  • Lara Djakovic

    (Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7)

  • Margarete Göbel

    (Julius-Maximilians-University Würzburg)

  • Kristina Döring

    (Julius-Maximilians-University Würzburg)

  • Jennifer Menegatti

    (Saarland University Medical School)

  • Robin Antrobus

    (University of Cambridge)

  • Nicholas J. Matheson

    (University of Cambridge)

  • Florian W. H. Künzig

    (Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7)

  • Guido Mastrobuoni

    (Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine)

  • Chris Bielow

    (Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine)

  • Stefan Kempa

    (Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine)

  • Chunguang Liang

    (Julius-Maximilians-University Würzburg)

  • Thomas Dandekar

    (Julius-Maximilians-University Würzburg)

  • Ralf Zimmer

    (Ludwig-Maximilians-Universität München)

  • Markus Landthaler

    (Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine)

  • Friedrich Grässer

    (Saarland University Medical School)

  • Paul J. Lehner

    (University of Cambridge)

  • Caroline C. Friedel

    (Ludwig-Maximilians-Universität München)

  • Florian Erhard

    (Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7)

  • Lars Dölken

    (Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7
    Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital
    Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI))

Abstract

The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution.

Suggested Citation

  • Adam W. Whisnant & Christopher S. Jürges & Thomas Hennig & Emanuel Wyler & Bhupesh Prusty & Andrzej J. Rutkowski & Anne L’hernault & Lara Djakovic & Margarete Göbel & Kristina Döring & Jennifer Menega, 2020. "Integrative functional genomics decodes herpes simplex virus 1," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15992-5
    DOI: 10.1038/s41467-020-15992-5
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