1. Immunology and Inflammation
  2. Microbiology and Infectious Disease
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Comparative analysis of viral RNA signatures on different RIG-I-like receptors

  1. Raul Y Sanchez David
  2. Chantal Combredet
  3. Odile Sismeiro
  4. Marie-Agnès Dillies
  5. Bernd Jagla
  6. Jean-Yves Coppée
  7. Marie Mura
  8. Mathilde Guerbois Galla
  9. Philippe Despres
  10. Frédéric Tangy
  11. Anastassia V Komarova  Is a corresponding author
  1. Institut Pasteur, France
  2. University of Texas Medical Branch, United States
  3. University of Reunion Island, France
Research Article
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Cite this article as: eLife 2016;5:e11275 doi: 10.7554/eLife.11275

Abstract

The RIG-I-like receptors (RLRs) play a major role in sensing RNA virus infection to initiate and modulate antiviral immunity. They interact with particular viral RNAs, most of them being still unknown. To decipher the viral RNA signature on RLRs during viral infection, we tagged RLRs (RIG-I, MDA5, LGP2) and applied tagged protein affinity purification followed by next-generation sequencing (NGS) of associated RNA molecules. Two viruses with negative- and positive-sense RNA genome were used: measles (MV) and chikungunya (CHIKV). NGS analysis revealed that distinct regions of MV genome were specifically recognized by distinct RLRs: RIG-I recognized defective interfering genomes, whereas MDA5 and LGP2 specifically bound MV nucleoprotein-coding region. During CHIKV infection, RIG-I associated specifically to the 3' untranslated region of viral genome. This study provides the first comparative view of the viral RNA ligands for RIG-I, MDA5 and LGP2 in the presence of infection.

Article and author information

Author details

  1. Raul Y Sanchez David

    Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  2. Chantal Combredet

    Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  3. Odile Sismeiro

    Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  4. Marie-Agnès Dillies

    Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Bernd Jagla

    Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  6. Jean-Yves Coppée

    Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  7. Marie Mura

    Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  8. Mathilde Guerbois Galla

    University of Texas Medical Branch, Galveston, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Philippe Despres

    Technology platform CYROI, University of Reunion Island, Saint-Clotilde, France
    Competing interests
    The authors declare that no competing interests exist.
  10. Frédéric Tangy

    Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  11. Anastassia V Komarova

    Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, France
    For correspondence
    stasy@pasteur.fr
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Xuetao Cao, Zhejiang University School of Medicine, China

Publication history

  1. Received: September 1, 2015
  2. Accepted: March 24, 2016
  3. Accepted Manuscript published: March 24, 2016 (version 1)
  4. Version of Record published: April 20, 2016 (version 2)

Copyright

© 2016, Sanchez David et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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