title: Comparative analysis of viral RNA signatures on different RIG-I-like receptors.
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.
authors.affiliation: Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.|Ecole doctorale, Biochimie, Biothérapies, Biologie Moléculaire et Infectiologie (B3MI), Université Paris Diderot - Paris 7, Paris, France.
authors.forename: Raul Y
authors.initials: RY
authors.lastname: Sanchez David
authors.affiliation: Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.
authors.forename: Chantal
authors.initials: C
authors.lastname: Combredet
authors.affiliation: Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France.
authors.forename: Odile
authors.initials: O
authors.lastname: Sismeiro
authors.affiliation: Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France.
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Dillies
authors.affiliation: Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France.
authors.forename: Bernd
authors.initials: B
authors.lastname: Jagla
authors.affiliation: Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France.
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Coppée
authors.affiliation: Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.|Unité Interactions Hôte-Agents Pathogens, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Mura
authors.affiliation: Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Guerbois Galla
authors.affiliation: Technology Platform CYROI, University of Reunion Island, Saint-Clotilde, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Despres
authors.affiliation: Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Tangy
authors.affiliation: Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.
authors.forename: Anastassia V
authors.identifier: http://orcid.org/0000-0002-9998-8447
authors.initials: AV
authors.lastname: Komarova
mesh_terms: D002460:Cell Line; D002646:Chikungunya virus / Q000276:immunology*; D000071457:DEAD Box Protein 58 / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D000072640:Interferon-Induced Helicase, IFIH1 / Q000302:isolation & purification / Q000378:metabolism*; D008459:Measles virus / Q000276:immunology*; D020365:RNA Helicases / Q000302:isolation & purification / Q000378:metabolism*; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D011971:Receptors, Immunologic / Q000302:isolation & purification / Q000378:metabolism*
chemical_list: D012367:RNA, Viral; D011971:Receptors, Immunologic; C520569:DHX58 protein, human; C452820:RIGI protein, human; C452815:IFIH1 protein, human; D000071457:DEAD Box Protein 58; D000072640:Interferon-Induced Helicase, IFIH1; D020365:RNA Helicases
keywords: PAMP; PRR; RIG-I-like receptors; human; immunology; infectious disease; innate immunity; microbiology; ribonucleoproteins; virus-host interactions