title: Innate immune system activation by viral RNA: How to predict it?
abstract: The immune system is able to identify foreign pathogens via different pathways. In the case of viral infection, recognition of the viral RNA is a crucial step, and many efforts have been made to understand which features of viral RNA are detected by the immune system. The biased viral RNA composition, measured as host-virus nucleotidic divergence, or CpG enrichment, has been proposed as salient signal. Peculiar structural features of these RNA could also be related to the immune system activation. Here, we gather multiple datasets and proceed to a meta-analysis to uncover the best predictors of immune system activation by viral RNA. "A" nucleotide content and Minimum Folding Energy are good predictors, and are more easily generalized than more complex indicators suggested previously. As RNA composition and structure are highly correlated, we suggest further experiments on synthetic sequences to identify the viral RNA sensing mechanisms by immune system receptors.
authors.affiliation: Atelier de Bioinformatique, Université Pierre et Marie Curie - Paris VI, 4 place Jussieu, 75005 Paris, France; Laboratoire Biométrie et Biologie Evolutive, Université Claude Bernard Lyon 1, CNRS, UMR5558, Bâtiment Gregor Mendel, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France.
authors.forename: M
authors.initials: M
authors.lastname: Kondili
authors.affiliation: Laboratoire Biométrie et Biologie Evolutive, Université Claude Bernard Lyon 1, CNRS, UMR5558, Bâtiment Gregor Mendel, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France.
authors.forename: M
authors.initials: M
authors.lastname: Roux
authors.affiliation: Unité de Génomique Virale et Vaccination, CNRS UMR-3569, Institut Pasteur, Paris, France.
authors.forename: N
authors.initials: N
authors.lastname: Vabret
authors.affiliation: Atelier de Bioinformatique, Université Pierre et Marie Curie - Paris VI, 4 place Jussieu, 75005 Paris, France; Laboratoire Biométrie et Biologie Evolutive, Université Claude Bernard Lyon 1, CNRS, UMR5558, Bâtiment Gregor Mendel, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. Electronic address: marc.bailly-bechet@univ-lyon1.fr.
authors.forename: M
authors.initials: M
authors.lastname: Bailly-Bechet
mesh_terms: D001482:Base Composition; D006801:Humans; D007113:Immunity, Innate; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics*; D014780:Viruses / Q000235:genetics* / Q000276:immunology*
chemical_list: D012367:RNA, Viral
keywords: Activation; Innate immune system; Meta-analysis; RNA virus