title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α).
abstract: Viruses that infect birds pose major threats-to the global supply of chicken, the major, universally-acceptable meat, and as zoonotic agents (e.g. avian influenza viruses H5N1 and H7N9). Controlling these viruses in birds as well as understanding their emergence into, and transmission amongst, humans will require considerable ingenuity and understanding of how different species defend themselves. The type I interferon-coordinated response constitutes the major antiviral innate defence. Although interferon was discovered in chicken cells, details of the response, particularly the identity of hundreds of stimulated genes, are far better described in mammals. Viruses induce interferon-stimulated genes but they also regulate the expression of many hundreds of cellular metabolic and structural genes to facilitate their replication. This study focusses on the potentially anti-viral genes by identifying those induced just by interferon in primary chick embryo fibroblasts. Three transcriptomic technologies were exploited: RNA-seq, a classical 3'-biased chicken microarray and a high density, "sense target", whole transcriptome chicken microarray, with each recognising 120-150 regulated genes (curated for duplication and incorrect assignment of some microarray probesets). Overall, the results are considered robust because 128 of the compiled, curated list of 193 regulated genes were detected by two, or more, of the technologies.
authors: Section of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK.
authors: Efstathios S
authors: ES
authors: Giotis
authors: Section of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK.
authors: Rebecca C
authors: RC
authors: Robey
authors: Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK.
authors: Natalie G
authors: NG
authors: Skinner
authors: Bioinformatics Support Service, Imperial College London, Sir Alexander Fleming Bldg, London, SW7 2AZ, UK.
authors: Christopher D
authors: CD
authors: Tomlinson
authors: Institute for Infection and Immunity, St. George's, University of London, London, SW17 0RE, UK.
authors: Stephen
authors: S
authors: Goodbourn
authors: Section of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK. m.skinner@imperial.ac.uk.
authors: Michael A
authors: 0000-0002-0050-4167
authors: MA
authors: Skinner
mesh_terms: D000818:Animals; D002642:Chick Embryo; D002645:Chickens / Q000235:genetics* / Q000276:immunology; D005347:Fibroblasts / Q000187:drug effects / Q000378:metabolism; D005796:Genes / Q000187:drug effects*; D016898:Interferon-alpha / Q000494:pharmacology*; D020411:Oligonucleotide Array Sequence Analysis / Q000662:veterinary*; D012313:RNA / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction / Q000662:veterinary
chemical_list: D016898:Interferon-alpha; D012313:RNA