Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts

• DOI: 10.4161/rna.29442
• Publication Date: 2014-06-12T22:15:08Z
• Authors: Laurence Josset; Nicolas Tchitchek; Lisa E Gralinski; Martin T Ferris; Amie J Eisfeld; Richard R Green; Matthew J Thomas; Jennifer Tisoncik-Go; Gary P Schroth; Yoshihiro Kawaoka; Fernando Pardo-Ma...; Ralph S Baric; Mark T Heise; Xinxia Peng; Michael G Katze
• Keywords: long non-coding rna; [SDV.IMM] Life Sciences [q-bio]/Immunology; Gene Expression Regulation/drug effects; Interferon-alpha/*administration & dosage/pharmacology; Inbred C57BL; Antiviral Agents; influenza virus; Cell Line; Mice; 03 medical and health sciences; sars-cov; RNA Virus Infections; Influenza A virus/drug effects/physiology; Animals; Antiviral Agents/*administration & dosage/pharmacology; Lung/metabolism/*virology; Lung; Molecular Biology; collaborative cross; Severe acute respiratory syndrome-related coronavirus/drug effects/physiology; 0303 health sciences; Sequence Analysis, RNA; Gene Expression Profiling; Interferon-alpha; Molecular Sequence Annotation; interferon; Cell Biology; 3. Good health; Mice, Inbred C57BL; RNA Virus Infections/*drug therapy/*genetics/virology; Gene Expression Regulation; Severe acute respiratory syndrome-related coronavirus; rna-seq; Influenza A virus; Long Noncoding/*genetics; RNA; Female; RNA, Long Noncoding; Sequence Analysis; Research Paper

The outcome of respiratory virus infection is determined by a complex interplay viral and host factors. Some potentially important factors for the antiviral response, whose functions remain largely unexplored, are long non-coding RNAs (lncRNAs). Here we systematically inferred regulatory lncRNAs in response to influenza A severe acute syndrome coronavirus (SARS-CoV) based on their similarity expression with genes known function. We performed total RNA-Seq viral-infected lungs from eight mouse strains, yielding large data set transcriptional responses. Overall 5,329 were differentially expressed after infection. Most co-expressed coding modules enriched associated lung homeostasis pathways or immune processes. Each lncRNA was further individually annotated using rank-based method, enabling us associate 5,295 at least one gene predict potential cis effects. validated predicted be interferon-stimulated profiling responses interferon-α treatment. Altogether, these results provide broad categorization identify subsets likely key roles pathogenesis. These fully accessible through MOuse NOn-Code Lung interactive database (MONOCLdb).