title: Deep sequencing reveals the eight facets of the influenza A/HongKong/1/1968 (H3N2) virus cap-snatching process.
abstract: The influenza A virus RNA polymerase cleaves the 5' end of host pre-mRNAs and uses the capped RNA fragments as primers for viral mRNA synthesis. We performed deep sequencing of the 5' ends of viral mRNAs from all genome segments transcribed in both human (A549) and mouse (M-1) cells infected with the influenza A/HongKong/1/1968 (H3N2) virus. In addition to information on RNA motifs present, our results indicate that the host primers are divergent between the viral transcripts. We observed differences in length distributions, nucleotide motifs and the identity of the host primers between the viral mRNAs. Mapping the reads to known transcription start sites indicates that the virus targets the most abundant host mRNAs, which is likely caused by the higher expression of these genes. Our findings suggest negligible competition amongst RdRp:vRNA complexes for individual host mRNA templates during cap-snatching and provide a better understanding of the molecular mechanism governing the first step of transcription of this influenza strain.
authors.affiliation: 1] Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada [2].
authors.forename: Dorota
authors.initials: D
authors.lastname: Sikora
authors.affiliation: 1] Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada [2].
authors.forename: Lynda
authors.initials: L
authors.lastname: Rocheleau
authors.affiliation: Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada.
authors.forename: Earl G
authors.initials: EG
authors.lastname: Brown
authors.affiliation: Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada.
authors.forename: Martin
authors.initials: M
authors.lastname: Pelchat
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D001483:Base Sequence; D045744:Cell Line, Tumor; D002874:Chromosome Mapping; D016384:Consensus Sequence; D017931:DNA Primers / Q000235:genetics; D015967:Gene Expression Regulation, Viral; D063990:Gene Ontology; D005814:Genes, Viral; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053122:Influenza A Virus, H3N2 Subtype / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D012333:RNA, Messenger / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D020121:5' Untranslated Regions; D017931:DNA Primers; D012333:RNA, Messenger; D012367:RNA, Viral