title: Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C.
abstract: BACKGROUND
  Influenza B and C are single-stranded RNA viruses that cause yearly epidemics and infections. Knowledge of RNA secondary structure generated by influenza B and C will be helpful in further understanding the role of RNA structure in the progression of influenza infection.
  
  
  RESULTS
  All available protein-coding sequences for influenza B and C were analyzed for regions with high potential for functional RNA secondary structure. On the basis of conserved RNA secondary structure with predicted high thermodynamic stability, putative structures were identified that contain splice sites in segment 8 of influenza B and segments 6 and 7 of influenza C. The sequence in segment 6 also contains three unused AUG start codon sites that are sequestered within a hairpin structure.
  
  
  CONCLUSIONS
  When added to previous studies on influenza A, the results suggest that influenza splicing may share common structural strategies for regulation of splicing. In particular, influenza 3' splice sites are predicted to form secondary structures that can switch conformation to regulate splicing. Thus, these RNA structures present attractive targets for therapeutics aimed at targeting one or the other conformation.
authors.forename: Lumbini I
authors.initials: LI
authors.lastname: Dela-Moss
authors.forename: Walter N
authors.initials: WN
authors.lastname: Moss
authors.affiliation: Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA. turner@chem.rochester.edu.
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D000595:Amino Acid Sequence; D018387:Codon, Initiator; D019295:Computational Biology; D016384:Consensus Sequence; D009980:Influenza A virus / Q000235:genetics*; D009981:Influenza B virus / Q000235:genetics*; D009982:Gammainfluenzavirus / Q000235:genetics*; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D018387:Codon, Initiator; D022821:RNA Splice Sites; D012367:RNA, Viral