title: Virtual screening of gene expression regulatory sites in non-coding regions of the infectious salmon anemia virus.
abstract: BACKGROUND
  Members of the Orthomyxoviridae family, which contains an important fish pathogen called the infectious salmon anemia virus (ISAV), have a genome consisting of eight segments of single-stranded RNA that encode different viral proteins. Each of these segments is flanked by non-coding regions (NCRs). In other Orthomyxoviruses, sequences have been shown within these NCRs that regulate gene expression and virulence; however, only the sequences of these regions are known in ISAV, and a biological role has not yet been attributed to these regions. This study aims to determine possible functions of the NCRs of ISAV.
  
  
  RESULTS
  The results suggested an association between the molecular architecture of NCR regions and their role in the viral life cycle. The available NCR sequences from ISAV isolates were compiled, alignments were performed to obtain a consensus sequence, and conserved regions were identified in this consensus sequence. To determine the molecular structure adopted by these NCRs, various bioinformatics tools, including RNAfold, RNAstructure, Sfold, and Mfold, were used. This hypothetical structure, together with a comparison with influenza, yielded reliable secondary structure models that lead to the identification of conserved nucleotide positions on an intergenus level. These models determined which nucleotide positions are involved in the recognition of the vRNA/cRNA by RNA-dependent RNA polymerase (RdRp) or mRNA by the ribosome.
  
  
  CONCLUSIONS
  The information obtained in this work allowed the proposal of previously unknown sites that are involved in the regulation of different stages of the viral cycle, leading to the identification of new viral targets that may assist future antiviral strategies.
authors: Alvaro
authors: A
authors: Díaz
authors: Katherine
authors: K
authors: García
authors: Andrea
authors: A
authors: Navarrete
authors: Gastón
authors: G
authors: Higuera
authors: Instituto de Nutrición y Tecnología de los Alimentos, INTA, Universidad de Chile, Avenida El Líbano #5524, Macul, Santiago, Chile. jromero@inta.cl.
authors: Jaime
authors: J
authors: Romero
mesh_terms: D001483:Base Sequence; D016384:Consensus Sequence / Q000235:genetics; D017124:Conserved Sequence; D015967:Gene Expression Regulation, Viral; D046829:Isavirus / Q000235:genetics* / Q000472:pathogenicity; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000235:genetics; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014584:User-Computer Interface
chemical_list: D009711:Nucleotides; D022661:RNA, Untranslated; D012367:RNA, Viral