title: The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures.
abstract: RNA is a versatile macromolecule that accommodates functional information in primary sequence and secondary and tertiary structure. We use a combination of chemical probing, RNA structure modeling, comparative sequence analysis, and functional assays to examine the role of RNA structure in the hepatitis C virus (HCV) genome. We describe a set of conserved but functionally diverse structural RNA motifs that occur in multiple coding regions of the HCV genome, and we demonstrate that conformational changes in these motifs influence specific stages in the virus' life cycle. Our study shows that these types of structures can pervade a genome, where they play specific mechanistic and regulatory roles, constituting a "code within the code" for controlling biological processes.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
authors.forename: Nathan
authors.initials: N
authors.lastname: Pirakitikulr
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Kohlway
authors.affiliation: Department of Microbial Pathogenesis, Yale University, New Haven, CT 06519, USA.
authors.forename: Brett D
authors.initials: BD
authors.lastname: Lindenbach
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address: anna.pyle@yale.edu.
authors.forename: Anna M
authors.initials: AM
authors.lastname: Pyle
mesh_terms: D016679:Genome, Viral; D016174:Hepacivirus / Q000235:genetics* / Q000502:physiology; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D059370:RNA Folding; D012367:RNA, Viral / Q000737:chemistry*; D014779:Virus Replication
chemical_list: D012367:RNA, Viral