The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures

Mol Cell. 2016 Apr 7;62(1):111-20. doi: 10.1016/j.molcel.2016.01.024. Epub 2016 Feb 25.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genome, Viral*
  • Hepacivirus / genetics*
  • Hepacivirus / physiology
  • Models, Molecular
  • Nucleic Acid Conformation
  • Open Reading Frames
  • RNA Folding
  • RNA, Viral / chemistry*
  • Virus Replication


  • RNA, Viral