Differential hepatitis C virus RNA target site selection and host factor activities of naturally occurring miR-122 3΄ variants

Nucleic Acids Res. 2017 May 5;45(8):4743-4755. doi: 10.1093/nar/gkw1332.

Abstract

In addition to suppressing cellular gene expression, certain miRNAs potently facilitate replication of specific positive-strand RNA viruses. miR-122, a pro-viral hepatitis C virus (HCV) host factor, binds and recruits Ago2 to tandem sites (S1 and S2) near the 5΄ end of the HCV genome, stabilizing it and promoting its synthesis. HCV target site selection follows canonical miRNA rules, but how non-templated 3΄ miR-122 modifications impact this unconventional miRNA action is unknown. High-throughput sequencing revealed that a 22 nt miRNA with 3΄G ('22-3΄G') comprised <63% of total miR-122 in human liver, whereas other variants (23-3΄A, 23-3΄U, 21-3΄U) represented 11-17%. All loaded equivalently into Ago2, and when tested individually functioned comparably in suppressing gene expression. In contrast, 23-3΄A and 23-3΄U were more active than 22-3΄G in stabilizing HCV RNA and promoting its replication, whereas 21-3΄U was almost completely inactive. This lack of 21-3΄U HCV host factor activity correlated with reduced recruitment of Ago2 to the HCV S1 site. Additional experiments demonstrated strong preference for guanosine at nt 22 of miR-122. Our findings reveal the importance of non-templated 3΄ miR-122 modifications to its HCV host factor activity, and identify unexpected differences in miRNA requirements for host gene suppression versus RNA virus replication.

MeSH terms

  • 3' Untranslated Regions / genetics
  • Argonaute Proteins / biosynthesis
  • Argonaute Proteins / genetics*
  • Binding Sites
  • Gene Expression Regulation / genetics
  • Hepacivirus / genetics*
  • Hepacivirus / pathogenicity
  • Hepatitis C / genetics
  • Hepatitis C / virology
  • Host-Pathogen Interactions / genetics*
  • Humans
  • Liver / metabolism
  • Liver / virology
  • MicroRNAs / genetics*
  • RNA, Viral / genetics
  • Virus Replication / genetics

Substances

  • 3' Untranslated Regions
  • AGO2 protein, human
  • Argonaute Proteins
  • MIRN122 microRNA, human
  • MicroRNAs
  • RNA, Viral