Masking the 5' terminal nucleotides of the hepatitis C virus genome by an unconventional microRNA-target RNA complex

• Published in: Proceedings of the National Academy of Sciences - PNAS 2011-02, Vol.108 (8), p.3193-3198
• Main Authors: Machlin, Erica S, Sarnow, Peter, Sagan, Selena M
• Format: Article
• Language: English
• Subjects: 5' Flanking Region - genetics; Abundance; Animals; Base Sequence; Binding Sites; Biological Sciences; Gene Expression Regulation; Genetic mutation; Genome, Viral; Genomes; Genomics; HeLa cells; Hepacivirus; Hepacivirus - genetics; Hepatitis; Hepatitis C; Hepatitis C virus; Hepatology; Host-Pathogen Interactions; Immune response; Liver; Messenger RNA; MicroRNA; MicroRNAs - metabolism; MicroRNAs - pharmacology; miRNA; Molecules; mRNA; Nucleic Acid Conformation; Nucleotides; Pan troglodytes; Ribonucleic acid; RNA; RNA viruses; RNA, Viral - metabolism; Tails; Viral RNA
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1012464108

Hepatitis C virus subverts liver-specific microRNA, miR-122, to upregulate viral RNA abundance in both infected cultured cells and in the liver of infected chimpanzees. These findings have identified miR-122 as an attractive antiviral target. Thus, it is imperative to know whether a distinct functional complex exists between miR-122 and the viral RNA versus its normal cellular target mRNAs. Toward this goal, effects on viral RNA abundance of mutated miR-122 duplex molecules, bound at each of the two target sites in the viral genome, were compared to effects on microRNA- or siRNA-mediated regulation of reporter target mRNAs. It was found that miR-122 formed an unusual microRNA complex with the viral RNA that is distinct from miR-122 complexes with reporter mRNAs. Notably, miR-122 forms an oligomeric complex in which one miR-122 molecule binds to the 5' terminus of the hepatitis C virus (HCV) RNA with 3' overhanging nucleotides, masking the 5' terminal sequences of the HCV genome. Furthermore, specific internal nucleotides as well as the 3' terminal nucleotides in miR-122 were absolutely required for maintaining HCV RNA abundance but not for microRNA function. Both miR-122 molecules utilize similar internal nucleotides to interact with the viral genome, creating a bulge and tail in the miR-122 molecules, revealing tandemly oriented oligomeric RNA complexes. These findings suggest that miR-122 protects the 5' terminal viral sequences from nucleolytic degradation or from inducing innate immune responses to the RNA terminus. Finally, this remarkable microRNA-mRNA complex could be targeted with compounds that inactivate miR-122 or interfere with this unique RNA structure.