In vitro selection of the 3′-untranslated regions of the human liver mRNA that bind to the HCV nonstructural protein 5B

•HCV NS5B has the potential of interacting with host RNA molecules.•High affinity binding mRNA molecules to NS5B were selected by iterative selection.•The 3′-UTR segments of Galectin-1 and RPS4X mRNA exhibited potent binding to NS5B.•These mRNA 3′-UTR segments can also serve as templates for NS5B RdRp.•Both of the mRNA molecules were shown to bind to NS5B in vivo by IP-RT-PCR.

Hepatitis C virus (HCV) nonstructural protein 5B (NS5B) has RNA-dependent RNA polymerase (RdRp) activity. Because NS5B recognizes various RNA motifs besides the HCV genome, NS5B has the potential of interacting with host RNA molecules. In this study, an RNA pool enriched with the 3′-UTR sequences was generated and mRNA molecules with high affinity binding to NS5B were selected by iterative selection. Among the high binding mRNA 3′-UTR segments, we analyzed the housekeeping ribosomal protein S4, X-linked [RPS4X] mRNA 3′-UTR and the 3′-UTR of galectin-1 (GAL-1) mRNA, which is known to be one of the genes upregulated in HCV-infected liver cells and to have a wide spectrum of biological properties. By means of IP-RT-PCR, it was demonstrated that both of the mRNA molecules bind to NS5B in the cytoplasm. Interestingly, GAL-1 and RPS4X mRNA can serve as templates for NS5B RdRp, suggesting these RNA molecules are regulated in vivo by NS5B.