miR-122 and the Hepatitis C RNA genome: more than just stability

Abstract

MicroRNA-122 (miR-122) plays a key role in hepatitis C virus (HCV) replication, but understanding exactly how it functions in the viral lifecycle has been elusive. HCV is a positive-strand virus with a messenger-sense RNA genome, to which miR-122 binds in a non-canonical fashion at two sites near the 5' end. Recent studies show that miR-122 recruits Ago-2 to the genomic RNA, stabilizing it and slowing its decay in infected cells. This led us to investigate decay pathways that mediate degradation of the viral RNA. We found HCV RNA is degraded primarily by the cytoplasmic 5' exonuclease Xrn1 in infected cells. miR-122 lost its stabilizing effect when cells were depleted of Xrn1 using an RNAi strategy, providing strong evidence that miR-122 acts to protect the viral RNA from Xrn1-mediated 5' exonucleolytic decay. However, Xrn1 depletion did not rescue replication of a viral mutant defective in miR-122 binding, indicating that there is much more to miR-122's actions than prevention of Xrn1 decay. Here, we consider the role of miR-122 in the viral lifecycle, and explore the possibility that it might function directly in viral RNA synthesis.

Keywords: PCBP2; RNA decay; RNA stability; Xrn1; hepatitis C virus; micro-RNA; replication; translation.

Figure 1. Two copies of miR-122 (red font) bind the extreme 5′ end of the positive-strand RNA genome of HCV (black font). The base-pair interactions shown have been established by genetic approaches and are important for viral replication. Seed sequence interactions are labeled S1 and S2. miR-122 recruits Ago2 to the RNA. PCPB2 binds to stem-loop 1 of the viral 5′NTR, formed by sequence within the most 5′ miR-122 binding site (S1).

Figure 2. Potential mechanisms by which miR-122 could function to promote the initiation of (A) negative-strand or (B) positive-strand HCV RNA synthesis. Positive-strand (genome sense) RNA is shown in black, and negative-strand RNA in red. See text for details. RF, replicative form RNA.