Competing and noncompeting activities of miR-122 and the 5' exonuclease Xrn1 in regulation of hepatitis C virus replication

Lineberger Comprehensive Cancer Center and Division of Infectious Diseases, Department of Medicine and Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 12/2012; 110(5). DOI: 10.1073/pnas.1213515110
Source: PubMed


Hepatitis C virus (HCV) replication is dependent on microRNA 122 (miR-122), a liver-specific microRNA that recruits Argonaute 2 to the 5' end of the viral genome, stabilizing it and slowing its decay both in cell-free reactions and in infected cells. Here we describe the RNA degradation pathways against which miR-122 provides protection. Transfected HCV RNA is degraded by both the 5' exonuclease Xrn1 and 3' exonuclease exosome complex, whereas replicating RNA within infected cells is degraded primarily by Xrn1 with no contribution from the exosome. Consistent with this, sequencing of the 5' and 3' ends of RNA degradation intermediates in infected cells confirmed that 5' decay is the primary pathway for HCV RNA degradation. Xrn1 knockdown enhances HCV replication, indicating that Xrn1 decay and the viral replicase compete to set RNA abundance within infected cells. Xrn1 knockdown and miR-122 supplementation have equal, redundant, and nonadditive effects on the rate of viral RNA decay, indicating that miR-122 protects HCV RNA from 5' decay. Nevertheless, Xrn1 knockdown does not rescue replication of a viral mutant defective in miR-122 binding, indicating that miR-122 has additional yet uncharacterized function(s) in the viral life cycle.

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    • "Pre-miRNAs occur as thermodynamically stable hairpin structures that are exported to the cytoplasm via the protein exportin and processed to active 21–22 nucleotide mature miRNAs by RNA endonuclease Dicer within the RNA silencing complex (RISC). Mature miRNAs are further processed in RISC by selecting one of two strands (−5p or −3p) and guided to their cognate mRNAs where they facilitate destabilization and eventual degradation of the target , prevent translation via recruitment of inhibitory factors, or in some cases can enhance RNA stability (Krol et al., 2010; Li et al., 2013). Humans express an estimated 1881 pre-miRNAs which produce 2588 mature miRNAs (Kozomara and Griffiths-Jones, 2014). "
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    • "Since HCV genome, as a viral genome, does not have cap structure and thus misses the associated proteins at its 5′ end, it eventually requires alternative mechanism to promote translation by recruiting translational components, eventually leading to increased RNA stability by inhibiting exonucleases digestion [69]. Indeed, it is proposed that miR-122 acts instead of cap structure in enhancing RNA expression by increasing its stability against Xrn1, accelerates the binding of ribosome, and exerts another Xrn1-independent role in stimulating HCV gene expression [110, 111]. Components such as RISC which are brought to HCV genome by miRNP would function as a shield in protecting single-stranded 5′ end of HCV from cytosolic exonucleases activities [111]. "
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