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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Available from: David Mcgivern, Oct 05, 2015
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    • "Nascent RNA genomes are translated to produce new viral proteins, serve as new/additional RNA templates for further RNA replication and are progressively assembled to form infectious virions. HCV replication is dependent on microRNA 122 (miR-122) [97], a liver-specific microRNA that recruits Argonaute 2 to the 5 0 end of the viral genome [98], stabilizing it and slowing its degradation by the 5 0 exonuclease Xrn1 [99]. "
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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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    • "Further studies revealed that miR-122 binds directly to the 5í¿GUTR of the HCV genome at two adjacent sites (Jopling et al., 2008; Machlin et al., 2011), stimulates HCV translation (Roberts et al., 2011a; Henke et al., 2014), and promotes HCV RNA accumulation by stabilizing the HCV genome (Shimakami et al., 2012b). Binding of miR-122 to the 5í¿GUTR of HCV RNA with 3í¿Goverhanging nucleotides was hypothesized to mask and protect the 5í¿Gend of the viral genome from 5í¿Gdecay mediated by 5í¿Gexonuclease Xrn1 (Li et al., 2013b). Even the exogenous expression of miR-122 famicroRNAs in HCV replication and related liver diseases 447 Fig. 2. Altered expression of miRNAs in association with HCV infection and their involvement in HCV-induced liver disease progression. "
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