Hepatitis C Virus RNA Functionally Sequesters miR-122

Abstract

Summary Hepatitis C virus uniquely requires the liver specific microRNA-122 for replication, yet global effects on endogenous miRNA targets during infection are unexplored. Here, high-throughput sequencing and crosslinking immunoprecipitation (HITS-CLIP) experiments of human Argonaute (Ago) during HCV infection showed robust Ago binding on the HCV 5′UTR, at known and predicted miR-122 sites. On the human transcriptome, we observed reduced Ago binding and functional mRNA de-repression of miR-122 targets during virus infection. This miR-122 “sponge” effect was relieved and redirected to miR-15 targets by swapping the miRNA tropism of the virus. Single-cell expression data from reporters containing miR-122 sites showed significant de-repression during HCV infection depending on expression level and site number. We describe a quantitative mathematical model of HCV induced miR-122 sequestration and propose that such miR-122 inhibition by HCV RNA may result in global de-repression of host miR-122 targets, providing an environment fertile for the long-term oncogenic potential of HCV.

Functional analysis of microRNA-122 binding sequences of hepatitis C virus and identification of variants with high resistance against a specific antagomir

“…however, its replication could be increased by the presence of miR-122 (Li et al, 2011a;Luna et al, 2015). These miravirsen-resistant mutant HCVs might depend on other unknown host factors or on the changed stem-loops permitting HCV growth in Huh7.5 cells without miR-122.…”

“…1c) (Li et al, 2011a), and Cell-U3 has been used as a control in miR-122 antagonism assays ( Fig. 2 and Li et al, 2011a) and in high-throughput sequencing and cross-linking immunoprecipitation experiments (Luna et al, 2015). However, Cell-U3 was attenuated and only produced infectivity titre of~10 3 f.f.u.…”

Heterogeneous Ribonucleoprotein K (hnRNP K) Binds miR-122, a Mature Liver-Specific MicroRNA Required for Hepatitis C Virus Replication

“…However, miR-122 may be partially stabilized by HCV RNA infection when the level of hnRNP K was reduced. The increase in miR-122 stability could be due to sequestration of miR-122 by the HCV RNA (25). Since hnRNP K can bind both the HCV RNA and miR-122, it may have a role in bringing miRNA-122 to the HCV RNA.…”

RNA-mediated degradation of microRNAs: A widespread viral strategy?

“…A recent report suggests this interaction may also inhibit the natural targets of miR-122 in the cell, though this is not expected to involve miRNA degradation. 56 . The majority of RNA viruses cause acute infections and it has been hypothesized that miRNAs lack the ability to regulate the host transcriptome in the time frame of most infections 57 since miRNA-mediated reductions in protein expression are contingent on protein turnover.…”