Human microRNAs targeting hepatitis C virus

microRNA (miRNA) is a post-transcriptional gene regulation mechanism that mediates sequence-specific degradation of the targeted RNA and thus provides an opportunity for the development of oligonucleotide-based drugs. Here, we propose a systematic approach for finding, selecting, and validating miRNAs that target conserved regions in the hepatitis C virus (HCV). Different factors, such as target conservation, target accessibility, miRNA and target RNA thermodynamics, are considered in our pipeline. The conservation profiles of six major genotypes of HCV have been analyzed and the potential conserved regions are selected for downstream analysis based on their entropy and length. An in silico protocol for predicting the miRNA targets in HCV highly conserved regions is devised, and a set of potential miRNAs is filtered and verified using different techniques. Some of the predicted miRNAs were previously experimentally validated, which gives support to our analysis.