In silico prediction of cellular gene targets of herpesvirus encoded microRNAs

Abstract

., miR-H1 [encoded by herpes simplex virus 1 (HSV1)] and miR-K12-3 [encoded by Kaposi sarcoma-associated herpesvirus (KSHV)] by identifying putative targets of viral miRNAs. We used our published microarray data (GSE107005) to identify the transcripts downregulated by the v-miRs. The 3' untranslated region (UTR) of these genes were extracted using BioMart tool on Ensembl and subjected to RNA:RNA interaction employing RNA Hybrid. We obtained hundreds of potential and novel miR-H1 and miR-K12-3 binding sites on the 3'UTR of the genes downregulated by these v-miRs. The information can provide likely regulatory mechanisms of the candidate v-miRs through which they can exert biological impact during herpesvirus infection and pathogenesis.