title: HITS-CLIP and PAR-CLIP advance viral miRNA targetome analysis.
abstract: MiRNAs regulate gene expression by binding predominantly to the 3' untranslated region (UTR) of target transcripts to prevent their translation and/or induce target degradation. In addition to the more than 1200 human miRNAs, human DNA tumor viruses such as Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) encode miRNAs. Target predictions indicate that each miRNA targets hundreds of transcripts, many of which are regulated by multiple miRNAs. Thus, target identification is a big challenge for the field. Most methods used currently investigate single miRNA-target interactions and are not able to analyze complex miRNA-target networks. To overcome these challenges, cross-linking and immunoprecipitation (CLIP), a recently developed method to study direct RNA-protein interactions in living cells, has been successfully applied to miRNA target analysis. It utilizes Argonaute (Ago)-immunoprecipitation to isolate native Ago-miRNA-mRNA complexes. In four recent publications, two variants of the CLIP method (HITS-CLIP and PAR-CLIP) were utilized to determine the targetomes of human and viral miRNAs in cells infected with the gamma-herpesviruses KSHV and EBV, which are associated with a number of human cancers. Here, we briefly introduce herpesvirus-encoded miRNAs and then focus on how CLIP technology has largely impacted our understanding of viral miRNAs in viral biology and pathogenesis.
authors.affiliation: Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA.
authors.forename: Irina
authors.initials: I
authors.lastname: Haecker
authors.affiliation: Department of Molecular Genetics and Microbiology, Shands Cancer Center, Genetics Institute, University of Florida, Gainesville, FL, USA.
authors.forename: Rolf
authors.initials: R
authors.lastname: Renne
mesh_terms: D020031:Epstein-Barr Virus Infections / Q000235:genetics / Q000378:metabolism* / Q000821:virology; D015967:Gene Expression Regulation, Viral; D004854:Herpesvirus 4, Human; D006801:Humans; D047468:Immunoprecipitation; D035683:MicroRNAs / Q000502:physiology*; D046228:Microarray Analysis; D012367:RNA, Viral
chemical_list: D035683:MicroRNAs; D012367:RNA, Viral