Identification of murine gammaherpesvirus 68 miRNA-mRNA hybrids reveals miRNA target conservation among gammaherpesviruses including host translation and protein modification machinery

Gammaherpesviruses, including the human pathogens Epstein-Barr virus and Kaposi’s sarcoma-associated herpesvirus, establish lifelong latent infection in B cells and are associated with a variety of tumors. In addition to protein coding genes, these viruses encode numerous microRNAs (miRNAs) within their genomes. While putative host targets of EBV and KSHV miRNAs have been previously identified, the specific functions of these miRNAs during in vivo infection are largely unknown. Murine gammaherpesvirus 68 is a natural pathogen of rodents that is genetically related to both EBV and KSHV, and thus serves as an excellent model for the study of EBV and KSHV elements such as miRNAs in the context of infection and disease. However, MHV68 the specific targets of miRNAs remain unknown. Using a technique known as quick CLASH (crosslinking, ligation, and sequencing of hybrids), we have now identified specific, Ago-associated mRNA targets of MHV68 miRNAs during lytic infection, latent infection and reactivation from latency. MHV68 infected cells were harvested from three biological conditions: latency (murine B cell line latently infected with MHV68), reactivation (reactivation of MHV68 from latently infected murine B cells), and lytic infection (MHV68 infected murine fibroblast cells. Cells were lysed, UV crosslinked and argonaute complexes were immunoprecipitated. Argonaute associated RNAs were ligated to one another, isolated, and sequenced.