Journal Article

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

Esemenli, Alim, Tibbetts, Scott A., Nirmalan, Shreya, Kara, Mehmet, Renne, Rolf, Sethuraman, Sunantha, Feswick, April, Bullard, Whitney L., Gay, Lauren A., Wang, Yiping, Hoffman, Brett A.

2019

Overview

Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV), 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 (MHV68) 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 genetic elements such as miRNAs in the context of infection and disease. However, the specific targets of MHV68 miRNAs remain completely unknown. Using a technique known as qCLASH (quick crosslinking, ligation, and sequencing of hybrids), we have now identified thousands of Ago-associated, direct miRNA-mRNA interactions during lytic infection, latent infection and reactivation from latency. Validating this approach, detailed molecular analyses of specific interactions demonstrated repression of numerous host mRNA targets of MHV68 miRNAs, including Arid1a, Ctsl, Ifitm3 and Phc3. Notably, of the 1,505 MHV68 miRNA-host mRNA targets identified in B cells, 86% were shared with either EBV or KSHV, and 64% were shared among all three viruses, demonstrating significant conservation of gammaherpesvirus miRNA targeting. Pathway analysis of MHV68 miRNA targets further revealed enrichment of cellular pathways involved in protein synthesis and protein modification, including eIF2 Signaling, mTOR signaling and protein ubiquitination, pathways also enriched for targets of EBV and KSHV miRNAs. These findings provide substantial new information about specific targets of MHV68 miRNAs and shed important light on likely conserved functions of gammaherpesvirus miRNAs.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Activation / Analysis / Animals / Apoptosis / B cells / Biology and life sciences / Cancer / Cell cycle / Conservation / Crosslinking / EDTA / Epstein-Barr virus / Gammaherpesvirinae - physiology / Gene expression / Gene Expression Regulation / Genes / Genetic aspects / Genomes / Genomics / Herpesviridae Infections - genetics / Herpesviridae Infections - metabolism / Herpesviridae Infections - virology / Herpesviruses / Host-virus relationships / Hybrids / Identification and classification / Infection / Infections / Kaposis sarcoma / Latency / Latent infection / Lymphocytes B / Lymphoma / Medicine and Health Sciences / Messenger RNA / Mice / MicroRNA / MicroRNAs / MicroRNAs - genetics / miRNA / mRNA / Pathogenic microorganisms / Pathogens / Pathways / Polymer crosslinking / Post-translational modification / Post-translational modifications / Protein biosynthesis / Protein Processing, Post-Translational / Protein synthesis / Proteins / RNA / RNA, Messenger - genetics / RNA, Messenger - metabolism / RNA, Viral - genetics / RNA, Viral - metabolism / Rodents / Sarcoma / Signal transduction / Signaling / Software / Target recognition / TOR protein / TOR Serine-Threonine Kinases - genetics / TOR Serine-Threonine Kinases - metabolism / Transcription Factors - genetics / Transcription Factors - metabolism / Translation (Genetics) / Tumors / Ubiquitin / Ubiquitination / Virus Replication / Viruses