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

PLoS Pathogens
Whitney L BullardScott A Tibbetts

Abstract

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, Cts...Continue Reading

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Citations

Apr 23, 2020·Annual Review of Genomics and Human Genetics·Grzegorz KudlaAleksandra Helwak
Jul 8, 2020·Seminars in Cell & Developmental Biology·Takanobu TagawaJoseph Ziegelbauer
Nov 20, 2020·Journal of Virology·Enrico R BarrozoDavid C Bloom
Sep 30, 2021·Annual Review of Virology·Yiping WangLaurie T Krug

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Methods Mentioned

BETA
immunoprecipitation
CLASH
CLIP
PCR
transfection
Assay
reverse transcription PCR
electrophoresis
ubiquitination
sumoylation

Software Mentioned

qCLASH scripts
quick CLASH ( qCLASH )
IPA
qCLASH
CLASH
iQ5
CLIP
Trimmomatic
Hyb
Ingenuity Pathway Analysis

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