Identification of cellular targets for virally-encoded miRNAs by ectopic expression and gene expression profiling

Since the first report in 2005, more than 120 microRNAs (miRNAs) have been identified in many double stranded DNA viruses-mainly herpesviruses and polyomaviruses [12, 68, 69, 82, 92]. MiRNAs are short 22 ± 3 nt RNA molecules that post-transcriptionally regulate gene expression by binding to 3′ UTRs of target mRNAs thereby inducing translational silencing and/or mRNA degradation [1, 3]. Because miRNAs require only limited complementarity, miRNA targets are difficult to determine [24]. Indeed, to date targets have only been experimentally verified for miRNAs of three viruses. SV40 encodes a miRNA which targets viral large T antigen expression [92]. Several KSHV miRNAs target Thrombospondin 1, a potent inhibitor of angiogenesis [82]. In addition, one KSHV miRNA, miR-K122-11, mimics a human miRNA, hsa-miR-155, involved in hematopoiesis and tumorigenesis. CMV miRNAs target both cellular and viral gene expression [31, 90]. Thus, virally encoded miRNAs regulate fundamental biological processes such as immune recognition, promotion of cell survival, and angiogenesis and may contribute to tumorigenesis. First, we briefly summarize our current knowledge on identification and expression of viral miRNAs with special emphasis on herpes-viruses. Next, we will discuss our work on KSHV-encoded miRNAs to illustrate how viral miRNAs provide a unique opportunity for target identification, and the challenges lying ahead in deciphering their potential roles in viral biology, and pathogenesis.