Human cytomegalovirus expresses novel microRNAs during productive viral infection

Abstract

SummaryMicroRNAs (miRNAs) are a large class of ~ 22-nucleotide non-coding RNAs that facilitate mRNA cleavage and translation repression through the RNA interference pathway. Until recently, miRNAs have been exclusively found in eukaryotic organisms. A nonimmunogenic molecule requiring minimal genomic investment, these RNAs may offer an efficient means for viruses to modulate both their own and the host's gene expression during a productive viral infection. In this study we report that human cytomegalovirus (HCMV) expresses miRNAs during its productive lytic infection of four clinically relevant human cell types: fibroblast, endothelial, epithelial and astrocyte cells. The sequences of the miRNAs, expressed from the UL23 and US24 loci of the viral genome, were conserved among all HCMV strains examined and in chimpanzee cytomegalovirus. Furthermore, their expression was detected from both a laboratoryadapted strain and a clinical isolate of HCMV. The conservation of these miRNAs and their expression in different cell types suggests that they represent an evolutionarily primitive feature in the viral genome, and that virus-encoded miRNAs may be more common than previously believed.

Identification and function of human cytomegalovirus microRNAs

“…Expression of five of the 13 miRNAs, miR-UL36-1, miR-UL70-1, miR-US4-1, miR-US5-1 and miR-US5-2, was confirmed through northern blot analysis (Grey et al, 2005). Following this study, and those of two other groups, a total of 11 miRNAs have been identified, including miR-UL22A-1, miR-UL112-1, miR-UL148D-1, miR-US25-1, US25-2, US33-1 and the five previously described (Dunn et al, 2005;Pfeffer et al, 2005).…”

“…It is now thought that regulation of gene expression by miRNAs is a mechanism common to all metazoan organisms (Bartel, 2004;Pfeffer et al, 2005;Pfeffer et al, 2004). In addition, a number of studies by multiple groups have clearly shown that mammalian DNA viruses, especially of the herpesvirus family, have evolved their own miRNA genes (Burnside et al, 2006;Cai et al, 2005;Cai et al, 2006;Cui et al, 2006;Dunn et al, 2005;Grey et al, 2005;Gupta et al, 2006;Lu and Cullen, 2004;Pfeffer et al, 2005;Pfeffer et al, 2004;Samols et al, 2005;Sano et al, 2006;Sullivan et al, 2005;Yao et al, 2007). In this review, the identification and characterization of miRNAs expressed by human cytomegalovirus, and the genes they target, will be discussed.…”

The Cell Biology of Cytomegalovirus: Implications for Transplantation

“…This tissue specificity suggests that CMV may activate multiple transcriptional programs depending on the The mechanisms underlying tissue specificity of viral gene expression may also relate to recently described and generally conserved microRNAs (miRNAs) of CMV (77)(78)(79)(80)(81). These small, noncoding RNA species have diverse effects including regulation of viral replication and immune evasion, which appear to vary by the cell type infected (77)(78)(79)(80)(81)(82)(83). HCMV-miR-UL112-3p, for example, appears to affect both the stress-induced ligand MICB and the antiviral interferon-response element IRF-1 (80,84).…”

Discrete Clusters of Virus-Encoded MicroRNAs Are Associated with Complementary Strands of the Genome and the 7.2-Kilobase Stable Intron in Murine Cytomegalovirus

“…Cloning of small RNAs has proven a successful method for experimentally identifying miRNAs in a variety of viruses (36). In two previous cloning studies with HCMV, either ϳ1% or ϳ18% of the total clones in each study possessed viral content, potentially due to differences in the infection conditions or cell lines (7,36). Thus, in order to screen for an efficient experimental design in our cloning studies, we initially sequenced a set of clones (ϳ200 each) from both infected MEF and BMM cells after 72 h. The ratio of viral to mouse RNA was assessed by BLAST analysis and was substantially greater in the MEF cells than in the BMM cells (ϳ30% viral clones compared to 0.5% viral clones, respectively).…”

“…Previous work has shown that HCMV encodes at least 11 miRNAs (7,13,36), and one of these miRNAs has been shown to target a host immune system gene (cited above). CMV is highly species specific; however, the pathogenesis of mouse CMV (MCMV) in mice is remarkably similar to that of HCMV in humans.…”