Combined agonist–antagonist genome-wide functional screening identifies broadly active antiviral microRNAs

Abstract

Although the functional parameters of microRNAs (miRNAs) have been explored in some depth, the roles of these molecules in viral infections remain elusive. Here we report a general method for global analysis of miRNA function that compares the significance of both overexpressing and inhibiting each mouse miRNA on the growth properties of different viruses. Our comparative analysis of representatives of all three herpesvirus subfamilies identified host miRNAs with broad anti-and proviral properties which extend to a singlestranded RNA virus. Specifically, we demonstrate the broad antiviral capacity of miR-199a-3p and illustrate that this individual hostencoded miRNA regulates multiple pathways required and/or activated by viruses, including PI3K/AKT and ERK/MAPK signaling, oxidative stress signaling, and prostaglandin synthesis. Global miRNA expression analysis further demonstrated that the miR-199a/miR-214 cluster is down-regulated in both murine and human cytomegalovirus infection and manifests similar antiviral properties in mouse and human cells. Overall, we report a general strategy for examining the contributions of individual host miRNAs in viral infection and provide evidence that these molecules confer broad inhibitory potential against multiple viruses.RNAi | herpesvirus | RNA virus | RNA processing | phosphatidylinositol-3-kinase-Akt signalling S ince the discovery of the first microRNA (miRNA) in Caenorhabditis elegans, research in diverse organisms has illuminated the role of this class of small RNA in a wide range of cellular processes (reviewed in ref.

Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target

“…We, therefore, conclude that the rescue of miR-27 levels in these experiments is not attributable to nonspecific effects of transfection or saturation of the RISC machinery by the siRNAs. The specificity of m169 function was confirmed by comparison with two other host miRNAs: miR-16, a miRNA that does not change in expression level in response to infection and miR-199a-3p, another miRNA that is down-regulated during infection (14). Neither miRNA displayed a significant change in expression level as a result of m169 knockdown (Fig.…”

“…All three miRNAs in this cluster target genes associated with cell proliferation, differentiation, and cancer and are predicted to function in a cooperative fashion (40). miR-24, in addition to miR-27, displays antiviral properties when overexpressed (14), and we show that the virus can be engineered to target miR-24 by mutation of 11 nt in the miRNA-binding site (Fig. 5C).…”

“…However, the factors driving the evolution of these interactions remain somewhat controversial, because they may relate to viral mechanisms for persistence and latency rather than host defense (8,9). At the same time, the expression levels of specific miRNAs can indirectly influence infections; miRNAs are key components of the innate immune response (10,11) and exert antiviral properties by modulating host cofactors and pathways required by viruses (12)(13)(14)(15). We previously showed that miR-27 limits the replication capacity of murine cytomegalovirus (MCMV) but is rapidly degraded during the lytic infection (16).…”

Chemical modification and design of anti-miRNA oligonucleotides

“…5 Recently, evidence has shown that miRNAs also have a role in viral infections, which include invoking an antiviral response; alternatively, the viruses themselves can encode miRNAs or regulate endogenous host miRNAs, which aid in the infection process. 6,7 There are currently 41000 putative miRNAs encoded in the human genome, and miRNAs are estimated to regulate up to 60% of protein-coding mammalian genes. 8 As the number of discovered miRNAs and their regulated targets continually increases, the biological importance of these small non-coding RNAs becomes more evident.…”

Functional high-throughput screening identifies the miR-15 microRNA family as cellular restriction factors for Salmonella infection

“…Only recently this approach has been extended to miRNAs 20,21 , and is yet to be applied for the identification of miRNAs critical for infection by bacterial pathogens.…”