Herpesviruses encode their own microRNAs.

Featured Article: Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grässer FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T. Identification of microRNAs of the herpesvirus family. Nat Methods 2005;2:269 –76. In 2001, the term microRNA (miRNA) was proposed for the first time after 3 groups reported the identification of hundreds of such small (22 nucleotides) noncoding RNAs in the nematode worm, Drosophila, and humans. Today, with the advent of next generation sequencing technologies, the number of validated miRNAs is nearing 2000 for humans alone, and the number of publications containing the keyword “miRNA” is up to 6000 for the year 2013. What are miRNAs? We now know quite a lot about their biogenesis, their modes of action, and their roles in a wide variety of biological processes (1 ). They derive from large primary transcripts, which are sequentially processed by the type III ribonucleases Drosha and Dicer to give rise to a small RNA duplex. One of the 2 strands of this duplex is maintained and loaded into an effector protein, a member of the Argonaute family. The small RNA then acts as a guide to mediate attachment of the Argonaute protein to specific target messenger RNAs via partial base pairing. This results in the regulation of the translation of the mRNA and its destabilization. Hence, miRNAs are essential regulators of gene expression at a posttranscriptional level. In 2004, we published the first report of miRNAs of viral origin (2 ). By cloning and sequencing small RNAs from cells latently infected with a member of the herpesvirus family, the Epstein-Barr virus (EBV), we identified 5 different viral RNAs, presenting the characteristics of miRNAs. Interestingly, EBV miRNAs did not share any sequence similarity with cellular miRNAs, which indicated that they were not acquired from the host but rather that evolution had shaped some of the EBV transcripts so that the host miRNA biogenesis machinery could process them. Stimulated by this finding, we then decided to extend our initial observations and to see whether other families of viruses could also encode their own miRNAs. In collaboration with the group of Mihaela Zavolan, from the University of Basel, Switzerland, we coupled a newly designed bioinformatic prediction tool with a small RNA cloning and sequencing approach to identify novel miRNAs in a subset of different virus families. Our results, published in the article featured here, showed that miRNAs were predicted only in viruses with a DNA genome and not in RNA viruses. Our cloning and sequencing efforts confirmed this hypothesis, because we found that viruses such as hepatitis C virus, yellow fever virus, and HIV 1 did not express miRNAs, whereas 3 viruses from the herpesvirus family (Kaposi’s sarcoma herpesvirus, human cytomegalovirus, and the mouse herpesvirus 68) all encoded miRNAs. Soon thereafter, another group showed that a different kind of DNA virus, the polyomavirus SV40, also contained an miRNA (3 ). In our Nature Methods article, we reported a total of 28 miRNAs encoded by the 3 viruses mentioned earlier. We also strengthened our initial hypothesis that each virus evolved its own strategy to express miRNAs, because again no significant sequence similarity was found between viral miRNAs, and more strikingly, their modes of expression varied widely between different virus families. Today, more than 400 viral miRNAs have been validated, the vast majority in the genome of DNA viruses. These pathogen-associated RNAs have been shown to regulate both cellular and viral targets and have been involved in pathways such as cell-mediated immunity, cell cycle regulation, and cell survival (4 ). The identification of virally encoded miRNAs unveiled a new mode of interaction between viruses and their hosts and epitomizes the ultimate mode of mimicry used by viruses. Indeed, miRNAs are nonimmunogenic molecules and allow viruses to modulate the expression of their host genome to establish an optimal environment while remaining undetected.