Mouse cytomegalovirus microRNAs dominate the cellular small RNAs profile during lytic infection and show features of post-transcriptional regulation

Max von Pettenkofer-Institut für Virologie, Ludwig-Maximilians-Universität München, Pettenkoferstr. 9a, 80336 München, Germany; IBMP-CNRS, 12, rue du Général Zimmer, 67084 Strasbourg cedex, France; Alnylam Europe AG, Fritz-Hornschuch-Str. 9, 95326 Kulmbach, Germany

^* To whom correspondence should be addressed. Email: sebastien.pfeffer{at}ibmp-ulp.u-strasbg.fr.

	Abstract

MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. Originally identified in a variety of organisms ranging from plants to mammals, miRNAs have recently been identified in several viruses. Viral miRNAs may play a role in modulating both viral and host gene expression. Here, we report on the identification and characterization of 18 viral miRNAs from mouse fibroblasts lytically infected with the murine cytomegalovirus (MCMV). The MCMV miRNAs are expressed at early times of infection and are scattered in small clusters throughout the genome with up to four distinct miRNAs processed from a single transcript. No significant homologies to human cytomegalovirus- (HCMV) encoded miRNAs were found. Remarkably, as soon as 24h after infection, MCMV miRNAs constituted about 35% of the total miRNAs pool and at 72h post infection this proportion was increased to more than 60%. However, despite the abundance of viral miRNAs during the early phase of infection, the expression of some MCMV miRNAs appeared to be regulated. Hence, for three miRNAs we observed polyuridylation of their 3' end, coupled to subsequent degradation. Individual knock-out mutants of two of the most abundant MCMV miRNAs miR-m01-4 and miR-M44-1, or a double knock-out mutant of miR-m21-1 and miR-M23-2, incurred no or only very mild growth deficit in murine embryonic fibroblasts in vitro.