Functional similarity analysis of human virus-encoded miRNAs

miRNAs, about 22 nucleotides in length, constitute a large family of non-coding RNAs that regulate gene expression posttranscriptionally, leading their target mRNAs to direct destructive cleavage or translational repression by base pairing with the 3' untranslated regions (3' UTRs). miRNA-mediated regulation plays crucial roles in a wide spectrum of biological processes, including proliferation [1], apoptosis [2], development [3], immune system regulation [4], and oncogenesis [5].Recent discoveries on viral miRNAs, mostly in herpesvirus family [6], threw lights on a new level of cross-talk between virus and host in viral infections and pathogenesis [7]. Viral miRNAs have been reported to participate in immune evasion by directly down-regulating host immune defence genes, and even to cooperate with viral proteins to target the same process [8]. The combination of protein-mediated and miRNA-mediated regulations forms an intricate strategy for viruses to resist host defence system and thus increase the opportunities of their survival.The research on viral miRNAs is still far from exhausted, with many unknown miRNA functions yet to be discovered. miRNA identification using computational tools is the most widely used method. In contrast to most eukaryotic miRNAs, virus-encoded miRNAs do not have homologs in other viral genomes or in the genome of the human host [6], and thus are difficult to be identified using existing miRNA gene prediction tools. Cloning and sequencing small RNA libraries to identify and characterize miRNAs is the basic method for miRNA discovery, since computationally predicted miRNAs should also be confirmed by experimental methods. Reverse ligation-mediated RT-PCR [9] is a widely used method in the identification of mature miRNAs and has been used to detect maturely processed MuHV-4 miRNAs [10]. Experimental validation is still a barrier in miRNA identification, especially in host cells infected by viruses. Currently, only a small fraction of viral