Viral Infection-Related MicroRNAs in Viral and Host Genomic Evolution
Yoichi R. Fujii and Nitin K. Saksena
from: RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity (Edited by: Kevin V. Morris). Caister Academic Press, U.K. (2008)
MicroRNA (miRNA) is a small RNA (~22 nucleotides). The miRNA genes have been discovered in plants, invertebrates, and vertebrates. These miRNAs can regulate gene expression to inhibit translation of target messenger RNAs (mRNAs), and sometimes direct many rounds of site-specific mRNA cleavage in mammalian cells. Beyond the cutting-edged criteria of RNA interference (RNAi) by complementarily pairing of short interfering RNA (siRNA), the miRNAs, which were incomplementarily paired, are also encoded by several viruses, such as herpesviruses and human immunodeficiency virus type 1 (HIV-1). Intriguingly, gene expression of HIV-1 genome has been recently shown to be epigenetically regulated via a novel process of transcriptional repression by the miRNA of virus itself. However, role of the viral miRNA for gene regulation is not still well understood mechanistically as compared with host miRNAs. Conversely, the experimental and computational methods used to detect and predict the miRNA target genes are common ones in genome informatics. We describe in this chapter about the target prediction of a viral miRNA, miR-N367 and the conservation of secondary structure of pre-miR-N367 into mir-98/let-7 and mir-181a-2 in human miRNAs whose targets in HIV-1 genome could be related to HIV-1 transcriptional system. Further, we show here that the sequences of viral nef si/miRNA are conserved in plant miRNAs and the nef si/miRNAs was enabled to express in Arabidopsis thaliana similar to human cell. Thus, we hypothesize that the orphaned non-selfish miRNAs may evolve and jump on to other RNAs, which can transposably lead to spread of these miRNAs from some plant and vertebrate genomes through feeding of miRNAs-containing foods, viruses, etc. Equivocally, miRNAs can be picked up into the lentiviral transposon, such as HIV-1. Therefore, the viral miR-N367 would necessarily be a HIV-1 silencer to be inclusively incorporated into HIV-1 itself. The virulence may be lost with recombination and mutation by miRNAs from the viral and host genome. The question is, whether the encoded miRNAs are mediating the viral and host genomic evolution, which remains to be answered read more ...