Background

The microRNAs, which are small RNA molecules, are ~22 nt sequences that regulate gene expression by interfering the post-transcriptional level, resulting in degradation of mRNAs and repression of translation by the base pair to 3’

untranslated regions (3'-UTR) of the mRNAs. Many studies have investigated miRNAs. Ambros et al. developed a uniform system for identifying and annotating new miRNAs in numerous organisms [1]. The miRBase [2] supports the information for published miRNA genes and miRNA targets. The miRNAMap provides known, putative miRNA and miRNA targets to browse.

Additionally, comparative sequence analysis, a fast and reliable method for identifying non-coding RNA structures [3], can be incorporated into the proposed resource to identify the conserved miRNA precursors in genomes of important in evolution, are developed by Washietl et al. In targets prediction, three tools, TargetScan [4], miRanda [5] and RNAHybrid [6] are commonly used to determine the most energetically most favorable hybridization sites of a small RNA to a large RNA. PicTar [7] is a computational method for identifying common targets of known miRNAs. Lu et al. developed an miRNA microarray for measuring the expression profiles of all known miRNAs in various normal tissues and tumors [8], which facilitate in accurately predicting miRNAs targets on viruses.

1.1.1 miRNA Biogenesis and Function

The microRNAs (miRNAs) are first discovered in C.elegan and regulate developmental stage. Currently, 44 species are found to produce miRNAs, not only in Eukaryotes, six virus species are also evidenced. More and more miRNAs are discovered, and have been shown to play important roles in a number of organisms at the level of development, apoptosis, and establishment of cell lineage. MicroRNA genes are one of the more abundant classes of regulatory genes in animals, estimated to comprise between 0.5 and 1 percent of the predicted genes in worms, flies, and humans, raising the prospect that they could have more regulatory functions than those uncovered to date [4]. The miRNAs are derived from precursor transcripts approximately 70–120 nts long sequences, which fold to form as stem-loop structures. These structures are believed to be recognized and taken out of nucleus by exportin 5. Pre-miRNA is then cleaved by Dicer (a ribonuclease III enzyme) to excise the mature miRNAs in the form of a small interfering RNA (siRNA) -like duplex, and asymmetrical assembly of the mature miRNA strands, which may be decided upon relative thermodynamic characteristics of the two 5 termini of strands, combining with the Argonaute proteins into effector complexes [9]. There are two ways to regulate gene expression: the common situation in plants, mRNA may be degraded when miRNA: mRNA perfectly complementary. In other situation,

always in animals, non-perfect complementary repress translation. The miRNAs appears to modulate methylation in chromatin level to silence chromatin, but this only occurs in yeast, some animals and plants. Figure 1.1 presents the biogenesis and functions of miRNAs.

Figure 1.1 The biogenesis and function of miRNAs [10].

1.1.2 Virus Infection and Propagation

In 1898, Friedrich Loeffler and Paul Frosch first found the nature of viruses, genetic entities that lie somewhere in the grey area between living and non-living states. Viruses are classified upon several characters, such as genome

type, shape, and life cycles depend on the host cells that they infect to reproduce.

There are three steps of virus infection: attachment, penetration, and uncoating.

When found outside of host cells, viruses exist as a protein coat or capsid, which encloses either DNA or RNA. Then it comes into contact with a host cell, a virus can penetrate, uncoat and insert its genetic material into host cell, literally taking over the host's functions. An infected cell produces more viral protein and genetic material instead of its usual products. Some viruses may remain dormant inside host cells for long periods, causing no obvious change in their host cells (a stage known as the lysogenic phase). But when a dormant virus is stimulated, it enters the lytic phase: new viruses are formed, self-assemble, and burst out of the host cell, killing the cell and going on to infect other cells. Viruses cause a number of diseases in eukaryotes. In humans, smallpox, the common cold, chickenpox, influenza, shingles, herpes, polio, rabies, Ebola, hanta fever, and AIDS are examples of viral diseases. Even some types of cancer - though definitely not all - have been linked to viruses.

1.1.3 The Relationship Between miRNAs and Viruses

Recently, the relationship between miRNAs and viruses appears to be interesting. Besides animals, insects and plants, miRNAs were also recently discoveredin viruses. Pfeffer et al [11] performeda small RNA profile of human cells infected by Epstein-Barrvirus to study therole that RNA silencing can play

during viral infection in animals. Besides host miRNAs, they identified five miRNAs originatingfrom the virus. Experimental verification of predictions in herpesviruses resulted in identification of several novel miRNAsfrom Kaposi sarcoma-associated virus, mouse gamma-herpes virus and human cytomegalovirus, SV40. Rhesus Lymphocryptovirus also encodes 16 microRNAs [12]. Additionally, virus miRNAs appear to have no homology between each other or with human miRNAs. Positions of miRNAs within different virus genomes were alsonot conserved in some viruses [13]. Although the function of most viral miRNAs seems unclear, the potential role in modulating virus activity is worthy to search. The miRNAs produced from viruses are considered to play a part in existence of virus by regulating virus own activity or host gene expression to escape immunity system. Besides, host miRNAs have been shown to target to viruses, such as PFV-1 [14], hepatitis C virus [15] and HIV [16], after they enter a host. Host miRNAs appear to cause different result in effecting virus. For example, experimental verification says that human miR-122a assists HCV replication in a host by targeting to the 3’

UTR on the HCV genome. However, HIV is suppressed by targeting several genes by human microRNAs.

These indicate two roles of virus in host: one is miRNAs can be produced from viruses, the other is that virus can be regulated by host microRNAs (Fig.

1.2). The relationship between viruses and host miRNAs is more various and worthy of further research. Research investigating miRNAs and viruses is at

initial stages, and the multi-relationships between viruses and miRNAs are valuable to investigate.

Figure 1.2 The relationship between microRNAs and virus [17].