ViTa: prediction of host microRNAs targets on viruses

Abstract

MicroRNAs (miRNAs) are involved in various biological processes by suppressing gene expression. A recent work has indicated that host miRNAs are also capable of regulating viral gene expression by targeting the virus genomes. To investigate regulatory relationships between host miRNAs and related viruses, we present a novel database, namely ViTa, to curate the known virus miRNA genes and the known/putative target sites of human, mice, rat and chicken miRNAs. Known miRNAs are obtained from miRBase. Virus data are collected and referred from ICTVdB, VBRC and VirGen. Experimentally validated miRNA targets on viruses were derived from literatures. Then, miRanda and TargetScan are utilized to predict miRNA targets within virus genomes. ViTa also provides the virus annotations, virus-infected tissues and tissue specificity of host miRNAs. This work also facilitates the comparisons between subtypes of viruses, such as influenza viruses, human liver viruses and the conserved regions between viruses. Both textual and graphical web interfaces are provided to facilitate the data retrieves in the ViTa database. The database is now freely available at .

Transcriptional Suppression of miR-181c by Hepatitis C Virus Enhances Homeobox A1 Expression

“…Lower minimum free energy (MFE) values of the miRNAs and the target sites revealed energetically more probable hybridizations between miRNAs and target genes (21). Our in silico analysis suggested a putative binding site for miR-181c in the HCV E1 and NS5A genes, with lower MFE values of Ϫ20.2 and Ϫ18.2, respectively (Fig.…”

“…Since overexpression of miR-181c downregulates HCV replication, we performed in silico analyses with ViTa algorithms (21) to identify whether miR-181c physically binds to the HCV genome. Lower minimum free energy (MFE) values of the miRNAs and the target sites revealed energetically more probable hybridizations between miRNAs and target genes (21).…”

Human MicroRNA hsa-miR-296-5p Suppresses Enterovirus 71 Replication by Targeting the Viral Genome

“…Identification of functional target sequences of hsa-miR-296-5p is necessary in order to define the regulatory mechanism of EV71 infection by this miRNA. By using ViTa algorithms (35) to predict viral targets of human miRNA, our analysis showed that the P1 region of the EV71 genome carries two putative hsa-miR-296-5p binding sites (nt 2115 to 2135 and nt 2896 to 2920) ( Fig. 4A and B).…”

The MicroRNA miR-199a-5p Down-regulation Switches on Wound Angiogenesis by Derepressing the v-ets Erythroblastosis Virus E26 Oncogene Homolog 1-Matrix Metalloproteinase-1 Pathway

“…miR-199a-5p Directly Targets Ets-1 by Interacting with the 3Ј UTR-To delineate the mechanisms underlying the angiostatic effect, bioinformatics analyses were performed to investigate the possible direct target using algorithms including Targetscan (22), Pictar (23), MiRanda (22), and miRDB (24). In silico analysis revealed that Ets-1 3Ј-UTR contains a highly conserved binding site at positions 2708 -2714 for miR-199a-5p ( Fig.…”