VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets

Abid Qureshi,Nishant Thakur,Isha Monga,Anamika Thakur,Manoj Kumar

doi:10.1093/database/bau103

Abid Qureshi, Nishant Thakur + Show 3 more

Open Access

https://doi.org/10.1093/database/bau103

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Abstract

Viral microRNAs (miRNAs) regulate gene expression of viral and/or host genes to benefit the virus. Hence, miRNAs play a key role in host–virus interactions and pathogenesis of viral diseases. Lately, miRNAs have also shown potential as important targets for the development of novel antiviral therapeutics. Although several miRNA and their target repositories are available for human and other organisms in literature, but a dedicated resource on viral miRNAs and their targets are lacking. Therefore, we have developed a comprehensive viral miRNA resource harboring information of 9133 entries in three subdatabases. This includes 1308 experimentally validated miRNA sequences with their isomiRs encoded by 44 viruses in viral miRNA ‘VIRmiRNA’ and 7283 of their target genes in ‘VIRmiRtar’. Additionally, there is information of 542 antiviral miRNAs encoded by the host against 24 viruses in antiviral miRNA ‘AVIRmir’. The web interface was developed using Linux-Apache-MySQL-PHP (LAMP) software bundle. User-friendly browse, search, advanced search and useful analysis tools are also provided on the web interface. VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets. This database would enhance the understanding of viral/host gene regulation and may also prove beneficial in the development of antiviral therapeutics.Database URL: http://crdd.osdd.net/servers/virmirna

Highlights

RNA interference (RNAi) is a process in which short double stranded RNA inhibits gene expression of complementary target sequence
VIRmiRNA subdatabase has information of 1308 viral miRNA including 538 isomiRs sequences that belong to 44 viruses infecting a range of host organisms, namely human (17 viruses), other mammals (16 viruses), birds (7 viruses), invertebrates (3 viruses) and plants (1 virus)
It includes a maximum of 287 miRNAs of Pseudorabies virus (PRV) followed by 111 miRNAs of Rhesus lymphocryptovirus (RLCV) and miRNAs of other important viruses like Epstein–Barr virus (EBV), Herpes simplex virus (HSV) and Duck enteritis virus (DEV) etc. (Supplementary Table S1)

Summary

Introduction

RNA interference (RNAi) is a process in which short double stranded RNA inhibits gene expression of complementary target sequence. MiRNAs are short double stranded 19–23 nucleotides long antisense molecules, which are endogenously produced and processed [4, 5]. They function as regulators of gene expression by exhibiting perfect or nearly perfect base pairing with target mRNA, inhibiting its expression at post-transcriptional level by either mRNA degradation or translational repression [6, 7]. Subsequent research indicated that more than 30% of human protein-coding genes are regulated by miRNAs [9]

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