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Computational identification of microRNAs in Anatid herpesvirus 1 genome

Jun Xiang1, Anchun Cheng123*, Mingshu Wang123*, Shunchuan Zhang1, Dekang Zhu23, Renyong Jia123, Shun Chen123, Yi Zhou2, Xiaoyu Wang3 and Xiaoyue Chen23

Author Affiliations

1 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu city, Sichuan, 611130, People’s Republic of China

2 Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, 46 Xinkang Road, Ya’an, Sichuan, 625014, People’s Republic of China

3 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu city, Sichuan, 611130, People’s Republic of China

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Virology Journal 2012, 9:93  doi:10.1186/1743-422X-9-93

Published: 14 May 2012

Abstract

Background

MicroRNAs (miRNAs) are a group of short (~22 nt) noncoding RNAs that specifically regulate gene expression at the post-transcriptional level. miRNA precursors (pre-miRNAs), which are imperfect stem loop structures of ~70 nt, are processed into mature miRNAs by cellular RNases III. To date, thousands of miRNAs have been identified in different organisms. Several viruses have been reported to encode miRNAs.

Findings

Here, we extended the analysis of miRNA-encoding potential to the Anatid herpesvirus 1 (AHV-1). Using computational approaches, we found that AHV-1 putatively encodes 12 mature miRNAs. We then compared the 12 mature miRNAs candidates with the all known miRNAs of the herpesvirus family. Interestingly, the “seed sequences” (nt 2 to 8) of 2 miRNAs were predicted to have the high conservation in position and/or sequence with the 2 miRNAs of Marek’s disease virus type 1 (MDV-1). Additionally, we searched the targets from viral mRNAs.

Conclusions

Using computational approaches, we found that AHV-1 putatively encodes 12 mature miRNAs and 2 miRNAs have the high conservation with the 2 miRNAs of MDV-1. The result suggested that AHV-1 and MDV-1 should have closed evolutionary relation, which provides a valuable evidence of classification of AHV-1. Additionally, seven viral gene targets were found, which suggested that AHV-1 miRNAs could affect its own gene expression.

Keywords:
Anatid herpesvirus 1; microRNA; Conservation; Computational analyses