J. Appl. Environ. Biol. Sci., 4(8S)34-39, 2014 © 2014, TextRoad Publication ISSN: 2090-4274 Journal of Applied Environmental and Biological Sciences www.textroad.com * Corresponding Author: Ayaz Ahmad, Department of Biotechnology, Abdul Wali Khan University Mardan, Pakistan. Phone# 0092-937-542046, E-mail: ahdayazb5@awkum.edu.pk Computational Analysis Reveals Three Micro-RN as in Hepatitis A Virus Genome Ayaz Ahmad 1,#, *, Muhammad Bilal 2,# , Khalid Khan 2 , Waheed Ahmad 3 , Islam-Ud-Din 4 , Sajid Ali 1 , Amjad Iqbal 5 , And Muhammad Jaseem 6 1 Department of Biotechnology, Abdul Wali Khan University Mardan, Pakistan 2 Department of Chemistry, Islamia College University Peshawar, Pakistan 3 Department of Computer Science, Abdul Wali Khan University Mardan, Pakistan 4 Department of Environmental Sciences, International Islamic University Islamabad, Pakistan 5 Department of Agriculture, Abdul wali Khan University Mardan, Pakistan 6 Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Pakistan Received: September 1, 2014 Accepted: November 13, 2014 ABSTRACT Micro RNAs (miRNAs) are a class of endogenous non-coding RNAs, 19—25 nt in length, that play pivotal role in the regulation of gene expression by degrading the messenger RNAs of target genes in a sequence-specific manner. Dysregulation of miRNAs results in abnormal gene expression and has been linked to the initiation, advancement and maintenance of some human diseases. Recent studies show that genomes of both virus and host have the potential to encode miRNAs, which may be beneficial either for host or for virus. Hepatitis A is one of the liver inflammations, instigated by the hepatitis A virus (HAV). In this study we, for the first time, computationally identified miRNAs in HAV genome. Initial searches through VMir software extracted 7 sequences with potential hairpin-like structures from HAV genome. MiPred program confirmed 6 candidates as real pre-miRNA hairpin structures. After measurements of free energy and applying other parameters, we confirmed three mature miRNAs in HAV genome. These findings will not only help researchers to explore the role of these miRNAs in viral pathogenesis but also in developing novel antiviral therapies. KEYWORDS: MicroRNAs, miRNAs, Hepatitis, Hepatitis A Virus, HAV. INTRODUCTION MiRNAs, previously known as small temporal RNAs (stRNAs), represent a class of 19—25 nt long, endogenous RNA molecules that play a vital role in post-transcriptional regulation of gene expression by guiding the RNA induced silencing complex (RISC) to bind the messenger RNAs of target genes in a sequence-specific manner thereby causing their cleavage or translational repression [1-3]. These tiny molecules have been implicated in plethora of cellular processes including developmental timing, cell fate determination, neuronal plasticity, cholesterol metabolism, immune responses, apoptosis, cell cycle and tumorigenesis [4]. Lines of evidences suggest that miRNAs are embedded not only in the intergenic regions of genomes but also in protein coding genes [2]. MiRNAs are first transcribed as long transcripts known a primary miRNA (pri-miRNAs). One to several precursors of miRNA (pre-miRNAs) may be embedded inside each pri-miRNA transcript. Consequently, the nuclear RNase III enzyme, Drosha processes each primary miRNA into its constituents of 60—70 nt long precursors of miRNA which fold into an imperfect stem-loop structure(s) and acquire characteristic hairpin shape while still in the nucleus. The resultant miRNA precursors are transported to the cellular cytoplasm by the exportin-5. Here these precursors are further sliced into ~22 nt long duplexes under the action of RNase III Dicer enzyme [2]. The mature miRNA then enters the multiprotein RNA induced silencing complex (RISC). RISC then leads to either degradation or translational silencing of the target mRNA, which in turn depends on the extent of complementarity among the RISC bound micro RNA and target messenger RNA [1, 5]. Beside animals, plants and insects, many virus genomes have been reported to contain miRNAs [4]. These virus encoded miRNAs have been shown to play key roles in virus-host interactions by targeting both host and virus mRNAs of various important genes [4]. The Epstein–Barr virus (EBV) genome was shown to encode five miRNAs, each of which has not only the capability to regulate the expression of virus gene 34