IN SILICO PREDICTION AND VALIDATION OF MICRORNAS FROM JAPANESE ENCEPHALITIS VIRUS (JEV)
Keywords:
MicroRNAs, Japanese encephalitis virus, Secondary structure prediction, MiPred, Genscan, Mirbase, RNApred, RNAfold, Mfold and minimum free energyAbstract
Objective: MicroRNAs are endogenous, small, single stranded, non coding RNAs having 19-25 nucleotides. These miRNAs are complementary to their target messenger RNAs that bind principally to its 3' un translated regions (3' UTRs). Small RNAs play crucial roles in the regulation of gene expression in many eukaryotes; therefore it is important to predict potential viral miRNAs which might be involved in an establishment of Japanese Encephalitis virus (JEV) disease. Different computational approaches and methods were used for predicting viral microRNAs from the JEV genome in this work.
Methods: In the present study, the use of genome-wide computational approach has been demonstrated to predict miRNAs and their target(s) in JEV genome. Two freely accessible softwares, MiPred and Genscan were used to predict the secondary structures of the potential miRNAs.
Results: In all, 36 miRNAs were predicted and characterized by conducting genome-wide homology search against all the reported miRNAs. These miRNAs were further validated by performing phylogenetic analyses and using statistical tools.Further, attempt was made to predict the 3′ untranslated regions of mRNAs from whole genome of JEV which may prove helpful in finding putative targets of these miRNAs.
Conclusion: This is the first study to identify and validate miRNAs in JEV which is an important step in identifying putative JEV miRNAs that utilize host cell machinery, and may play a crucial role in neuroinflammation and silencing of host genes, thus demonstrating the role of viral miRNAs in establishing viral pathogenesis.
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