title: Identification of new stress-induced microRNA and their targets in wheat using computational approach.
abstract: MicroRNAs (miRNAs) are a class of short endogenous non-coding small RNA molecules of about 18-22 nucleotides in length. Their main function is to downregulate gene expression in different manners like translational repression, mRNA cleavage and epigenetic modification. Computational predictions have raised the number of miRNAs in wheat significantly using an EST based approach. Hence, a combinatorial approach which is amalgamation of bioinformatics software and perl script was used to identify new miRNA to add to the growing database of wheat miRNA. Identification of miRNAs was initiated by mining the EST (Expressed Sequence Tags) database available at National Center for Biotechnology Information. In this investigation, 4677 mature microRNA sequences belonging to 50 miRNA families from different plant species were used to predict miRNA in wheat. A total of five abiotic stress-responsive new miRNAs were predicted and named Ta-miR5653, Ta-miR855, Ta-miR819k, Ta-miR3708 and Ta-miR5156. In addition, four previously identified miRNA, i.e., Ta-miR1122, miR1117, Ta-miR1134 and Ta-miR1133 were predicted in newly identified EST sequence and 14 potential target genes were subsequently predicted, most of which seems to encode ubiquitin carrier protein, serine/threonine protein kinase, 40S ribosomal protein, F-box/kelch-repeat protein, BTB/POZ domain-containing protein, transcription factors which are involved in growth, development, metabolism and stress response. Our result has increased the number of miRNAs in wheat, which should be useful for further investigation into the biological functions and evolution of miRNAs in wheat and other plant species.
authors.affiliation: Plant Biotechnology; Directorate of Wheat Research; Karnal, India; Department of Biotechnology; Birla Institute of Technology; Mesra, India.
authors.forename: Bharati
authors.initials: B
authors.lastname: Pandey
authors.forename: Om Prakash
authors.initials: OP
authors.lastname: Gupta
authors.forename: Dev Mani
authors.initials: DM
authors.lastname: Pandey
authors.forename: Indu
authors.initials: I
authors.lastname: Sharma
authors.forename: Pradeep
authors.initials: P
authors.lastname: Sharma
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D016415:Sequence Alignment; D013312:Stress, Physiological / Q000235:genetics*; D014908:Triticum / Q000235:genetics* / Q000502:physiology*
chemical_list: D035683:MicroRNAs
keywords: EST; computational prediction; miRNA; target prediction; wheat