title: Computational prediction of rice (Oryza sativa) miRNA targets.
abstract: Bioinformatic approaches have complemented experimental efforts to inventorize plant miRNA targets. We carried out global computational analysis of rice (Oryza sativa) transcriptome to generate a comprehensive list of putative miRNA targets. Our predictions (684 unique transcripts) showed that rice miRNAs mediate regulation of diverse functions including transcription (41%), catalysis (28%), binding (18%), and transporter activity (11%). Among the predicted targets, 61.7% hits were in coding regions and nearly 72% targets had a solitary miRNA hit. The study predicted more than 70 novel targets of 34 miRNAs putatively regulating functions like stress-response, catalysis, and binding. It was observed that more than half (55%) of the targets were conserved between O. sativa indica and O. sativa japonica. Members of 31 miRNA families were found to possess conserved targets between rice and at least one of other grass family members. About 44% of the unique targets were common between two dissimilar miRNA prediction algorithms. Such an extent of cross-species conservation and algorithmic consensus confers confidence in the list of rice miRNA targets predicted in this study.
authors.affiliation: Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500076, India.
authors.forename: Sunil
authors.initials: S
authors.lastname: Archak
authors.forename: J
authors.initials: J
authors.lastname: Nagaraju
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D023281:Genomics / Q000706:statistics & numerical data; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008957:Models, Genetic; D012275:Oryza / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D006109:Poaceae / Q000145:classification / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D013045:Species Specificity
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant