Archak Sunil, Nagaraju J
Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500076, India.
Genomics Proteomics Bioinformatics. 2007 Dec;5(3-4):196-206. doi: 10.1016/S1672-0229(08)60007-8.
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.
生物信息学方法补充了对植物miRNA靶标的实验研究。我们对水稻（Oryza sativa）转录组进行了全面的计算分析，以生成一份推定的miRNA靶标的综合清单。我们的预测结果（684个独特转录本）表明，水稻miRNA介导多种功能的调控，包括转录（41%）、催化（28%）、结合（18%）和转运活性（11%）。在预测的靶标中，61.7%的命中位于编码区，近72%的靶标有单个miRNA命中。该研究预测了34个miRNA的70多个新靶标，这些miRNA可能调控应激反应、催化和结合等功能。据观察，超过一半（55%）的靶标在籼稻和粳稻之间是保守的。发现31个miRNA家族的成员在水稻和至少一种其他禾本科成员之间拥有保守靶标。约44%的独特靶标在两种不同的miRNA预测算法之间是相同的。这种跨物种保守性和算法一致性程度为该研究预测的水稻miRNA靶标清单提供了可信度。
