Computational prediction of miRNAs in Arabidopsis thaliana
Computational prediction of miRNAs in Arabidopsis thaliana
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DOI：
10.1101/gr.2908205
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发表时间：
2005-01-01
期刊：
影响因子：
7
通讯作者：
Sundaresan, V
中科院分区：
文献类型：
--
作者：
Adai, A;Johnson, C;Sundaresan, V
microRNA（miRNAs）是动植物基因表达的转录后调节因子。比较基因组计算方法已被开发用于预测蠕虫、苍蝇和人类中的新miRNA。在这里，我们提出了一种新的单基因组方法检测拟南芥中的miRNA。这是通过使用称为findMiRNA的算法产生候选miRNA靶数据集来启动的，该算法预测候选前体序列内的潜在miRNA，这些候选前体序列在转录本内具有相应的靶位点。从这个数据集中，我们使用miRNA前体家族的特征性分歧模式来选择13个潜在的新miRNA进行实验验证，并发现至少8个候选miRNA可以检测到相应的小RNA。这些miRNAs中的一些的表达似乎受到发育控制。我们的研究结果是一致的想法，小RNA的目标涵盖了广泛的转录本，包括F-盒因子，泛素共轭，富含亮氨酸的重复蛋白，和代谢酶，和小RNA的调节可能是广泛的基因组。拟南芥基因组中的全部注释转录物已经通过findMiRNA进行了分析，以产生一个数据集，该数据集将能够识别针对任何靶基因的潜在miRNAs。
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in animals and plants. Comparative genomic computational methods have been developed to predict new miRNAs in worms, flies, and humans. Here, we present a novel single genome approach for the detection of miRNAs in Arabidopsis thaliana. This was initiated by producing a candidate miRNA-target data set using an algorithm called findMiRNA, which predicts potential miRNAs within candidate precursor sequences that have corresponding target sites within transcripts. From this data set, we used a characteristic divergence pattern of miRNA precursor families to select 13 potential new miRNAs for experimental verification, and found that corresponding small RNAs could be detected for at least eight of the candidate miRNAs. Expression of some of these miRNAs appears to be under developmental control. Our results are consistent with the idea that targets of miRNAs encompass a wide range of transcripts, including those for F-box factors, ubiquitin conjugases, Leucine-rich repeat proteins, and metabolic enzymes, and that regulation by miRNAs might be widespread in the genome. The entire set of annotated transcripts in the Arabidopsis genome has been run through findMiRNA to yield a data set that will enable identification of potential miRNAs directed against any target gene.