Identification of homologous microRNAs in 56 animal genomes
Identification of homologous microRNAs in 56 animal genomes
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DOI：
10.1016/j.ygeno.2010.03.009
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发表时间：
2010-07-01
期刊：
影响因子：
4.4
通讯作者：
Lin, Wen-chang
中科院分区：
文献类型：
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作者：
Li, Sung-Chou;Chan, Wen-Ching;Lin, Wen-chang
MicroRNA (miRNA) 是大约 22 个核苷酸的内源性非蛋白质编码 RNA。已经在多种生物体中（通过计算和/或实验）鉴定出数千个 miRNA 基因，这表明 miRNA 基因已在物种之间广泛共享和分布。在这里，我们使用独特的 miRNA 序列模式扫描 56 个两侧对称动物物种的基因组序列，以首先定位候选 miRNA。然后提取以这些候选 miRNA 为中心的区域进行折叠并计算其二级结构的特征。使用支持向量机（SVM）作为分类器，结合这些特征，我们鉴定了额外的 13,091 个直系同源或旁系同源候选 pre-miRNA，以及它们相应的候选成熟 miRNA。使用茎环RT-PCR和深度测序方法在人体中对预测结果进行实验验证。青鳉和兔子。我们的预测流程可以快速有效地发现大量基因组中的同源 miRNA。 (C) 2010 Elsevier Inc. 保留所有权利。
MicroRNAs (miRNAs) are endogenous non-protein-coding RNAs of approximately 22 nucleotides. Thousands of miRNA genes have been identified (computationally and/or experimentally) in a variety of organisms, which suggests that miRNA genes have been widely shared and distributed among species. Here, we used unique miRNA sequence patterns to scan the genome sequences of 56 bilaterian animal species for locating candidate miRNAs first. The regions centered surrounding these candidate miRNAs were then extracted for folding and calculating the features of their secondary structure. Using a support vector machine (SVM) as a classifier combined with these features, we identified an additional 13,091 orthologous or paralogous candidate pre-miRNAs, as well as their corresponding candidate mature miRNAs. Stem-loop RT-PCR and deep sequencing methods were used to experimentally validate the prediction results in human. medaka and rabbit. Our prediction pipeline allows the rapid and effective discovery of homologous miRNAs in a large number of genomes. (C) 2010 Elsevier Inc. All rights reserved.