MetaMirClust: Discovery of miRNA cluster patterns using a data-mining approach
MetaMirClust: Discovery of miRNA cluster patterns using a data-mining approach
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DOI：
10.1016/j.ygeno.2012.06.007
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发表时间：
2012-09-01
期刊：
影响因子：
4.4
通讯作者：
Lin, Wen-Chang
中科院分区：
文献类型：
--
作者：
Chan, Wen-Ching;Ho, Meng-Ru;Lin, Wen-Chang
最近对ncRNA的全基因组调查显示，相当一部分miRNA基因可能形成簇。然而，成簇的miRNAs的进化和生物学功能的影响仍然是难以捉摸的。本研究通过对不同最大miRNA间距（MID）下的miRNA基因进行聚类分析，利用计算算法揭示后生动物中这些聚类的miRNA基因的进化保守模式。例如，在9个选定的物种中，总共15-35%的已知和预测的miRNA基因在1 kb至50 kb的MID范围内构成簇。有趣的是，在56个后生动物基因组中的37个后生动物miRNA簇中，有33个与它们的上游/下游相邻的蛋白质编码基因共保守。同时，在mir-133-1簇中，miR-1和miR-133 a的共表达模式已被实验证实。因此，MetaMirClust数据库为生物学家提供了一个有用的生物信息资源，以促进对miRNA簇的组成及其进化模式的高级查询。(C)2012 Elsevier Inc. All rights reserved.
Recent genome-wide surveys on ncRNA have revealed that a substantial fraction of miRNA genes is likely to form clusters. However, the evolutionary and biological function implications of clustered miRNAs are still elusive. After identifying clustered miRNA genes under different maximum inter-miRNA distances (MIDs), this study intended to reveal evolution conservation patterns among these clustered miRNA genes in metazoan species using a computation algorithm. As examples, a total of 15-35% of known and predicted miRNA genes in nine selected species constitute clusters under the MIDs ranging from 1 kb to 50 kb. Intriguingly, 33 out of 37 metazoan miRNA clusters in 56 metazoan genomes are co-conserved with their up/down-stream adjacent protein-coding genes. Meanwhile, a co-expression pattern of miR-1 and miR-133a in the mir-133-1 cluster has been experimentally demonstrated. Therefore, the MetaMirClust database provides a useful bioinformatic resource for biologists to facilitate the advanced interrogations on the composition of miRNA clusters and their evolution patterns. (C) 2012 Elsevier Inc. All rights reserved.