Conservation and divergence of plant microRNA genes
Conservation and divergence of plant microRNA genes
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DOI：
10.1111/j.1365-313x.2006.02697.x
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发表时间：
2006-04-01
期刊：
影响因子：
7.2
通讯作者：
Anderson, TA
中科院分区：
文献类型：
--
作者：
Zhang, BH;Pan, XP;Anderson, TA
MicroRNA（miRNA）是一类新发现的非编码小RNA，在转录后基因调控中发挥着重要作用。所有的miRNAs都具有相似的二级发夹结构，其中许多在进化上是保守的。这表明了一种预测其他物种中新的miRNA直系同源物或同源物存在的强有力的方法。我们开发了一个全面的战略，以确定新的miRNA同源物，挖掘可用的EST库。从600多万个植物EST序列中共鉴定出481个miRNAs，分属于71种不同植物的37个miRNAs家族。EST和蛋白质数据库也阐明了EST预测的miRNAs的潜在靶点，为这些miRNAs在给定植物物种中的真实的存在提供了额外的证据。一些植物miRNA在物理上聚集在一起，这表明这些miRNA具有相似的基因表达模式，并作为多顺反子一起转录，如在动物miRNA中观察到的那样。尿嘧啶核苷酸在5'成熟miRNA的第一位置中占优势。我们的研究结果表明，许多miRNA家族在所有主要的植物谱系中是进化保守的，包括苔藓，裸子植物，单子叶植物和真双子叶植物。此外，发现的miRNAs的数量与可用EST的数量直接相关，而与拟南芥的进化相关性无关，表明miRNAs是保守的，在这些miRNAs存在或不存在的情况下几乎不存在系统发育信号。miRNAs对基因表达的调控似乎存在于植物进化的最早阶段，并且在超过4.25亿年的时间里一直受到严格的限制（功能上）。
MicroRNA (miRNA) is one class of newly identified, small, non-coding RNAs that play versatile and important roles in post-transcriptional gene regulation. All miRNAs have similar secondary hairpin structures; many of these are evolutionarily conserved. This suggests a powerful approach to predict the existence of new miRNA orthologs or homologs in other species. We developed a comprehensive strategy to identify new miRNA homologs by mining the repository of available ESTs. A total of 481 miRNAs, belonging to 37 miRNA families in 71 different plant species, were identified from more than 6 million EST sequences in plants. The potential targets of the EST-predicted miRNAs were also elucidated from the EST and protein databases, providing additional evidence for the real existence of these miRNAs in the given plant species. Some plant miRNAs were physically clustered together, suggesting that these miRNAs have similar gene expression patterns and are transcribed together as a polycistron, as observed among animal miRNAs. The uracil nucleotide is dominant in the first position of 5' mature miRNAs. Our results indicate that many miRNA families are evolutionarily conserved across all major lineages of plants, including mosses, gymnosperms, monocots and eudicots. Additionally, the number of miRNAs discovered was directly related to the number of available ESTs and not to evolutionary relatedness to Arabidopsis thaliana, indicating that miRNAs are conserved and little phylogenetic signal exists in the presence or absence of these miRNAs. Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years.