Zhang Baohong, Pan Xiaoping, Cannon Charles H, Cobb George P, Anderson Todd A
The Institute of Environmental and Human Health (TIEHH), and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409-1163, USA.
Plant J. 2006 Apr;46(2):243-59. doi: 10.1111/j.1365-313X.2006.02697.x.
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.
微小RNA（miRNA）是一类新发现的小的非编码RNA，在转录后基因调控中发挥着多方面的重要作用。所有的miRNA都具有相似的二级发夹结构；其中许多在进化上是保守的。这提示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有效方法。我们开发了一种综合策略，通过挖掘可用EST文库来鉴定新的miRNA同源物。从植物中超过600万个EST序列中，共鉴定出属于71种不同植物中37个miRNA家族的481个miRNA。还从EST和蛋白质数据库中阐明了EST预测的miRNA的潜在靶标，为这些miRNA在特定植物物种中的真实存在提供了额外证据。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，并作为一个多顺反子一起转录，这与动物miRNA的情况类似。尿嘧啶核苷酸在5'成熟miRNA的第一位占主导地位。我们的结果表明，许多miRNA家族在植物的所有主要谱系中都是进化保守的，包括苔藓植物、裸子植物、单子叶植物和双子叶植物。此外，发现的miRNA数量与可用EST的数量直接相关，而与与拟南芥的进化关系无关，这表明miRNA是保守的，并且在这些miRNA的存在或不存在方面几乎没有系统发育信号。miRNA对基因表达的调控似乎在植物进化的最早阶段就已存在，并且在功能上已经受到严格限制超过4.25亿年。
