Identification and characterization of new plant microRNAs using EST analysis
Identification and characterization of new plant microRNAs using EST analysis
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DOI：
10.1038/sj.cr.7290302
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发表时间：
2005-05
期刊：
影响因子：
44.1
通讯作者：
Baohong Zhang;Xiaoping Pan;Qing-lian Wang;G. Cobb;T. Anderson
中科院分区：
文献类型：
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作者：
Baohong Zhang;Xiaoping Pan;Qing-lian Wang;G. Cobb;T. Anderson
75种已知的植物microRNA（miRNAs）根据其基因序列的一致性被分为14个家族。通过BLAST算法将所有先前已知的拟南芥miRNAs与GenBank的植物EST数据库进行比较，在GenBank EST数据库中发现了总共18，694个植物表达序列标签（EST）。在去除具有高数目（超过2个）错配核苷酸的EST序列后，总共鉴定出812个EST重叠群。使用mFold软件对812个EST序列的RNA二级结构进行预测和评分后，在60种植物中鉴定出338种新的潜在miRNA。miRNAs广泛存在。一些microRNA在植物界中可能高度保守，它们可能在非常早期的进化中具有相同的祖先。在许多植物物种中，大多数miRNA没有核苷酸取代。一些新发现的潜在miRNAs可能受到环境生物和非生物胁迫的诱导和调节。有些可能优先在特定组织中表达，并受发育转换的调节。这些发现表明，EST分析是一个很好的替代策略，用于识别新的miRNA候选者，它们的靶标和其他基因。大量的miRNAs存在于不同的植物物种中，在植物的发育转换、植物对环境非生物和生物胁迫的响应以及信号转导中发挥重要作用。环境胁迫和发育转换可能是植物miRNAs合成和调控的信号。一个模型的miRNA诱导和表达，并通过miRNA的基因调控进行了假设。
Seventy-five previously known plant microRNAs (miRNAs) were classified into 14 families according to their gene sequence identity. A total of 18,694 plant expressed sequence tags (EST) were found in the GenBank EST databases by comparing all previously known Arabidopsis miRNAs to GenBank's plant EST databases with BLAST algorithms. After removing the EST sequences with high numbers (more than 2) of mismatched nucleotides, a total of 812 EST contigs were identified. After predicting and scoring the RNA secondary structure of the 812 EST sequences using mFold software, 338 new potential miRNAs were identified in 60 plant species. miRNAs are widespread. Some microRNAs may highly conserve in the plant kingdom, and they may have the same ancestor in very early evolution. There is no nucleotide substitution in most miRNAs among many plant species. Some of the new identified potential miRNAs may be induced and regulated by environmental biotic and abiotic stresses. Some may be preferentially expressed in specific tissues, and are regulated by developmental switching. These findings suggest that EST analysis is a good alternative strategy for identifying new miRNA candidates, their targets, and other genes. A large number of miRNAs exist in different plant species and play important roles in plant developmental switching and plant responses to environmental abiotic and biotic stresses as well as signal transduction. Environmental stresses and developmental switching may be the signals for synthesis and regulation of miRNAs in plants. A model for miRNA induction and expression, and gene regulation by miRNA is hypothesized.