Genome-wide survey of rice microRNAs and microRNA–target pairs in the root of a novel auxin-resistant mutant
Genome-wide survey of rice microRNAs and microRNA–target pairs in the root of a novel auxin-resistant mutant
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DOI：
10.1007/s00425-009-0994-3
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发表时间：
2009-08
期刊：
影响因子：
4.3
通讯作者：
Y. Meng;Fangliang Huang;Qingyun Shi;Jun-Xia Cao;Dijun Chen;Jinwei Zhang;J. Ni;Ping Wu;Ming Chen
中科院分区：
文献类型：
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作者：
Y. Meng;Fangliang Huang;Qingyun Shi;Jun-Xia Cao;Dijun Chen;Jinwei Zhang;J. Ni;Ping Wu;Ming Chen
生长素是植物体内的一种中枢激素，而生长素反应因子(ARF)是生长素早期反应的关键调节因子。MicroRNAs(MiRNAs)在生长素信号转导中起着重要作用，但人们对miRNAs和生长素信号转导蛋白编码基因(如ARF)之间的调控网络的了解仍然有限。在这项研究中，我们使用了一个新的具有生长素抗性的水稻突变体，利用基因芯片技术研究了miRNA的表达模式。与野生型相比，突变体中的许多miRNAs对生长素的敏感性降低，这与突变体的生长素抗性表型一致。Northern印迹进一步证实了突变体中四个表达模式发生显著变化的miRNAs，这支持了我们的微阵列数据。聚类分析发现在根中发现了一些新的生长素敏感的miRNAs。对miRNA复制和表达模式的分析表明，miRNAs和蛋白质编码基因之间存在进化保守。MiRNA启动子分析表明，大多数植物miRNAs可能与其他由RNA聚合酶II转录的非植物真核基因具有相似的转录机制。生长素反应元件被证明更多地存在于生长素相关的miRNA启动子中。对miRNA和编码蛋白质的基因表达数据集的比较分析发现了许多相互表达的miRNA-靶点对，这可能为miRNA下游分析提供一些线索。基于这些发现，我们还提出了miRNA(S)和ARF(S)之间的反馈电路。这些结果可以作为进一步深入研究植物miRNAs参与生长素信号转导的基础。
Auxin is one of the central hormones in plants, and auxin response factor (ARF) is a key regulator in the early auxin response. MicroRNAs (miRNAs) play an essential role in auxin signal transduction, but knowledge remains limited about the regulatory network between miRNAs and protein-coding genes (e.g. ARFs) involved in auxin signalling. In this study, we used a novel auxin-resistant rice mutant with plethoric root defects to investigate the miRNA expression patterns using microarray analysis. A number of miRNAs showed reduced auxin sensitivity in the mutant compared with the wild type, consistent with the auxin-resistant phenotype of the mutant. Four miRNAs with significantly altered expression patterns in the mutant were further confirmed by Northern blot, which supported our microarray data. Clustering analysis revealed some novel auxin-sensitive miRNAs in roots. Analysis of miRNA duplication and expression patterns suggested the evolutionary conservation between miRNAs and protein-coding genes. MiRNA promoter analysis suggested the possibility that most plant miRNAs might share the similar transcriptional mechanisms with other non-plant eukaryotic genes transcribed by RNA polymerase II. Auxin response elements were proved to be more frequently present in auxin-related miRNA promoters. Comparative analysis of miRNA and protein-coding gene expression datasets uncovered many reciprocally expressed miRNA–target pairs, which could provide some hints for miRNA downstream analysis. Based on these findings, we also proposed a feedback circuit between miRNA(s) and ARF(s). The results presented here could serve as the basis for further in-depth studies of plant miRNAs involved in auxin signalling.