Toward microRNA-mediated gene regulatory networks in plants
Toward microRNA-mediated gene regulatory networks in plants
复制标题
植物中 microRNA 介导的基因调控网络
DOI：
10.1093/bib/bbq091
复制
发表时间：
2011-11-01
影响因子：
9.5
通讯作者：
Chen, Ming
中科院分区：
文献类型：
--
作者：
Meng, Yijun;Shao, Chaogang;Chen, Ming
目前，植物microRNA （miRNA）的研究成果令人鼓舞。分子克隆和功能解析极大地促进了我们对这种小RNA物种的认识。作为最终目标之一，许多研究都致力于全面了解mirna介导的植物基因调控网络。许多生物信息学工具胜任网络分析已经可用。然而，网络建设最重要的一点是在充分的实验数据基础上获得可靠的分析结果。在这里，我们介绍了一个通用的工作流来检索和分析作为网络构建基石的所需数据集。对于miRNA基因的上游分析，需要对miRNA启动子的序列特征进行表征。转录因子（TFs）与miRNA基因之间的调控关系有待进一步研究。对于下游部分，我们强调高通量降解组测序数据对于真正的mirna -靶对鉴定特别有用。miRNA靶点的功能表征对于深入了解某些miRNA介导的途径至关重要。对于mirna本身，本文讨论了其器官或组织特异性表达模式和自我调节机制的研究。此外，还需要进行详尽的文献挖掘，以进一步支持或完善已建立的网络。希望所介绍的miRNA介导的网络构建框架是及时和有用的，并能在miRNA研究领域激发更多的研究努力。
Current achievements in plant microRNA (miRNA) research area are inspiring. Molecular cloning and functional elucidation have greatly advanced our understanding of this small RNA species. As one of the ultimate goals, many research efforts devoted to draw a comprehensive view of miRNA-mediated gene regulatory networks in plants. Numerous bioinformatics tools competent for network analysis have been available. However, the most important point for network construction is to obtain reliable analytical results based on sufficient experimental data. Here, we introduced a general workflow to retrieve and analyze the desired data sets that serve as the cornerstones for network construction. For the upstream analyses of miRNA genes, the sequence feature of miRNA promoters should be characterized. And, regulatory relationships between transcription factors (TFs) and miRNA genes need to be investigated. For the downstream part, we emphasized that the high-throughput degradome sequencing data were especially useful for genuine miRNA-target pair identification. Functional characterization of the miRNA targets is essential to provide deep biological insights into certain miRNA-mediated pathways. For miRNAs themselves, studies on their organ- or tissue-specific expression patterns and the mechanism of self-regulation were discussed. Besides, exhaustive literature mining is required to further support or improve the established networks. It is desired that the introduced framework for miRNA-mediated network construction is timely and useful and could inspire more research efforts in the miRNA research area.