A reversed framework for the identification of microRNA-target pairs in plants
A reversed framework for the identification of microRNA-target pairs in plants
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用于识别植物中 microRNA-靶标对的反向框架
DOI：
10.1093/bib/bbs040
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发表时间：
2013-05-01
影响因子：
9.5
通讯作者：
Meng, Yijun
中科院分区：
文献类型：
--
作者：
Shao, Chaogang;Chen, Ming;Meng, Yijun
大多数植物microrna （mirna）通过靶切割来完成它们的抑制调控。目标转录本上的切片位点可以通过测序3'-裂解残基来绘制，称为降解测序。mirna与靶点之间的高度序列互补性极大地促进了植物mirna靶点预测工具的发展。然后对预测结果进行基于降解组测序数据的验证，通过该验证提取了许多mirna -靶标相互作用。然而，在使用这种正向方法时，一些缺点是不可避免的。从本质上讲，在进行靶标预测和验证之前，应该先获得已知的植物mirna列表。这成为发现新的mirna及其靶标的障碍。在回顾了目前可用的植物mirna -靶标对反向识别算法之后，我们使用了一个新建立的具有可调参数的框架进行了案例研究。在这个工作流程中，建议整合降解组和富含ARGONAUTE 1的小RNA测序数据，进行相对全面和可靠的搜索。此外，还使用了BLAST、靶图和RNA二级结构预测等计算算法。结果表明，在揭示植物中mirna -靶标相互作用方面，反向方法具有普遍的实用性。
Most plant microRNAs (miRNAs) perform their repressive regulation through target cleavages. The resulting slicing sites on the target transcripts could be mapped by sequencing of the 3'-cleavage remnants, called degradome sequencing. The high sequence complementarity between miRNAs and their targets has greatly facilitated the development of the target prediction tools for plant miRNAs. The prediction results were then subjected to degradome sequencing data-based validation, through which numerous miRNA-target interactions have been extracted. However, some drawbacks are unavoidable when using this forward approach. Essentially, a known list of plant miRNAs should be obtained in advance of target prediction and validation. This becomes an obstacle to discover novel miRNAs and their targets. Here, after reviewing the current available algorithms for reverse identification of miRNA-target pairs in plants, a case study was performed by using a newly established framework with adjustable parameters. In this workflow, integration of degradome and ARGONAUTE 1-enriched small RNA sequencing data was recommended to do a relatively comprehensive and reliable search. Besides, several computational algorithms such as BLAST, target plots and RNA secondary structure prediction were used. The results demonstrated the prevalent utility of the reversed approach for uncovering miRNA-target interactions in plants.