Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants: a bioinformatics workflow
Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants: a bioinformatics workflow
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研究植物中新生核转录本的 microRNA 介导的调控：生物信息学工作流程
DOI：
10.1093/bib/bbx069
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发表时间：
2018
影响因子：
9.5
通讯作者：
Meng Yijun
中科院分区：
文献类型：
--
作者：
Yu Dongliang;Tang Zhonghai;Shao Chaogang;Ma Xiaoxia;Xiang Taihe;Fan Zhihong;Wang Huizhong;Meng Yijun
大多数microRNAs(MiRNAs)通过转录后靶标衰退或翻译抑制发挥其调节作用。对于植物和动物，这些调控事件以前被认为发生在细胞质中，因为观察到成熟的miRNAs被输出到细胞质中，用于ArgAerte(AGO)的装载和随后的靶结合。最近，在动物细胞中发现了与AGO相关的miRNAs的核输入和作用的证据越来越多，这一观点受到了挑战。据报道，该工厂的miRNAs也采用了核局部调控模式。然而，仍缺乏证据表明miRNA介导的调控在植物细胞核中的普遍性和保守性。在这里，我们介绍了一种生物信息学工作流程，用于全基因组研究miRNA引导的、基于切割的新生核转录调控。在PmiRNTSA(植物microRNA介导的新生转录切片分析仪)工具包的帮助下，植物生物学家可以全面搜索位于目标转录本的内含子或外显子-内含子/内含子-外显子连接内的miRNA切片位点，这是由降解组测序数据支持的。这些结果使研究人员能够检查特定植物物种的miRNAs的共转录调控模型。此外，还对两个模式植物的外显子-内含子/内含子-外显子连接中的片断位置进行了个案研究。通过一个案例研究，验证了该工作流的可行性和可靠性。总之，我们希望这项工作能够激发更多的创新研究努力，以扩大目前对植物中miRNA作用模式的理解。
Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO) loading and subsequent target binding. Recently, this notion was challenged by increasing pieces of evidence in the animal cells that uncovered the nuclear importation and action of the AGO-associated miRNAs. The nuclear-localized regulatory mode was also reported for the plant miRNAs. However, evidence is still lacking to show the universality and conservation of the miRNA-mediated regulation in the plant nuclei. Here, we introduced a bioinformatics workflow for genome-wide investigation of miRNA-guided, cleavage-based regulation of the nascent nuclear transcripts. Facilitated by the tool package PmiRNTSA (Plant microRNA-mediated nascent transcript slicing analyzer), plant biologists could perform a comprehensive search for the miRNA slicing sites located within the introns or the exon-intron/intron-exon junctions of the target transcripts, which are supported by degradome sequencing data. The results enable the researchers to examine the co-transcriptional regulatory model of the miRNAs for a specific plant species. Moreover, a case study was performed to search for the slicing sites located within the exon-intron/intron-exon junctions in two model plants. A case study was performed to show the feasibility and reliability of our workflow. Together, we hope that this work could inspire much more innovative research efforts to expand the current understanding of the miRNA action modes in plants.