Integrative expression network analysis of microRNA and gene isoforms in sacred lotus
Integrative expression network analysis of microRNA and gene isoforms in sacred lotus
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圣莲中 microRNA 和基因亚型的整合表达网络分析
DOI：
10.1186/s12864-020-06853-y
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发表时间：
2020
期刊：
影响因子：
4.4
通讯作者：
Shi Tao
中科院分区：
文献类型：
--
作者：
Zhang Yue;Rahmani Razgar Seyed;Yang Xingyu;Chen Jinming;Shi Tao
背景基因表达是一个复杂的过程，受多种分子机制的调控，如miRNA介导的基因抑制和前体mRNA的选择性剪接。然而，具有不同剪接异构体的miRNA之间的相互作用的协调以及剪接异构体响应于不同细胞环境的变化在植物中很大程度上未被探索。在这项研究中，我们分析了miRNA和mRNA转录组从莲（莲），一个重要的经济开花植物。ResultsThrough RNA-seq分析的miRNA和它们的靶基因（异构体）之间的6个组织，大多数miRNA的表达似乎是负相关的，其目标，并倾向于组织特异性。此外，我们的研究结果表明，在一个与叶高度相关的共表达模块中，miRNAs和hub基因亚型之间的优先相互作用。有趣的是，对于许多基因，它们相应的异构体被分配到不同的共表达模块，并且它们表现出更趋异的mRNA结构，包括miRNA结合位点的存在和不存在，这表明许多异构体的功能差异是由结构和表达差异引起的。进一步的功能富集分析表明，miRNA通过调控植物的转录相关通路基因参与了荷花生长发育的调控。ConclusionsTogether，我们对miRNA和mRNA转录组的综合分析阐明了miRNA与不同剪接异构体之间相互作用的协调性，并突出了荷花中同一位点的许多转录异构体的功能差异。
BackgroundGene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant.ResultsThrough RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets and tend to be tissue-specific. Further, our results showed that preferential interactions between miRNAs and hub gene isoforms in one coexpression module which is highly correlated with leaf. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes.ConclusionsTaken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.