Integrative expression network analysis of microRNA and gene isoforms in sacred lotus
文献类型：期刊论文
| 作者 | Zhang,Yue1,2,3; Rahmani,Razgar Seyed4; Yang,Xingyu5; Chen,Jinming1,2; Shi,Tao1,2 |
| 刊名 | BMC Genomics
 |
| 出版日期 | 2020-06-25 |
| 卷号 | 21期号:1 |
| 关键词 | microRNA Transcript isoforms Co-expression network Sacred lotus |
| DOI | 10.1186/s12864-020-06853-y |
| 英文摘要 | AbstractBackgroundGene 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. |
| 语种 | 英语 |
| WOS记录号 | BMC:10.1186/S12864-020-06853-Y |
| 出版者 | BioMed Central |
| 源URL | [http://202.127.146.157/handle/2RYDP1HH/14362]  |
| 专题 | 中国科学院武汉植物园 |
| 通讯作者 | Chen,Jinming; Shi,Tao |
| 作者单位 | 1.Chinese Academy of Sciences; Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden 2.Chinese Academy of Sciences; Center of Conservation Biology, Core Botanical Gardens 3.University of Chinese Academy of Sciences 4.Ghent University; Department of Plant Biotechnology and Bioinformatics 5.Wuhan Institute of Landscape Architecture |
| 推荐引用方式 GB/T 7714 | Zhang,Yue,Rahmani,Razgar Seyed,Yang,Xingyu,et al. Integrative expression network analysis of microRNA and gene isoforms in sacred lotus[J]. BMC Genomics,2020,21(1). |
| APA | Zhang,Yue,Rahmani,Razgar Seyed,Yang,Xingyu,Chen,Jinming,&Shi,Tao.(2020).Integrative expression network analysis of microRNA and gene isoforms in sacred lotus.BMC Genomics,21(1). |
| MLA | Zhang,Yue,et al."Integrative expression network analysis of microRNA and gene isoforms in sacred lotus".BMC Genomics 21.1(2020). |
入库方式： OAI收割
来源：武汉植物园
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