Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice.
Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice.
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DOI：
10.6026/97320630009072
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发表时间：
2013
期刊：
影响因子：
1.9
通讯作者：
Bansal KC
中科院分区：
文献类型：
--
作者：
Smita S;Katiyar A;Pandey DM;Chinnusamy V;Archak S;Bansal KC
鉴定在不同组织和环境胁迫中共同表达的基因具有生物学意义，因为它们可能在类似的生物过程中发挥协调作用。使用转录组数据的共表达网络分析可以最好地识别具有相关表达模式的基因。在本研究中，我们分析了干旱胁迫下水稻根、叶和穗中基因表达的时空协调性，并利用WGCNA和Cytoscape构建了网络。共有2199个差异表达基因在至少三个或三个以上的组织中被鉴定，其中88个基因在干旱胁迫下的所有六个组织中具有协调表达谱。这88个高度协调的基因进一步在共表达网络中进行模块鉴定。根据主要的拓扑结构特征，我们鉴定了ABC转运蛋白、ATP结合蛋白、脱水蛋白、蛋白磷酸酶2C、LTPL153-酶抑制因子、磷脂酰乙醇胺结合蛋白、乳糖通透酶相关基因、NADP依赖的苹果酸酶等18个HUB基因，Motif富集分析表明，62%的协同表达基因启动子中含有Abre顺式元件。我们的结果表明，干旱胁迫介导的上调基因表达是通过依赖于ABA的信号通路在组织中协调的，至少对于本研究中确定的基因亚集来说是这样，而下调似乎受到组织特有途径的调节。
Identification of genes that are coexpressed across various tissues and environmental stresses is biologically interesting, since they may play coordinated role in similar biological processes. Genes with correlated expression patterns can be best identified by using coexpression network analysis of transcriptome data. In the present study, we analyzed the temporal-spatial coordination of gene expression in root, leaf and panicle of rice under drought stress and constructed network using WGCNA and Cytoscape. Total of 2199 differentially expressed genes (DEGs) were identified in at least three or more tissues, wherein 88 genes have coordinated expression profile among all the six tissues under drought stress. These 88 highly coordinated genes were further subjected to module identification in the coexpression network. Based on chief topological properties we identified 18 hub genes such as ABC transporter, ATP-binding protein, dehydrin, protein phosphatase 2C, LTPL153 - Protease inhibitor, phosphatidylethanolaminebinding protein, lactose permease-related, NADP-dependent malic enzyme, etc. Motif enrichment analysis showed the presence of ABRE cis-elements in the promoters of > 62% of the coordinately expressed genes. Our results suggest that drought stress mediated upregulated gene expression was coordinated through an ABA-dependent signaling pathway across tissues, at least for the subset of genes identified in this study, while down regulation appears to be regulated by tissue specific pathways in rice.