Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
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DOI：
10.1371/journal.pbio.0040143
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发表时间：
2006-05
期刊：
影响因子：
9.8
通讯作者：
Benfey PN
中科院分区：
文献类型：
--
作者：
Levesque MP;Vernoux T;Busch W;Cui H;Wang JY;Blilou I;Hassan H;Nakajima K;Matsumoto N;Lohmann JU;Scheres B;Benfey PN
干细胞在器官发生过程中的作用是发育生物学中的一个关键问题。转录因子短根(Short-Root，SHR)是拟南芥根发育过程中的一个重要组成部分，它既调节根干细胞生态位的指定，又调节部分干细胞的分化潜能。为了全面了解SHR途径，我们使用了一种称为荟萃分析的统计方法，结合了几个微阵列实验的结果，测量了调节SHR活性后整体表达谱的变化。Meta分析首先被用来确定SHR的直接靶点，方法是结合由其内源启动子异位表达驱动的SHR的诱导形式的结果，然后进行细胞分类和突变体与野生型根的比较。我们确定了SHR的八个假定的直接靶点，所有的表达模式都包含了天然SHR表达结构域的子集。SHR直接调控的进一步证据来自于体内SHR与8个假定靶点中的4个的启动子区域的结合。根据几个直接靶点的表达模式预测了SHR在血管圆柱体中的新作用，并用独立的标记进行了证实。随后使用荟萃分析方法对SHR的间接目标进行了全球调查。我们的分析表明，SHR途径不仅通过一个大型的转录调控网络调节根的发育，而且还通过激素途径和使用受体样激酶的信号途径来调节根的发育。综上所述，我们的结果不仅确定了SHR通路中的第一个节点和SHR在血管组织发育中的新功能，而且揭示了这一发育通路的整体结构。结合几个微阵列实验结果的荟萃分析揭示了转录因子短根在维管组织发育中的新功能。
Stem cell function during organogenesis is a key issue in developmental biology. The transcription factor SHORT-ROOT (SHR) is a critical component in a developmental pathway regulating both the specification of the root stem cell niche and the differentiation potential of a subset of stem cells in the Arabidopsis root. To obtain a comprehensive view of the SHR pathway, we used a statistical method called meta-analysis to combine the results of several microarray experiments measuring the changes in global expression profiles after modulating SHR activity. Meta-analysis was first used to identify the direct targets of SHR by combining results from an inducible form of SHR driven by its endogenous promoter, ectopic expression, followed by cell sorting and comparisons of mutant to wild-type roots. Eight putative direct targets of SHR were identified, all with expression patterns encompassing subsets of the native SHR expression domain. Further evidence for direct regulation by SHR came from binding of SHR in vivo to the promoter regions of four of the eight putative targets. A new role for SHR in the vascular cylinder was predicted from the expression pattern of several direct targets and confirmed with independent markers. The meta-analysis approach was then used to perform a global survey of the SHR indirect targets. Our analysis suggests that the SHR pathway regulates root development not only through a large transcription regulatory network but also through hormonal pathways and signaling pathways using receptor-like kinases. Taken together, our results not only identify the first nodes in the SHR pathway and a new function for SHR in the development of the vascular tissue but also reveal the global architecture of this developmental pathway. Meta-analysis to combine the results of several microarray experiments reveals a new function for the transcription factor SHORT-ROOT in the development of vascular tissue.
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