Levesque Mitchell P, Vernoux Teva, Busch Wolfgang, Cui Hongchang, Wang Jean Y, Blilou Ikram, Hassan Hala, Nakajima Keiji, Matsumoto Noritaka, Lohmann Jan U, Scheres Ben, Benfey Philip N
Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA.
PLoS Biol. 2006 May;4(5):e143. doi: 10.1371/journal.pbio.0040143. Epub 2006 May 2.
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.
器官发生过程中的干细胞功能是发育生物学中的一个关键问题。转录因子SHORT-ROOT（SHR）是调控拟南芥根中干细胞龛的特化以及一部分干细胞分化潜能的发育途径中的关键组成部分。为了全面了解SHR途径，我们使用了一种称为元分析的统计方法，将几个微阵列实验的结果结合起来，这些实验测量了调节SHR活性后全局表达谱的变化。元分析首先通过结合由其内源启动子驱动的诱导型SHR、异位表达的结果，随后进行细胞分选以及突变体与野生型根的比较，来鉴定SHR的直接靶标。鉴定出了8个推定的SHR直接靶标，其表达模式均包含天然SHR表达域的子集。SHR直接调控的进一步证据来自SHR在体内与8个推定靶标中的4个的启动子区域的结合。根据几个直接靶标的表达模式预测了SHR在维管束中的新作用，并通过独立标记进行了证实。然后使用元分析方法对SHR间接靶标进行全局调查。我们的分析表明，SHR途径不仅通过一个大型转录调控网络，还通过激素途径和使用类受体激酶的信号传导途径来调节根的发育。综上所述，我们的结果不仅确定了SHR途径中的首个节点以及SHR在维管组织发育中的新功能，还揭示了该发育途径的全局架构。
