A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors.
A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors.
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DOI：
10.1371/journal.pgen.1000396
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发表时间：
2009-02
期刊：
影响因子：
4.5
通讯作者：
Grotewold, Erich
中科院分区：
文献类型：
--
作者：
Morohashi, Kengo;Grotewold, Erich
位置依赖性细胞命运决定和模式形成是植物结构发育的独特方面。拟南芥中多能表皮（原表皮）细胞形成单细胞叶毛（毛状体）为确定参与细胞命运决定的基因调控网络提供了一个强大的系统。为了全面了解与拟南芥表皮细胞分化为毛状体相关的调控事件，我们对毛状体发育选择因子GLABRA3（GL3）和GLABRA1（GL1）分别进行了表达分析和全基因组定位分析（ChIP - chip），它们分别编码碱性螺旋 - 环 - 螺旋（bHLH）和MYB转录因子。利用元分析将野生型与gl3或gl1突变体的全基因组表达结果对比，并结合可诱导形式的GL3和GL1随时间变化的基因表达情况进行整合。这导致鉴定出一组与表皮细胞分化为毛状体相关的最少基因集。ChIP - chip实验，辅以对已知参与毛状体起始或模式形成的因子的针对性检测，鉴定出约20个新的GL3/GL1直接靶标。除了参与基因表达控制的基因，如转录因子SCL8和MYC1，我们还鉴定出SIM（SIAMESE），它编码一种细胞周期蛋白依赖性激酶抑制剂，以及RBR1（视网膜母细胞瘤相关蛋白1），它对应于细胞周期转录因子E2F的负调控因子，作为GL3/GL1的直接靶标，这直接表明这些毛状体调控因子参与内循环的控制。许多已鉴定的GL3/GL1直接靶标的表达在毛状体起始的极早期阶段具有特异性，表明它们参与了一些已知的与原表皮细胞分化相关的最早过程。通过将这些知识与毛状体形成相关基因的分析相结合，我们的结果揭示了参与表皮细胞分化和毛状体形成的调控网络层次结构的顶层架构。
从多能表皮（原表皮）细胞建立单细胞叶毛（毛状体）为确定参与植物细胞命运决定的基因调控网络提供了一个强大的系统。两种转录因子——GL1和GL3——与毛状体形成的起始有关；然而，之前仅有少数GL1 - GL3调控的基因得到了表征。在这项研究中，我们结合在多种不同基因型中进行的表达分析，鉴定出一组约500个与毛状体形成相关的最少基因集。我们还使用ChIP - chip鉴定出一组约20个作为GL3和GL1直接靶标的基因。更多的基因是GL1或GL3的靶标，可能是与其他bHLH或MYB伙伴合作的结果，但不是GL1和GL3共同的靶标。正如对参与表皮细胞命运决定起始的基因所预测的那样，几个GL3/GL1直接靶标在毛状体形成早期表达，包括转录因子MYC1（bHLH）、SCL8（GRAS）以及参与内循环调节的基因（SIM和RBR1）。共表达分析使我们能够鉴定出可能位于GL3/GL1调控的转录因子下游的靶基因集，为构建与原表皮细胞分化为毛状体相关的调控网络迈出了第一步。
Position-dependent cell fate determination and pattern formation are unique aspects of the development of plant structures. The establishment of single-celled leaf hairs (trichomes) from pluripotent epidermal (protodermal) cells in Arabidopsis provides a powerful system to determine the gene regulatory networks involved in cell fate determination. To obtain a holistic view of the regulatory events associated with the differentiation of Arabidopsis epidermal cells into trichomes, we combined expression and genome-wide location analyses (ChIP-chip) on the trichome developmental selectors GLABRA3 (GL3) and GLABRA1 (GL1), encoding basic helix-loop-helix (bHLH) and MYB transcription factors, respectively. Meta-analysis was used to integrate genome-wide expression results contrasting wild type and gl3 or gl1 mutants with changes in gene expression over time using inducible versions of GL3 and GL1. This resulted in the identification of a minimal set of genes associated with the differentiation of epidermal cells into trichomes. ChIP-chip experiments, complemented by the targeted examination of factors known to participate in trichome initiation or patterning, identified about 20 novel GL3/GL1 direct targets. In addition to genes involved in the control of gene expression, such as the transcription factors SCL8 and MYC1, we identified SIM (SIAMESE), encoding a cyclin-dependent kinase inhibitor, and RBR1 (RETINOBLASTOMA RELATED1), corresponding to a negative regulator of the cell cycle transcription factor E2F, as GL3/GL1 immediate targets, directly implicating these trichome regulators in the control of the endocycle. The expression of many of the identified GL3/GL1 direct targets was specific to very early stages of trichome initiation, suggesting that they participate in some of the earliest known processes associated with protodermal cell differentiation. By combining this knowledge with the analysis of genes associated with trichome formation, our results reveal the architecture of the top tiers of the hierarchical structure of the regulatory network involved in epidermal cell differentiation and trichome formation. The establishment of single-celled leaf hairs (trichomes) from pluripotent epidermal (protodermal) cells provides a powerful system to determine the gene regulatory networks involved in plant cell fate determination. Two transcription factors—GL1 and GL3—have been associated with the initiation of trichome formation; yet only a handful of GL1-GL3–regulated genes have previously been characterized. In this study, we combined expression analyses performed in a number of different genotypes to identify a minimal set of about 500 genes associated with trichome formation. We also used ChIP-chip to identify a set of about 20 genes that are immediate targets of GL3 and GL1. Many more genes are targeted by GL1 or by GL3, likely in cooperation with other bHLH of MYB partners, but not by both GL1 and GL3. As predicted for genes involved in the initiation of epidermal cell fate determination, several of the GL3/GL1 direct targets are expressed early during trichome formation, including the transcription factors MYC1 (bHLH), SCL8 (GRAS), and genes involved in the regulation of the endocycle (SIM and RBR1). Co-expression analyses permitted us to identify sets of target genes likely downstream of the GL3/GL1 regulated transcription factors, providing the first steps towards building the regulatory network associated with the differentiation of protodermal cells into trichomes.
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影响因子：
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