A gene regulatory network for root epidermis cell differentiation in Arabidopsis.
A gene regulatory network for root epidermis cell differentiation in Arabidopsis.
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DOI：
10.1371/journal.pgen.1002446
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发表时间：
2012-01
期刊：
影响因子：
4.5
通讯作者：
Schiefelbein J
中科院分区：
文献类型：
--
作者：
Bruex A;Kainkaryam RM;Wieckowski Y;Kang YH;Bernhardt C;Xia Y;Zheng X;Wang JY;Lee MM;Benfey P;Woolf PJ;Schiefelbein J
拟南芥的根表皮为研究细胞命运和分化的分子基础提供了一个特殊的模型。为了获得根表皮细胞分化的系统水平的观点，我们使用全基因组转录组的方法来定义和组织大量的基因到转录调控网络中。利用只产生两种表皮细胞类型中的一种的细胞命运突变体，结合荧光激活的细胞分选优先分析根表皮转录组，我们鉴定了在根毛或非毛细胞类型中差异表达的1,582个基因，其中包括208个“核心”根表皮基因。通过使用17个不同的根表皮突变体和2个激素处理来扰乱系统并评估对每个基因转录积累的影响，完成了核心基因的网络组织。此外，来自发育时间序列数据集的时间基因表达信息和来自贝叶斯建模方法的预测基因关联被用来帮助在网络中定位基因。此外，对该网络中可能的bHLH调控基因进行了详细的功能分析，包括MYC1、bHLH54、bHLH66和bHLH82，结果表明，bHLH蛋白的三个亚家族以阶段特异性的方式参与根表皮的发育。遗传、基因组和计算分析的集成为根表皮转录网络的组成、结构和逻辑提供了一个新的视角，并展示了综合系统方法在解剖复杂调控网络方面的有效性。目前发育生物学领域的一个挑战是定义指导细胞、组织和器官的模式和分化的基因网络的组成和组织。在这项研究中，我们使用拟南芥根表皮发育来解决这个问题，这是一个相对简单的模型，用于研究植物细胞模式的形成和分化。我们使用组织特异性细胞分类方法定义了1500多个基因，这些基因的转录产物在发育中的根表皮中差异积累。对17个根表皮突变体和2个植物激素处理进行了一系列的转录组分析，分析了208个核心基因之间的调控关系。此外，来自发育时间序列数据集的基因表达信息被用来在时间上组织基因。这些结果提供了对发育基因调控网络的组成、组织和逻辑的洞察。此外，这项工作还展示了综合分析在使用遗传、基因组和计算方法构建基因调控网络中的作用。
The root epidermis of Arabidopsis provides an exceptional model for studying the molecular basis of cell fate and differentiation. To obtain a systems-level view of root epidermal cell differentiation, we used a genome-wide transcriptome approach to define and organize a large set of genes into a transcriptional regulatory network. Using cell fate mutants that produce only one of the two epidermal cell types, together with fluorescence-activated cell-sorting to preferentially analyze the root epidermis transcriptome, we identified 1,582 genes differentially expressed in the root-hair or non-hair cell types, including a set of 208 “core” root epidermal genes. The organization of the core genes into a network was accomplished by using 17 distinct root epidermis mutants and 2 hormone treatments to perturb the system and assess the effects on each gene's transcript accumulation. In addition, temporal gene expression information from a developmental time series dataset and predicted gene associations derived from a Bayesian modeling approach were used to aid the positioning of genes within the network. Further, a detailed functional analysis of likely bHLH regulatory genes within the network, including MYC1, bHLH54, bHLH66, and bHLH82, showed that three distinct subfamilies of bHLH proteins participate in root epidermis development in a stage-specific manner. The integration of genetic, genomic, and computational analyses provides a new view of the composition, architecture, and logic of the root epidermal transcriptional network, and it demonstrates the utility of a comprehensive systems approach for dissecting a complex regulatory network. A current challenge in the field of developmental biology is to define the composition and organization of gene networks that direct the pattern and differentiation of cells, tissues, and organs. In this study, we address this problem using Arabidopsis root epidermis development, a relatively simple model for studies of cell pattern formation and differentiation in plants. We used a tissue-specific cell sorting approach to define more than 1,500 genes whose transcripts differentially accumulate in the developing root epidermis. A series of transcriptome analyses were performed with 17 root epidermal mutants and 2 plant hormone treatments to dissect the regulatory relationships between 208 core genes. In addition, gene expression information from a developmental time series dataset was used to organize genes temporally. The results provide insight into the composition, organization, and logic of a developmental gene regulatory network. Furthermore, this work demonstrates the utility of an integrated analysis in gene regulatory network construction using genetic, genomic, and computational approaches.
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影响因子：
9.2
作者：
Berger, F;Haseloff, J;Dolan, L
通讯作者：
Dolan, L
影响因子：
4.6
作者：
Bernhardt, C;Zhao, MZ;Schiefelbein, J
通讯作者：
Schiefelbein, J
影响因子：
4.6
作者：
Bernhardt, C;Lee, MM;Schiefelbein, J
通讯作者：
Schiefelbein, J
影响因子：
11.8
作者：
Deal, Roger B.;Henikoff, Steven
通讯作者：
Henikoff, Steven
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y