拟南芥中转录因子的功能分析
Functional analysis of transcription factors in Arabidopsis.
作者信息
Mitsuda Nobutaka, Ohme-Takagi Masaru
机构信息
Research Institute of Genome-Based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), Central 4, Higashi, Tsukuba, Japan.
出版信息
Plant Cell Physiol. 2009 Jul;50(7):1232-48. doi: 10.1093/pcp/pcp075. Epub 2009 May 28.
Abstract
Transcription factors (TFs) regulate the expression of genes at the transcriptional level. Modification of TF activity dynamically alters the transcriptome, which leads to metabolic and phenotypic changes. Thus, functional analysis of TFs using 'omics-based' methodologies is one of the most important areas of the post-genome era. In this mini-review, we present an overview of Arabidopsis TFs and introduce strategies for the functional analysis of plant TFs, which include both traditional and recently developed technologies. These strategies can be assigned to five categories: bioinformatic analysis; analysis of molecular function; expression analysis; phenotype analysis; and network analysis for the description of entire transcriptional regulatory networks.
摘要
转录因子（TFs）在转录水平上调控基因的表达。TF活性的改变会动态地改变转录组，进而导致代谢和表型变化。因此，利用“组学”方法对TFs进行功能分析是后基因组时代最重要的领域之一。在本综述中，我们概述了拟南芥转录因子，并介绍了植物转录因子功能分析的策略，包括传统技术和最近开发的技术。这些策略可分为五类：生物信息学分析；分子功能分析；表达分析；表型分析；以及用于描述整个转录调控网络的网络分析。
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2
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Science. 2009 Mar 13;323(5920):1481-5. doi: 10.1126/science.1167206.
3
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PLoS Genet. 2009 Feb;5(2):e1000396. doi: 10.1371/journal.pgen.1000396. Epub 2009 Feb 27.
4
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Science. 2009 Feb 20;323(5917):1053-7. doi: 10.1126/science.1166386.
5
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Nat Rev Genet. 2009 Mar;10(3):161-72. doi: 10.1038/nrg2522.
6
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Plant J. 2009 May;58(3):450-63. doi: 10.1111/j.1365-313X.2009.03796.x. Epub 2009 Jan 8.
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Nat Protoc. 2009;4(1):71-7. doi: 10.1038/nprot.2008.217.
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