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Plant and Cell Physiology Advance Access originally published online on May 28, 2009
Plant and Cell Physiology 2009 50(7):1232-1248; doi:10.1093/pcp/pcp075
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© The Author 2009. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and the Japanese Society of Plant Physiologists are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

This article appears in the following Plant and Cell Physiology issue: Special Issue Articles: Omics and Bioinformatics [View the issue table of contents]

Special Issue - Mini Review

Functional Analysis of Transcription Factors in Arabidopsis

Nobutaka Mitsuda and Masaru Ohme-Takagi*

Research Institute of Genome-Based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), Central 4, Higashi 1-1-1, Tsukuba, 305-8562 Japan

*Corresponding author: E-mail, m-takagi{at}aist.go.jp; Fax, +81-29-861-3026.


  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.

Keywords: Arabidopsis - Bioinformatics - Functional analysis - Methodology - Transcription factor

Abbreviations: AD, activation domain; CaMV, cauliflower mosaic virus; CD, conserved domain; ChIP, chromatin immunoprecipitation; CHX, cycloheximide; CRES-T, chimeric repressor silencing technology; DBD, DNA-binding domain; DEG, differentially expressed gene; DEX, dexamethasone; EAR, ERF-associated amphiphilic repression; ER, estrogen receptor; FDR, false discovery rate; FOX, full-length cDNA overexpressor; GFP, green fluorescent protein; GO, gene ontology; GR, glucocorticoid receptor; GUS, β-glucuronidase; LUC, luciferase; miRNA, microRNA; PPI, protein–protein interaction; RD, repression domain; RT–PCR, reverse transcription–PCR; SRDX, modified EAR motif plant-specific repression domain showing strong repression activity; ta-siRNA, trans-acting small interfering RNA; TF, transcription factor; Y1H, yeast one-hybrid screening

(Received April 8, 2009; Accepted May 26, 2009)
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