Literature DB >> 19478073

Functional analysis of transcription factors in Arabidopsis.

Nobutaka Mitsuda1, Masaru Ohme-Takagi.   

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.

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Year:  2009        PMID: 19478073      PMCID: PMC2709548          DOI: 10.1093/pcp/pcp075

Source DB:  PubMed          Journal:  Plant Cell Physiol        ISSN: 0032-0781            Impact factor:   4.927


  127 in total

1.  A predicted interactome for Arabidopsis.

Authors:  Jane Geisler-Lee; Nicholas O'Toole; Ron Ammar; Nicholas J Provart; A Harvey Millar; Matt Geisler
Journal:  Plant Physiol       Date:  2007-08-03       Impact factor: 8.340

2.  Arabidopsis TRANSPARENT TESTA GLABRA2 is directly regulated by R2R3 MYB transcription factors and is involved in regulation of GLABRA2 transcription in epidermal differentiation.

Authors:  Tetsuya Ishida; Sayoko Hattori; Ryosuke Sano; Kayoko Inoue; Yumiko Shirano; Hiroaki Hayashi; Daisuke Shibata; Shusei Sato; Tomohiko Kato; Satoshi Tabata; Kiyotaka Okada; Takuji Wada
Journal:  Plant Cell       Date:  2007-08-31       Impact factor: 11.277

3.  Arabidopsis MALE STERILITY1 encodes a PHD-type transcription factor and regulates pollen and tapetum development.

Authors:  Takuya Ito; Noriko Nagata; Yoshu Yoshiba; Masaru Ohme-Takagi; Hong Ma; Kazuo Shinozaki
Journal:  Plant Cell       Date:  2007-11-21       Impact factor: 11.277

4.  Functional analysis of the epidermal-specific MYB genes CAPRICE and WEREWOLF in Arabidopsis.

Authors:  Rumi Tominaga; Mineko Iwata; Kiyotaka Okada; Takuji Wada
Journal:  Plant Cell       Date:  2007-07-20       Impact factor: 11.277

5.  Distinct and overlapping roles of single-repeat MYB genes in root epidermal patterning.

Authors:  Marissa Simon; Myeong Min Lee; Yan Lin; Lindsey Gish; John Schiefelbein
Journal:  Dev Biol       Date:  2007-09-14       Impact factor: 3.582

6.  AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.

Authors:  Jian Cui; Peng Li; Guang Li; Feng Xu; Chen Zhao; Yuhua Li; Zhongnan Yang; Guang Wang; Qingbo Yu; Yixue Li; Tieliu Shi
Journal:  Nucleic Acids Res       Date:  2007-10-25       Impact factor: 16.971

7.  Update of ASRP: the Arabidopsis Small RNA Project database.

Authors:  Tyler W H Backman; Christopher M Sullivan; Jason S Cumbie; Zachary A Miller; Elisabeth J Chapman; Noah Fahlgren; Scott A Givan; James C Carrington; Kristin D Kasschau
Journal:  Nucleic Acids Res       Date:  2007-11-13       Impact factor: 16.971

8.  An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets.

Authors:  Debbie Winter; Ben Vinegar; Hardeep Nahal; Ron Ammar; Greg V Wilson; Nicholas J Provart
Journal:  PLoS One       Date:  2007-08-08       Impact factor: 3.240

9.  WoLF PSORT: protein localization predictor.

Authors:  Paul Horton; Keun-Joon Park; Takeshi Obayashi; Naoya Fujita; Hajime Harada; C J Adams-Collier; Kenta Nakai
Journal:  Nucleic Acids Res       Date:  2007-05-21       Impact factor: 16.971

10.  Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins.

Authors:  Jue Zeng; Jizhou Yan; Ting Wang; Deborah Mosbrook-Davis; Kyle T Dolan; Ryan Christensen; Gary D Stormo; David Haussler; Richard H Lathrop; Rainer K Brachmann; Shawn M Burgess
Journal:  Nucleic Acids Res       Date:  2007-12-17       Impact factor: 16.971

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  97 in total

1.  Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana.

Authors:  Tao Lu; Yuedong Yang; Bo Yao; Song Liu; Yaoqi Zhou; Chi Zhang
Journal:  Protein Sci       Date:  2012-05-01       Impact factor: 6.725

2.  Expression and function of a modified AP2/ERF transcription factor from Brassica napus enhances cold tolerance in transgenic Arabidopsis.

Authors:  Ai-Sheng Xiong; Hai-Hua Jiang; Jing Zhuang; Ri-He Peng; Xiao-Fen Jin; Bo Zhu; Feng Wang; Jian Zhang; Quan-Hong Yao
Journal:  Mol Biotechnol       Date:  2013-02       Impact factor: 2.695

3.  Identification of recognition sequence of ANAC078 protein by the cyclic amplification and selection of targets technique.

Authors:  Yukinori Yabuta; Teruyuki Morishita; Yusuke Kojima; Takanori Maruta; Ayako Nishizawa-Yokoi; Shigeru Shigeoka
Journal:  Plant Signal Behav       Date:  2010-06-01

4.  NEMATIC: a simple and versatile tool for the in silico analysis of plant-nematode interactions.

Authors:  Javier Cabrera; Regla Bustos; Bruno Favery; Carmen Fenoll; Carolina Escobar
Journal:  Mol Plant Pathol       Date:  2014-02-12       Impact factor: 5.663

5.  Mapping transcription factor interactome networks using HaloTag protein arrays.

Authors:  Junshi Yazaki; Mary Galli; Alice Y Kim; Kazumasa Nito; Fernando Aleman; Katherine N Chang; Anne-Ruxandra Carvunis; Rosa Quan; Hien Nguyen; Liang Song; José M Alvarez; Shao-Shan Carol Huang; Huaming Chen; Niroshan Ramachandran; Stefan Altmann; Rodrigo A Gutiérrez; David E Hill; Julian I Schroeder; Joanne Chory; Joshua LaBaer; Marc Vidal; Pascal Braun; Joseph R Ecker
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-29       Impact factor: 11.205

6.  Phosphorylation of the Nicotiana benthamiana WRKY8 transcription factor by MAPK functions in the defense response.

Authors:  Nobuaki Ishihama; Reiko Yamada; Miki Yoshioka; Shinpei Katou; Hirofumi Yoshioka
Journal:  Plant Cell       Date:  2011-03-08       Impact factor: 11.277

7.  Omics and bioinformatics: an essential toolbox for systems analyses of plant functions beyond 2010.

Authors:  Kazuo Shinozaki; Hitoshi Sakakibara
Journal:  Plant Cell Physiol       Date:  2009-07       Impact factor: 4.927

Review 8.  Genomics and bioinformatics resources for crop improvement.

Authors:  Keiichi Mochida; Kazuo Shinozaki
Journal:  Plant Cell Physiol       Date:  2010-03-05       Impact factor: 4.927

9.  Identification of transcription factors linked to cell cycle regulation in Arabidopsis.

Authors:  Fatemeh Dehghan Nayeri
Journal:  Plant Signal Behav       Date:  2014

10.  Functional divergence within class B MADS-box genes TfGLO and TfDEF in Torenia fournieri Lind.

Authors:  Katsutomo Sasaki; Ryutaro Aida; Hiroyasu Yamaguchi; Masahito Shikata; Tomoya Niki; Takaaki Nishijima; Norihiro Ohtsubo
Journal:  Mol Genet Genomics       Date:  2010-09-26       Impact factor: 3.291

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