In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants

Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki, Lam Son Phan Tran

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

The interactions between transcription factors (TFs) and cis-regulatory DNA sequences control gene expression, constituting the essential functional linkages of gene regulatory networks. The aim of this study is to identify and integrate all putative TFs from six grass species: Brachypodium distachyon, maize, rice, sorghum, barley, and wheat with significant information into an integrative database (GramineaeTFDB) for comparative genomics and functional genomics. For each TF, sequence features, promoter regions, domain alignments, GO assignment, FL-cDNA information, if available, and cross-references to various public databases and genetic resources are provided. Additionally, GramineaeTFDB possesses a tool which aids the users to search for putative cis-elements located in the promoter regions of TFs and predict the functions of the TFs using cis-element-based functional prediction approach. We also supplied hyperlinks to expression profiles of those TF genes of maize, rice, and barley, for which data are available. Furthermore, information about the availability of FOX and Ds mutant lines for rice and maize TFs, respectively, are also accessible through hyperlinks. Our study provides an important user-friendly public resource for functional analyses and comparative genomics of grass TFs, and understanding of the architecture of transcriptional regulatory networks and evolution of the TFs in agriculturally important cereal crops.

Original languageEnglish
Pages (from-to)321-332
Number of pages12
JournalDNA Research
Volume18
Issue number5
DOIs
Publication statusPublished - Oct 2011
Externally publishedYes

Fingerprint

Poaceae
Computer Simulation
Transcription Factors
Genomics
Zea mays
Gene Regulatory Networks
Hordeum
Genetic Promoter Regions
Brachypodium
Genetic Databases
Sorghum
Triticum
Complementary DNA
Databases
Gene Expression

Keywords

  • abiotic stress
  • cis-motif
  • database
  • grasses
  • transcription factor

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

Cite this

In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants. / Mochida, Keiichi; Yoshida, Takuhiro; Sakurai, Tetsuya; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo; Tran, Lam Son Phan.

In: DNA Research, Vol. 18, No. 5, 10.2011, p. 321-332.

Research output: Contribution to journalArticle

Mochida, Keiichi ; Yoshida, Takuhiro ; Sakurai, Tetsuya ; Yamaguchi-Shinozaki, Kazuko ; Shinozaki, Kazuo ; Tran, Lam Son Phan. / In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants. In: DNA Research. 2011 ; Vol. 18, No. 5. pp. 321-332.
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