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, Kazuko; Tran, Lam-Son Phan

doi:10.1093/dnares/dsr019

In Silico Analysis of Transcription Factor Repertoires and Prediction of Stress-Responsive Transcription Factors from Six Major Gramineae Plants

Journal Article · Mon Jul 04 00:00:00 EDT 2011 · DNA Research

DOI:https://doi.org/10.1093/dnares/dsr019· OSTI ID:1625314

Mochida, Keiichi ^[1]; Yoshida, Takuhiro ^[2]; Sakurai, Tetsuya ^[2]; Yamaguchi-Shinozaki, Kazuko ^[3]; Shinozaki, Kazuko ^[4]; Tran, Lam-Son Phan ^[2]

RIKEN Plant Science Center, Yokohama (Japan); RIKEN Biomass Engineering Program, Yokohama (Japan); Yokohama City Univ. (Japan). Kihara Inst. for Biological Research; DOE/OSTI
RIKEN Plant Science Center, Yokohama (Japan)
Japan International Center of Agricultural Sciences, Ibaraki (Japan)
RIKEN Plant Science Center, Yokohama (Japan); RIKEN Biomass Engineering Program, Yokohama (Japan)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: Ministry of Education, Culture, Sports, Science and Technology of Japan; RIKEN; USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625314

Journal Information:: DNA Research, Journal Name: DNA Research Journal Issue: 5 Vol. 18; ISSN 1340-2838

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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