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DNA Research Advance Access published online on November 2, 2009
DNA Research, doi:10.1093/dnares/dsp023
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© The Author 2009. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

In silico Analysis of Transcription Factor Repertoire and Prediction of Stress Responsive Transcription Factors in Soybean

Keiichi Mochida1,*, Takuhiro Yoshida1, Tetsuya Sakurai1, Kazuko Yamaguchi-Shinozaki2, Kazuo Shinozaki1 and Lam-Son Phan Tran1,*

1 RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
2 Japan International Center of Agricultural Sciences, Ibaraki 305-8686, Japan

Received 27 July 2009 ; accepted 5 October 2009.

Sequence-specific DNA-binding transcription factors (TFs) are often termed as ‘master regulators’ which bind to DNA and either activate or repress gene transcription. We have computationally analysed the soybean genome sequence data and constructed a proper set of TFs based on the Hidden Markov Model profiles of DNA-binding domain families. Within the soybean genome, we identified 4342 loci encoding 5035 TF models which grouped into 61 families. We constructed a database named SoybeanTFDB (http://soybeantfdb.psc.riken.jp) containing the full compilation of soybean TFs and significant information such as: functional motifs, full-length cDNAs, domain alignments, promoter regions, genomic organization and putative regulatory functions based on annotations of gene ontology (GO) inferred by comparative analysis with Arabidopsis. With particular interest in abiotic stress signalling, we analysed the promoter regions for all of the TF encoding genes as a means to identify abiotic stress responsive cis-elements as well as all types of cis-motifs provided by the PLACE database. SoybeanTFDB enables scientists to easily access cis-element and GO annotations to aid in the prediction of TF function and selection of TFs with functions of interest. This study provides a basic framework and an important user-friendly public information resource which enables analyses of transcriptional regulation in soybean.

Key words: soybean; transcription factors; abiotic stress; database

* To whom correspondence should be addressed. Tel. +81 45-503-9593. E-mail: mochida{at}psc.riken.jp (K.M.) or tran{at}psc.riken.jp (L.-S.P.T.)

Edited by Dr. Katsumi Isono


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