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

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

doi:10.1093/dnares/dsp023

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

Journal Article · Mon Nov 02 00:00:00 EST 2009 · DNA Research

DOI:https://doi.org/10.1093/dnares/dsp023· OSTI ID:1625313

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

RIKEN Plant Science Center, Yokohama (Japan); DOE/OSTI
RIKEN Plant Science Center, Yokohama (Japan)
Japan International Center of Agricultural Sciences, Ibaraki (Japan)

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.

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; USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625313

Journal Information:: DNA Research, Journal Name: DNA Research Journal Issue: 6 Vol. 16; ISSN 1340-2838

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Genetics & Heredity
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database
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transcription factors

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

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