Open Access Highly Accessed Open Badges Research article

Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data

Yoshiharu Y Yamamoto1*, Yohei Yoshioka1, Mitsuro Hyakumachi1, Kyonoshin Maruyama2, Kazuko Yamaguchi-Shinozaki2, Mutsutomo Tokizawa1 and Hiroyuki Koyama1

Author Affiliations

1 Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu 501-1193, Japan

2 Japan International Research Center for Agricultural Sciences, Ohwashi 1-1, Tsukuba, Ibaraki 305-8686, Japan

For all author emails, please log on.

BMC Plant Biology 2011, 11:39  doi:10.1186/1471-2229-11-39

Published: 24 February 2011



Phytohormones organize plant development and environmental adaptation through cell-to-cell signal transduction, and their action involves transcriptional activation. Recent international efforts to establish and maintain public databases of Arabidopsis microarray data have enabled the utilization of this data in the analysis of various phytohormone responses, providing genome-wide identification of promoters targeted by phytohormones.


We utilized such microarray data for prediction of cis-regulatory elements with an octamer-based approach. Our test prediction of a drought-responsive RD29A promoter with the aid of microarray data for response to drought, ABA and overexpression of DREB1A, a key regulator of cold and drought response, provided reasonable results that fit with the experimentally identified regulatory elements. With this succession, we expanded the prediction to various phytohormone responses, including those for abscisic acid, auxin, cytokinin, ethylene, brassinosteroid, jasmonic acid, and salicylic acid, as well as for hydrogen peroxide, drought and DREB1A overexpression. Totally 622 promoters that are activated by phytohormones were subjected to the prediction. In addition, we have assigned putative functions to 53 octamers of the Regulatory Element Group (REG) that have been extracted as position-dependent cis-regulatory elements with the aid of their feature of preferential appearance in the promoter region.


Our prediction of Arabidopsis cis-regulatory elements for phytohormone responses provides guidance for experimental analysis of promoters to reveal the basis of the transcriptional network of phytohormone responses.