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

BACKGROUND: 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 ut...

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Autores principales: Yamamoto, Yoshiharu Y, Yoshioka, Yohei, Hyakumachi, Mitsuro, Maruyama, Kyonoshin, Yamaguchi-Shinozaki, Kazuko, Tokizawa, Mutsutomo, Koyama, Hiroyuki
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058078/
https://www.ncbi.nlm.nih.gov/pubmed/21349196
http://dx.doi.org/10.1186/1471-2229-11-39
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author Yamamoto, Yoshiharu Y
Yoshioka, Yohei
Hyakumachi, Mitsuro
Maruyama, Kyonoshin
Yamaguchi-Shinozaki, Kazuko
Tokizawa, Mutsutomo
Koyama, Hiroyuki
author_facet Yamamoto, Yoshiharu Y
Yoshioka, Yohei
Hyakumachi, Mitsuro
Maruyama, Kyonoshin
Yamaguchi-Shinozaki, Kazuko
Tokizawa, Mutsutomo
Koyama, Hiroyuki
author_sort Yamamoto, Yoshiharu Y
collection PubMed
description BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.
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spelling pubmed-30580782011-03-16 Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data Yamamoto, Yoshiharu Y Yoshioka, Yohei Hyakumachi, Mitsuro Maruyama, Kyonoshin Yamaguchi-Shinozaki, Kazuko Tokizawa, Mutsutomo Koyama, Hiroyuki BMC Plant Biol Research Article BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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. BioMed Central 2011-02-24 /pmc/articles/PMC3058078/ /pubmed/21349196 http://dx.doi.org/10.1186/1471-2229-11-39 Text en Copyright ©2011 Yamamoto et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Yamamoto, Yoshiharu Y
Yoshioka, Yohei
Hyakumachi, Mitsuro
Maruyama, Kyonoshin
Yamaguchi-Shinozaki, Kazuko
Tokizawa, Mutsutomo
Koyama, Hiroyuki
Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
title Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
title_full Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
title_fullStr Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
title_full_unstemmed Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
title_short Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
title_sort prediction of transcriptional regulatory elements for plant hormone responses based on microarray data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058078/
https://www.ncbi.nlm.nih.gov/pubmed/21349196
http://dx.doi.org/10.1186/1471-2229-11-39
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