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      ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis

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          Abstract

          Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction database (ATTED-II) that provides co-regulated gene relationships based on co-expressed genes deduced from microarray data and the predicted cis elements. ATTED-II ( http://www.atted.bio.titech.ac.jp) includes the following features: (i) lists and networks of co-expressed genes calculated from 58 publicly available experimental series, which are composed of 1388 GeneChip data in A.thaliana; (ii) prediction of cis-regulatory elements in the 200 bp region upstream of the transcription start site to predict co-regulated genes amongst the co-expressed genes; and (iii) visual representation of expression patterns for individual genes. ATTED-II can thus help researchers to clarify the function and regulation of particular genes and gene networks.

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          Cluster analysis and display of genome-wide expression patterns.

          P. T. Spellman, P. O. Brown, D Botstein … (1998)
          A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression. The output is displayed graphically, conveying the clustering and the underlying expression data simultaneously in a form intuitive for biologists. We have found in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function, and we find a similar tendency in human data. Thus patterns seen in genome-wide expression experiments can be interpreted as indications of the status of cellular processes. Also, coexpression of genes of known function with poorly characterized or novel genes may provide a simple means of gaining leads to the functions of many genes for which information is not available currently.
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            JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis.

            Óscar Lorenzo, Jose M Chico, José Sánchez-Serrano … (2004)
            In spite of the importance of jasmonates (JAs) as plant growth and stress regulators, the molecular components of their signaling pathway remain largely unknown. By means of a genetic screen that exploits the cross talk between ethylene (ET) and JAs, we describe the identification of several new loci involved in JA signaling and the characterization and positional cloning of one of them, JASMONATE-INSENSITIVE1 (JAI1/JIN1). JIN1 encodes AtMYC2, a nuclear-localized basic helix-loop-helix-leucine zipper transcription factor, whose expression is rapidly upregulated by JA, in a CORONATINE INSENSITIVE1-dependent manner. Gain-of-function experiments confirmed the relevance of AtMYC2 in the activation of JA signaling. AtMYC2 differentially regulates the expression of two groups of JA-induced genes. The first group includes genes involved in defense responses against pathogens and is repressed by AtMYC2. Consistently, jin1 mutants show increased resistance to necrotrophic pathogens. The second group, integrated by genes involved in JA-mediated systemic responses to wounding, is activated by AtMYC2. Conversely, Ethylene-Response-Factor1 (ERF1) positively regulates the expression of the first group of genes and represses the second. These results highlight the existence of two branches in the JA signaling pathway, antagonistically regulated by AtMYC2 and ERF1, that are coincident with the alternative responses activated by JA and ET to two different sets of stresses, namely pathogen attack and wounding.
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              ABFs, a family of ABA-responsive element binding factors.

              H. Choi, J. Hong, J. Ha … (2000)
              Abscisic acid (ABA) plays an important role in environmental stress responses of higher plants during vegetative growth. One of the ABA-mediated responses is the induced expression of a large number of genes, which is mediated by cis-regulatory elements known as abscisic acid-responsive elements (ABREs). Although a number of ABRE binding transcription factors have been known, they are not specifically from vegetative tissues under induced conditions. Considering the tissue specificity of ABA signaling pathways, factors mediating ABA-dependent stress responses during vegetative growth phase may thus have been unidentified so far. Here, we report a family of ABRE binding factors isolated from young Arabidopsis plants under stress conditions. The factors, isolated by a yeast one-hybrid system using a prototypical ABRE and named as ABFs (ABRE binding factors) belong to a distinct subfamily of bZIP proteins. Binding site selection assay performed with one ABF showed that its preferred binding site is the strong ABRE, CACGTGGC. ABFs can transactivate an ABRE-containing reporter gene in yeast. Expression of ABFs is induced by ABA and various stress treatments, whereas their induction patterns are different from one another. Thus, a new family of ABRE binding factors indeed exists that have the potential to activate a large number of ABA/stress-responsive genes in Arabidopsis.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (pmc): nar
                Journal ID (publisher-id): Nucleic Acids Research
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): January 2007
                Publication date (Electronic): 27 November 2006
                Publication date PMC-release: 27 November 2006
                Volume: 35
                Issue: Database issue
                Pages: D863-D869
                Affiliations
                1Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
                2Graduate School of Pharmaceutical Sciences, Chiba University Chiba 263-8522, Japan
                3Core Research for Evolutional Science and Technology, Japan Science and Technology Agency 4-1-8, Saitama 332-0012, Japan
                4Human Genome Center, Institute of Medical Science, The University of Tokyo 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
                5Structure and Function of Biomolecules, SORST JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
                6Graduate School of Information Science and Engineering, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
                7Kazusa DNA Research Institute, Kisarazu Chiba 292-0812, Japan
                8RIKEN Plant Science Center, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama 230-0045, Japan
                9Research Center for the Evolving Earth and Planets, 4259-B-14 Nagatsuta-cho Midori-ku, Yokohama 226-8501, Japan
                Author notes
                *To whom correspondence should be addressed at Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan. Tel: +81 45 924 5736; Fax: +81 45 924 5823; Email: atted@ 123456bio.titech.ac.jp
                Article
                DOI: 10.1093/nar/gkl783
                PMC ID: 1716726
                PubMed ID: 17130150
                SO-VID: 23894aff-f23a-4b28-a609-c33a5edab6b3
                Copyright © © 2006 The Author(s)
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 15 August 2006
                Date revision received : 25 September 2006
                Date accepted : 29 September 2006
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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