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

BackgroundPhytohormones 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.ResultsWe 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.ConclusionsOur 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.

[1]  S. Yanagisawa.  Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. , 2004, Plant & cell physiology.

[2]  Kazuo Shinozaki,et al.  Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems. , 2004, The Plant journal : for cell and molecular biology.

[3]  T. Sakurai,et al.  Identification of plant promoter constituents by analysis of local distribution of short sequences , 2007, BMC Genomics.

[4]  G. Hagen,et al.  Dimerization and DNA binding of auxin response factors. , 1999, The Plant journal : for cell and molecular biology.

[5]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[6]  J. Sheen,et al.  Emerging connections in the ethylene signaling network. , 2009, Trends in plant science.

[7]  K. Shinozaki,et al.  Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. , 2003, The Plant journal : for cell and molecular biology.

[8]  A. Lovegrove,et al.  Gibberellin and abscisic acid signalling in aleurone. , 2000, Trends in plant science.

[9]  Kathleen Marchal,et al.  A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes , 2001, RECOMB.

[10]  G. Paliyath,et al.  Influence of Salicylic Acid on H2O2 Production, Oxidative Stress, and H2O2-Metabolizing Enzymes (Salicylic Acid-Mediated Oxidative Damage Requires H2O2) , 1997, Plant physiology.

[11]  Kenta Nakai,et al.  Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions , 2007, Nucleic Acids Res..

[12]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[13]  K. Shinozaki,et al.  'Omics' analyses of regulatory networks in plant abiotic stress responses. , 2010, Current opinion in plant biology.

[14]  K. Shinozaki,et al.  A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. , 1994, The Plant cell.

[15]  K. Shinozaki,et al.  Two Transcription Factors, DREB1 and DREB2, with an EREBP/AP2 DNA Binding Domain Separate Two Cellular Signal Transduction Pathways in Drought- and Low-Temperature-Responsive Gene Expression, Respectively, in Arabidopsis , 1998, Plant Cell.

[16]  R. Foster,et al.  Plant bZIP proteins gather at ACGT elements , 1994, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[17]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.

[18]  E. Bornberg-Bauer,et al.  The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. , 2007, The Plant journal : for cell and molecular biology.

[19]  K. Akiyama,et al.  Functional Annotation of a Full-Length Arabidopsis cDNA Collection , 2002, Science.

[20]  Q. Shen,et al.  WRKY transcription factors. , 2010, Trends in plant science.

[21]  M. Matsui,et al.  Global classification of transcriptional responses to light stress in Arabidopsis thaliana , 2004 .

[22]  Jun S. Liu,et al.  Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. , 1993, Science.

[23]  Kazuo Shinozaki,et al.  The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. , 2008, The Plant journal : for cell and molecular biology.

[24]  P. Rushton,et al.  Engineering plants with increased disease resistance: what are we going to express? , 2005, Trends in biotechnology.

[25]  B. Poovaiah,et al.  A Calmodulin-binding/CGCG Box DNA-binding Protein Family Involved in Multiple Signaling Pathways in Plants* 210 , 2002, The Journal of Biological Chemistry.

[26]  P. Heifetz,et al.  Functional analysis of regulatory sequences controlling PR-1 gene expression in Arabidopsis. , 1998, The Plant journal : for cell and molecular biology.

[27]  C. Gatz,et al.  The Arabidopsis PR-1 Promoter Contains Multiple Integration Sites for the Coactivator NPR1 and the Repressor SNI1[W] , 2010, Plant Physiology.

[28]  Jonathan D. G. Jones,et al.  Role of plant hormones in plant defence responses , 2009, Plant Molecular Biology.

[29]  M. Ivanchenko,et al.  Ethylene regulates lateral root formation and auxin transport in Arabidopsis thaliana , 2008, The Plant journal : for cell and molecular biology.

[30]  Q. Shen,et al.  Modular nature of abscisic acid (ABA) response complexes: composite promoter units that are necessary and sufficient for ABA induction of gene expression in barley. , 1996, The Plant cell.

[31]  Ingo Dreyer,et al.  Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice , 2007, BMC Genomics.

[32]  M. Grant,et al.  Arabidopsis Auxin Mutants Are Compromised in Systemic Acquired Resistance and Exhibit Aberrant Accumulation of Various Indolic Compounds1[W][OA] , 2010, Plant Physiology.

[33]  Junichi Obokata,et al.  ppdb: a plant promoter database , 2007, Nucleic Acids Res..

[34]  K. Shinozaki,et al.  DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. , 2002, Biochemical and biophysical research communications.

[35]  Alona S. Russe.  Computational biology : new research , 2009 .

[36]  C. Vinson,et al.  Clustering of DNA sequences in human promoters. , 2004, Genome research.

[37]  T. Sakurai,et al.  Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. , 2009, The Plant journal : for cell and molecular biology.

[38]  K. Ljung,et al.  Ethylene Regulates Root Growth through Effects on Auxin Biosynthesis and Transport-Dependent Auxin Distribution[W] , 2007, The Plant Cell Online.

[39]  K. Shinozaki,et al.  Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters. , 2005, Trends in plant science.

[40]  Transcription Factor CBF4 Is a Regulator of Drought Adaptation in Arabidopsis1 , 2002, Plant Physiology.