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

Abstract

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.

Bipartite Promoter Element Required for Auxin Response

“…Genome-wide surveys and computational analyses of auxin and brassinosteroid targets have provided clues into the regulatory landscape required for hormone response (Nemhauser et al, 2004;Priest et al, 2009;Keilwagen et al, 2011;Yamamoto et al, 2011). However, these approaches have a limited ability to define the function of specific cis-elements.…”

Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics

“…We used k-mer motifs to illustrate the MERCED algorithm for k = 8, while k could be any number between 6 and 14. We used 8-mers, because the most dominant length of motifs in the TRANSFAC database is eight (Wingender et al, 1996), and many previous studies have successfully identified meaningful motifs in plants and other species using 8-mers (Mariño-Ramírez et al, 2004;Yamamoto et al, 2011). We also predicted 7-mer and 9-mer motifs.…”

The Responses of Arabidopsis Early Light-Induced Protein2 to Ultraviolet B, High Light, and Cold Stress Are Regulated by a Transcriptional Regulatory Unit Composed of Two Elements

“…We recently developed a unique methodology for identifying promoter elements, utilizing frequency comparison of short nucleotide sequences present in a library of promoter regions (Yamamoto et al, 2011). Our method is simple but offers considerable advantages in terms of the accuracy and sensitivity of predictions compared with established methods such as Gibbs Sampling and Multiple Expectation Maximization for Motif Elicidation that are based upon extraction of consensus sequences .…”

“…As a first step in our work, we made use of these microarray data to analyze the ELIP2 promoter using our octamer-based frequency comparison method (Yamamoto et al, 2011). Promoter scans that express the frequency of individual octamers in stress-induced promoters relative to their frequency in all promoters in the genome (the relative appearance ratio [RAR], degree of overrepresentation) provide a means of visualizing regions within a specific promoter that display octamers that are enriched within the population of stress-induced promoters.…”

“…An apparent enrichment in Element C (-781) in promoters that respond to HL was not significant as determined by Fisher's Exact Test (P , 0.05), but significant enrichment was observed in promoters responding to cold stress. Among the three elements, Element A shows similarity to the Morning Element, and Element C contains a known DNA motif (CGCG box) that is a target sequence of Calcium-Binding Transcription Factor (CAMTA)/Arabidopsis SignalResponsive (AtSR) proteins (Yamamoto et al, 2011). Element B does not have high similarity to known DNA motifs; however, a closely related sequence with a onebase mismatch (designated B9) was found in the complementary strand (Fig.…”