Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice

Yusuke Kakei,Takashi Yamakawa,Naoko K Nishizawa,Reiko N Itai,Takanori Kobayashi,Yuko Ogo,Hiromi Nakanishi

doi:10.1186/1939-8433-6-22

Abstract

BackgroundCis-acting elements are essential genomic sequences that control gene expression. In higher eukaryotes, a series of cis-elements function cooperatively. However, further studies are required to examine the co-regulation of multiple cis-elements on a promoter. The aim of this study was to propose a model of cis-element networks that cooperatively regulate gene expression in rice under iron (Fe) deficiency.ResultsWe developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. Based on sequences of Oryza sativa genes upregulated by Fe deficiency, MAMA returned experimentally identified cis-elements responsible for Fe deficiency in O. sativa. When this method was applied to O. sativa subjected to zinc deficiency and Arabidopsis thaliana subjected to salt stress, several novel candidate cis-acting elements that overlap with known cis-acting elements, such as ZDRE, ABRE, and DRE, were identified. After optimization, MAMA accurately simulated more than 87% of gene expression. Predicted motifs strongly co-localized in the upstream regions of regulated genes and sequences around transcription start sites. Furthermore, in many cases, the separation (in bp) between co-localized motifs was conserved, suggesting that predicted motifs and the separation between them were important in the co-regulation of gene expression.ConclusionsOur results are suggestive of a typical sequence model for Fe deficiency-responsive promoters and some strong candidate cis-elements that function cooperatively with known cis-elements.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-22) contains supplementary material, which is available to authorized users.

Highlights

Cis-acting elements are essential genomic sequences that control gene expression
A model of transcriptional regulation under Fe deficiency Based on our predictions, we propose the following model of transcriptional regulation in rice under Fedeficiency stress (Figure 6)
The Fe-deficiency signal initially activates transcription factors involved in Fedeficiency responses such as IDEF1

Summary

Introduction

Cis-acting elements are essential genomic sequences that control gene expression. For more than 10 years, during which time a variety of genomes have been fully sequenced, much effort has been devoted to the development of in silico methods for predicting novel cis-acting sequences or motifs in prokaryotes and eukaryotes. These methods are categorized into two general groups Predicting a series of cis-elements that function cooperatively has become increasingly important to understand transcriptional regulation in higher eukaryotes

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