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

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.

Spatial transcriptomes of iron‐deficient and cadmium‐stressed rice

“…To investigate the cis elements related to changes in spatial gene expression triggered by Fe deficiency and Cd stress, we used MAMA, which is an in silico tool for predicting cis ‐acting elements based on expression ratios by microarray analysis (Kakei et al ., ). MAMA detects cis motifs that occur frequently in a set of promoter sequences of up‐regulated genes, based on sequence similarities and the expression ratio of each up‐regulated gene.…”

“…a). We previously reported that DCEp1 and TATA‐box‐like motifs are important as a unit of the basic transcription machinery to function with other colocalized cis motifs, including stress‐related motifs such as IDEF1‐binding core motif and FAM1 (Kakei et al ., ). The present study suggests that DCEp1 is required for the up‐regulation of Fe deficiency‐inducible genes in all root tissues, while DCEp2 is important in the VB and Cor.…”

“…The microarray‐associated motif analyzer is an in silico application for the prediction of cis motifs that occur frequently in up‐regulated genes (Kakei et al ., ). First, candidate cis motif sequences were selected from the promoters of a few dozen of the most highly up‐regulated genes in the microarray.…”

“…Sequences similar to the candidate cis motifs that occur frequently in the promoters of genes with a high expression ratio will have high MAMA scores. The MAMA was performed as described previously (Kakei et al ., ) with minor modifications. Briefly, MAMA scores were calculated using the 500 bp promoters and expression ratios of those genes whose average signal values were > 50 in at least one tissue type or condition.…”

Rice and chickpea GDPDs are preferentially influenced by low phosphate and CaGDPD1 encodes an active glycerophosphodiester phosphodiesterase enzyme

“…None of the CaGDPDs possessed PHO (CACGTS) and P responsive (ATGCCAT) elements. Further, we found only one Fe responsive cis-regulatory elements, IDEF1BS (Kakei et al 2013) …”