An Integrated Bioinformatics Approach to the Discovery of Cis -regulatory Elements Involved in Plant Gravitropic Signal Transduction

Gravity is a common stimulus affecting plant growth and development, from seed germination to positioning of flowers for pollination and seeds for dispersal. Classic models of plant gravitropism have revolved around biophysical perception of the gravity stimulus and the effects of plant growth regulators on the growth response. Transcriptional regulation of the gravitropic mechanism has been largely ignored. The aim of this experiment is to identify putative regulatory functional elements, including transcription factor binding sites and cis-regulatory modules involved in gravitropic signal transduction. In this article, we detailed a strategy to identify putative cis-regulatory elements by analyzing gene expression data from microarray experiments. Genes involved in the gravitropic perception– response pathway were identified based on their changes in expression level after gravity stimulation. Genes were clustered according to their expression patterns (transcriptional regulation profiles), and gene promoter were analyzed using genomics regulatory analysis software to identify candidate cis-regulatory elements and cis-regulatory modules. Analysis of the microarray data indicated that 154 genes were involved in the gravitropic response. The genes were grouped into 9 clusters based on expression profile similarities. An analysis of the promoters of the 154 genes resulted in the identification of 32 putative regulatory elements and 55 putative regulatory modules. Some of the elements are associated with individual clusters and other elements are associated with multiple clusters, potentially indicating elements involved in specific and in general gravitropic response processes, respectively.