X. Liang, K. Shen, J. Lichtenberg, S.E. Wyatt, and L.R. Welch
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Gravitropism, motif discovery, regulatory genomics, module discov-ery, gene expression∗ School of Electrical Engineering and Computer Science, OhioUniversity, Athens, Ohio, USA∗∗ Department of Environmental and Plant Biology, Ohio Uni-versity, Athens, Ohio, USA∗∗∗ Molecular and Cellular Biology Program, Ohio University,Athens, Ohio, USA∗∗∗∗ Biomedical Engineering Program, Ohio Uni-versity, Athens, Ohio, USA; e-mail:{xl187007,ks280007,lichtenj,wyatts,welch}@ohio.edu
Gravity is a common stimulus affecting plant growth and develop- ment, from seed germination to positioning of flowers for pollina- tion 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 bind- ing 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 mi- croarray experiments. Genes involved in the gravitropic perception– response pathway were identified based on their changes in ex- pression level after gravity stimulation. Genes were clustered ac- cording to their expression patterns (transcriptional regulation pro- files), 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.
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