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SYSTEMS BIOLOGY, MOLECULAR BIOLOGY, AND GENE REGULATION

Conservation, Convergence, and Divergence of Light-Responsive, Circadian-Regulated, and Tissue-Specific Expression Patterns during Evolution of the Arabidopsis GATA Gene Family^1,[W],[OA]

Centre for Plant Sciences, Institute for Integrative and Comparative Biology (I.W.M., P.M.G.), and Institute for Molecular and Cellular Biology (C.-H.J., D.R.W.), Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom; and School of Biological Sciences, Royal Holloway, University of London, Egham, TW20 0EX, United Kingdom (P.F.D.)

In vitro analyses of plant GATA transcription factors have implicated some proteins in light-mediated and circadian-regulated gene expression, and, more recently, the analysis of mutants has uncovered further diverse roles for plant GATA factors. To facilitate function discovery for the 29 GATA genes in Arabidopsis (Arabidopsis thaliana), we have experimentally verified gene structures and determined expression patterns of all family members across adult tissues and suspension cell cultures, as well as in response to light and signals from the circadian clock. These analyses have identified two genes that are strongly developmentally light regulated, expressed predominantly in photosynthetic tissue, and with transcript abundance peaking before dawn. In contrast, several GATA factor genes are light down-regulated. The products of these light-regulated genes are candidates for those proteins previously implicated in light-regulated transcription. Coexpression of these genes with well-characterized light-responsive transcripts across a large microarray data set supports these predictions. Other genes show additional tissue-specific expression patterns suggesting novel and unpredicted roles. Genome-wide analysis using coexpression scatter plots for paralogous gene pairs reveals unexpected differences in cocorrelated gene expression profiles. Clustering the Arabidopsis GATA factor gene family by similarity of expression patterns reveals that genes of recent descent do not uniformly show conserved current expression profiles, yet some genes showing more distant evolutionary origins have acquired common expression patterns. In addition to defining developmental and environmental dynamics of GATA transcript abundance, these analyses offer new insights into the evolution of gene expression profiles following gene duplication events.

² Present address: Genome Research Centre (VYMGC), National Yang-Ming University, 155 Li-Nong St., Taipei City 112, Taiwan.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Philip M. Gilmartin (p.m.gilmartin{at}leeds.ac.uk).

^[W] The online version of this article contains Web-only data.

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.106.090761

^* Corresponding author; e-mail p.m.gilmartin{at}leeds.ac.uk; fax 0044–113–343–3144.

Received October 11, 2006; accepted December 10, 2006; published January 5, 2007.

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