Plant Physiology 136:3009-3022 (2004)
© 2004 American Society of Plant Biologists
GENOME ANALYSIS
Transcriptional Similarities, Dissimilarities, and Conservation of cis-Elements in Duplicated Genes of Arabidopsis1,[w]
Georg Haberer,
Tobias Hindemitt,
Blake C. Meyers and
Klaus F.X. Mayer*
Munich Information Center for Protein Sequences, Institute for Bioinformatics, GSF Research Center for Environment and Health, 85758 Neuherberg, Germany (G.H., T.H., K.M.); and Department of Plant and Soil Sciences, Delaware Biotechnology Institute, Newark, Delaware 19711 (B.C.M.)
In plants, duplication of individual genes, long chromosomal regions, and complete genomes provides a major source for evolutionary innovation. We investigated two different types of duplications, tandem and segmental duplications, in Arabidopsis for correlation, conservation, and differences of expression characteristics by making use of large genome-wide expression data as measured by the massively parallel signature sequencing method. Our analysis indicates that large fractions of duplicated gene pairs still share transcriptional characteristics. However, our results also indicate that expression divergence occurs frequently between duplicated gene pairs, a process which frequently might be employed for the retention of sequence redundant gene pairs. Preserved overall similarity between promoters of duplicated genes as well as preservation of individual cis-elements within the respective promoters indicates that the process of transcriptional neo- and subfunctionalization is restricted to only a fraction of cis-elements. We show that sequence similarities and shared regulatory properties within duplicated promoters provide a powerful means to undertake large-scale cis-regulatory element identification by applying an intragenomic phylogenetic footprinting approach. Our work lays a foundation for future comparative studies to elucidate the molecular manifestation of regulatory similarities and dissimilarities of duplicated genes.
1 This work was supported by the Deutsche Forschungsgemeinschaft (grant no. MA 2522/1–1 to K.F.X.M.) and by the National Science Foundation Plant Genome Research Program (DBI–0110528 to B.C.M.).
[w] The online version of this article contains Web-only data.
www.plantphysiol.org/cgi/doi/10.1104/pp.104.046466.
* Corresponding author; e-mail k.mayer{at}gsf.de; fax 49–89–3187–3585.
Received May 14, 2004;
returned for revision July 28, 2004;
accepted July 29, 2004.
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