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First published online August 26, 2005; 10.1104/pp.105.066290

Plant Physiology 139:316-328 (2005)
© 2005 American Society of Plant Biologists

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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Genome-Wide Identification of Potential Plant E2F Target Genes1,[w]

Klaas Vandepoele2, Kobe Vlieghe2, Kobe Florquin, Lars Hennig, Gerrit T.S. Beemster, Wilhelm Gruissem, Yves Van de Peer, Dirk Inzé* and Lieven De Veylder

Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9052 Gent, Belgium (K.V., K.V., K.F., G.T.S.B., Y.V.d.P., D.I., L.D.V.); and Institute of Plant Sciences, Swiss Federal Institute of Technology, Eidgenössische Technische Hochschule Center, LFW E57.1, CH–8092 Zürich, Switzerland (L.H., W.G.)

Entry into the S phase of the cell cycle is controlled by E2F transcription factors that induce the transcription of genes required for cell cycle progression and DNA replication. Although the E2F pathway is highly conserved in higher eukaryotes, only a few E2F target genes have been experimentally validated in plants. We have combined microarray analysis and bioinformatics tools to identify plant E2F-responsive genes. Promoter regions of genes that were induced at the transcriptional level in Arabidopsis (Arabidopsis thaliana) seedlings ectopically expressing genes for the E2Fa and DPa transcription factors were searched for the presence of E2F-binding sites, resulting in the identification of 181 putative E2F target genes. In most cases, the E2F-binding element was located close to the transcription start site, but occasionally could also be localized in the 5' untranslated region. Comparison of our results with available microarray data sets from synchronized cell suspensions revealed that the E2F target genes were expressed almost exclusively during G1 and S phases and activated upon reentry of quiescent cells into the cell cycle. To test the robustness of the data for the Arabidopsis E2F target genes, we also searched for the presence of E2F-cis-acting elements in the promoters of the putative orthologous rice (Oryza sativa) genes. Using this approach, we identified 70 potential conserved plant E2F target genes. These genes encode proteins involved in cell cycle regulation, DNA replication, and chromatin dynamics. In addition, we identified several genes for potentially novel S phase regulatory proteins.

1 This work was supported by grants from the Interuniversity Poles of Attraction Program-Belgian Science Policy (P5/13), the European Union (European Cell Cycle Consortium QLG2–CT1999–00454), the Swiss National Science Foundation (3100–061398), the Functional Genomics Center–Zurich, the Instituut voor de aanmoediging van Innovatie door Wetenschap en Technologie in Vlaanderen (predoctoral fellowships to K.V. and K.V.), and the Fund for Scientific Research (Flanders; postdoctoral fellowship to L.D.V.).

2 These authors contributed equally to the paper.

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

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.105.066290.

* Corresponding author; e-mail dirk.inze{at}psb.ugent.be; fax 32–9–3313809.

Received May 27, 2005; returned for revision July 7, 2005; accepted July 13, 2005.




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