Genome-Wide Identification of Potential Plant E2F Target Genes (original) (raw)

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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.)

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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.)

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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.)

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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.)

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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.)

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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.)

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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.)

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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.)

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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.)

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Revision received:

07 July 2005

Published:

26 August 2005

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Klaas Vandepoele, Kobe Vlieghe, Kobe Florquin, Lars Hennig, Gerrit T.S. Beemster, Wilhelm Gruissem, Yves Van de Peer, Dirk Inzé, Lieven De Veylder, Genome-Wide Identification of Potential Plant E2F Target Genes, Plant Physiology, Volume 139, Issue 1, September 2005, Pages 316–328, https://doi.org/10.1104/pp.105.066290
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Abstract

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.

© 2005 American Society of Plant Biologists

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