First published online April 29, 2005; 10.1104/pp.104.053884
Plant Physiology 138:734-743 (2005)
© 2005 American Society of Plant Biologists
DEVELOPMENT AND HORMONE ACTION
Genome-Wide Analysis of Gene Expression Profiles Associated with Cell Cycle Transitions in Growing Organs of Arabidopsis1,[w]
Gerrit T.S. Beemster,
Lieven De Veylder,
Steven Vercruysse,
Gerrit West,
Debbie Rombaut,
Paul Van Hummelen,
Arnaud Galichet,
Wilhelm Gruissem,
Dirk Inzé* and
Marnik Vuylsteke
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9052 Ghent, Belgium (G.T.S.B., L.D.V., S.V., G.W., D.R., D.I., M.V.); Microarray Facility, Flanders Interuniversity Institute for Biotechnology, 3000 Louvain, Belgium (P.V.H.); and Institute of Plant Sciences, Swiss Federal Institute of Plant Sciences, Swiss Federal Institute of Technology, CH–8092 Zurich, Switzerland (A.G., W.G.)
Organ growth results from the progression of component cells through subsequent phases of proliferation and expansion before reaching maturity. We combined kinematic analysis, flowcytometry, and microarray analysis to characterize cell cycle regulation during the growth process of leaves 1 and 2 of Arabidopsis (Arabidopsis thaliana). Kinematic analysis showed that the epidermis proliferates until day 12; thereafter, cells expand until day 19 when leaves reach maturity. Flowcytometry revealed that endoreduplication occurs from the time cell division rates decline until the end of cell expansion. Analysis of 10 time points with a 6k-cDNA microarray showed that transitions between the growth stages were closely reflected in the mRNA expression data. Subsequent genome-wide microarray analysis on the three main stages allowed us to categorize known cell cycle genes into three major classes: constitutively expressed, proliferative, and inhibitory. Comparison with published expression data obtained from root zones corresponding to similar developmental stages and from synchronized cell cultures supported this categorization and enabled us to identify a high confidence set of 131 proliferation genes. Most of those had an M phase-dependent expression pattern and, in addition to many known cell cycle-related genes, there were at least 90 that were unknown or previously not associated with proliferation.
1 This work was supported by the Interuniversity Poles of Attraction Programme-Belgian Science Policy (grant no. P5/13) and by the European Commission Quality of Life and Management of Living Resources program (grant no. QLK5–CT–2001–01871).
[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.104.053884.
* Corresponding author; e-mail dirk.inze{at}psb.ugent.be; fax 32–(0)9–33–13–809.
Received September 22, 2004;
returned for revision December 23, 2004;
accepted December 23, 2004.
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