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Plant Cell Advance Online Publication
Published on April 18, 2008; 10.1105/tpc.107.057075

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Received November 21, 2007
Returned for revision February 19, 2008
Accepted March 24, 2008

Distinct Light-Initiated Gene Expression and Cell Cycle Programs in the Shoot Apex and Cotyledons of Arabidopsis

Enrique López-Juez 1*, Edyta Dillon 1, Zoltán Magyar 2, Safina Khan 1, Saul Hazeldine 3, Sarah M. de Jager 4, James A.H. Murray 4, Gerrit T.S. Beemster 5, László Bögre 1, and Hugh Shanahan 3

1 School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom
2 School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom; Institute of Plant Biology, Biological Research Center, H-6701 Szeged, Hungary
3 Department of Computer Science, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom
4 Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, United Kingdom
5 Department of Plant Systems Biology, Flanders Institute of Biotechnology, B-9052 Gent, Belgium; Department of Molecular Genetics, Gent University, B-9052 Gent, Belgium

* To whom correspondence should be addressed. E-mail: e.lopez{at}rhul.ac.uk.

In darkness, shoot apex growth is repressed, but it becomes rapidly activated by light. We show that phytochromes and cryptochromes play largely redundant roles in this derepression in Arabidopsis thaliana. We examined the light activation of transcriptional changes in a finely resolved time course, comparing the shoot apex (meristem and leaf primordia) and the cotyledon and found >5700 differentially expressed genes. Early events specific to the shoot apices included the repression of genes for Really Interesting New Gene finger proteins and basic domain/leucine zipper and basic helix-loop-helix transcription factors. The downregulation of auxin and ethylene and the upregulation of cytokinin and gibberellin hormonal responses were also characteristic of shoot apices. In the apex, genes involved in ribosome biogenesis and protein translation were rapidly and synchronously induced, simultaneously with cell proliferation genes, preceding visible organ growth. Subsequently, the activation of signaling genes and transcriptional signatures of cell wall expansion, turgor generation, and plastid biogenesis were apparent. Furthermore, light regulates the forms and protein levels of two transcription factors with opposing functions in cell proliferation, E2FB and E2FC, through the Constitutively Photomorphogenic1 (COP1), COP9-Signalosome5, and Deetiolated1 light signaling molecules. These data provide the basis for reconstruction of the regulatory networks for light-regulated meristem, leaf, and cotyledon development.






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