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First published online March 24, 2006; 10.1104/pp.105.076331 Plant Physiology 141:85-96 (2006) © 2006 American Society of Plant Biologists Identification of Primary Target Genes of Phytochrome Signaling. Early Transcriptional Control during Shade Avoidance Responses in Arabidopsis1Departament de Genètica Molecular (Institut de Biologia Molecular de Barcelona), Laboratori de Genètica Vegetal, Consorci CSIC-IRTA, 08034 Barcelona, Spain (I.R.-V., J.B., C.S., J.F.M.-G.); School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom (P.F.D.); and Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain (J.F.M.-G.)
The phytochrome (phy) photoreceptors modulate plant development after perception of light. Upon illumination of etiolated seedlings, phys initiate a transcriptional cascade by directly transducing light signals to the promoters of genes encoding regulators of morphogenesis. In light-grown plants, however, little is known about the transcriptional cascade modulated by phys in response to changes in light. The phy entry points in this cascade are completely unknown. We are particularly interested in the shade avoidance syndrome (SAS). Here we describe a subset of six genes whose expression is rapidly modulated by phys during both deetiolation and SAS in Arabidopsis (Arabidopsis thaliana). Using cycloheximide, we provide evidence that four of these phy rapidly regulated (PAR) genes are direct targets of phy signaling during SAS, revealing these genes as upstream components of the transcriptional cascade. Promoter-
1 This work was supported by the Spanish Ministerio de Educación y Ciencia-Fonds Européen de Développement Régional (grant nos. BIO20002–00298 and BIO2005–00154 to J.F.M.-G.); the Consejo Superior de Investigaciones Cientificas and the Royal Society (grant nos. 2004GB00016 to J.F.M.-G. and 2004/R1–EU to P.F.D.); and the University of London Central Research Fund (grant no. AR/CRF/B to P.F.D.). I.R.-V. is the recipient of a predoctoral fellowship from the Spanish Ministerio de Educación y Ciencia (reference no. BES–2003–1873); J.B. and C.S. are funded by postdoctoral contracts from the Departament d'Universitats Recerca i Societat de la Informació, Generalitat de Catalunya (reference nos. 2004 CRED 10003 and 2004 CRED 00058, respectively). We are part of the Grup de Recerca Emergent (grant no. 2005SGR 00284). The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Jaime F. Martínez-García (jmggmg{at}ibmb.csic.es). Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.105.076331. * Corresponding author; e-mail jmggmg{at}ibmb.csic.es; fax 34–93–204–5904. Received December 27, 2005; returned for revision March 20, 2006; accepted March 20, 2006. This article has been cited by other articles:
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-glucuronidase fusions confirmed that PAR genes are photoregulated at the transcriptional level. Analysis of gene expression in light signal transduction mutants showed that COP1 and DET1 (but not DET2 or HY5) play a role in modulating PAR expression in response to shade in light-grown seedlings. Moreover, genetic analyses showed that one of the genes identified as a direct target of phy signaling was phy-interacting factor 3-like-1 (PIL1). PIL1 has previously been implicated in SAS in response to transient shade, but we show here that it also plays a key role in response to long-term shade. The action of PIL1 was particularly apparent in a phyB background, suggesting an important negative role for PIL1 under dense vegetation canopies. 
