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First published online March 2, 2007; 10.1105/tpc.106.047688

The Plant Cell 19:731-749 (2007)
© 2007 American Society of Plant Biologists

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Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development[W]

Jungeun Leea,b,1, Kun Hec,1, Viktor Stolca,d, Horim Leeb, Pablo Figueroaa, Ying Gaoa,c, Waraporn Tongprasite, Hongyu Zhaof, Ilha Leeb,2 and Xing Wang Denga,c,2

a Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
b Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea
c Peking–Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering and College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
d Genome Research Facility, NASA Ames Research Center, Moffett Field, California 94035
e Eloret Corporation, Sunnyvale, California 94087
f Department of Epidemiology and Public Health, School of Medicine, Yale University, New Haven, Connecticut 06520

2 To whom correspondence should be addressed. E-mail ilhalee{at}snu.ac.kr or xingwang.deng{at}yale.edu; fax 822-872-1993 or 203-432-3854.

The transcription factor LONG HYPOCOTYL5 (HY5) acts downstream of multiple families of the photoreceptors and promotes photomorphogenesis. Although it is well accepted that HY5 acts to regulate target gene expression, in vivo binding of HY5 to any of its target gene promoters has yet to be demonstrated. Here, we used a chromatin immunoprecipitation procedure to verify suspected in vivo HY5 binding sites. We demonstrated that in vivo association of HY5 with promoter targets is not altered under distinct light qualities or during light-to-dark transition. Coupled with DNA chip hybridization using a high-density 60-nucleotide oligomer microarray that contains one probe for every 500 nucleotides over the entire Arabidopsis thaliana genome, we mapped genome-wide in vivo HY5 binding sites. This analysis showed that HY5 binds preferentially to promoter regions in vivo and revealed >3000 chromosomal sites as putative HY5 binding targets. HY5 binding targets tend to be enriched in the early light-responsive genes and transcription factor genes. Our data thus support a model in which HY5 is a high hierarchical regulator of the transcriptional cascades for photomorphogenesis.


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