Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development.
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.
Lee
Jungeun
J
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Conecticut 06520-8104, USA.
He
Kun
K
Stolc
Viktor
V
Lee
Horim
H
Figueroa
Pablo
P
Gao
Ying
Y
Tongprasit
Waraporn
W
Zhao
Hongyu
H
Lee
Ilha
I
Deng
Xing Wang
XW
D000217:Acyltransferases / Q000235:genetics / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development* / Q000528:radiation effects*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D050976:Basic-Leucine Zipper Transcription Factors / Q000378:metabolism*; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D002940:Circadian Rhythm / Q000235:genetics / Q000528:radiation effects; D000939:Epitopes; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics* / Q000528:radiation effects; D008027:Light; D009687:Nuclear Proteins / Q000378:metabolism*; D009928:Organ Specificity / Q000235:genetics / Q000528:radiation effects; D010788:Photosynthesis / Q000235:genetics / Q000528:radiation effects; D030821:Plants, Genetically Modified; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding / Q000528:radiation effects
D029681:Arabidopsis Proteins; D050976:Basic-Leucine Zipper Transcription Factors; D000939:Epitopes; C109254:HY5 protein, Arabidopsis; D009687:Nuclear Proteins; D000217:Acyltransferases; C020141:flavanone synthetase