title: An arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro.
abstract: To analyze transcription factor-promoter interactions in Arabidopsis, a general strategy for generating a promoter microarray has been established. This includes an integrated platform for promoter sequence extraction and the design of primers for the PCR amplification of the promoter regions of annotated genes in the Arabidopsis genome. A web-interfaced primer-retrieval program was used to obtain up to 10 primer pairs with a suitability ranking given to each gene. We selected primer pairs for the promoters of about 3800 genes, and greater than 95% of the promoter fragments from the total genomic DNA were successfully amplified by PCR. These PCR products were purified and used to print an Arabidopsis promoter microarray. This initial promoter microarray was used to study the in vitro binding of the transcription factor HY5 to its promoter targets. A set of promoter fragments exhibited consistent and strong interaction with the HY5 protein in vitro, and computational analysis revealed that they were enriched with the HY5 consensus binding G-box motif. Thus, a promoter microarray can be a useful tool for identifying transcription factor binding sites at the genomic scale in higher plants.
authors.affiliation: Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, PR China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Gao
authors.forename: Jinming
authors.initials: J
authors.lastname: Li
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Strickland
authors.forename: Sujun
authors.initials: S
authors.lastname: Hua
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.forename: Zhangliang
authors.initials: Z
authors.lastname: Chen
authors.forename: Lijia
authors.initials: L
authors.lastname: Qu
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism*; D001483:Base Sequence; D050976:Basic-Leucine Zipper Transcription Factors; D001665:Binding Sites / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D030561:Databases, Nucleic Acid; D018745:Genome, Plant; D046228:Microarray Analysis / Q000379:methods* / Q000592:standards; D009687:Nuclear Proteins / Q000378:metabolism*; D016133:Polymerase Chain Reaction / Q000379:methods; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D015203:Reproducibility of Results
chemical_list: D029681:Arabidopsis Proteins; D050976:Basic-Leucine Zipper Transcription Factors; D017931:DNA Primers; D018744:DNA, Plant; C109254:HY5 protein, Arabidopsis; D009687:Nuclear Proteins