An arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro.
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.
Gao
Ying
Y
Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, PR China.
Li
Jinming
J
Strickland
Elizabeth
E
Hua
Sujun
S
Zhao
Hongyu
H
Chen
Zhangliang
Z
Qu
Lijia
L
Deng
Xing Wang
XW
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
D029681:Arabidopsis Proteins; D050976:Basic-Leucine Zipper Transcription Factors; D017931:DNA Primers; D018744:DNA, Plant; C109254:HY5 protein, Arabidopsis; D009687:Nuclear Proteins