An arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro

Plant Molecular Biology
Ying GaoXing Wang Deng

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.

Citations

Jan 20, 2007·Omics : a Journal of Integrative Biology·David W Galbraith
Jun 29, 2011·BMC Bioinformatics·Changqing ZhangXiang Gao
Jan 16, 2007·The Plant Journal : for Cell and Molecular Biology·Filip VandenbusscheMargaret Ahmad
Dec 23, 2011·Physiologia Plantarum·Christina Lang-MladekMarie-Theres Hauser
Sep 19, 2006·Current Opinion in Plant Biology·Séverine LorrainChristian Fankhauser
Nov 28, 2006·Genomics, Proteomics & Bioinformatics·Asad Jan, Setsuko Komatsu
Mar 20, 2012·Protein & Cell·Jigang LiXing Wang Deng

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