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An Arabidopsis Promoter Microarray and its Initial Usage in the Identification of HY5 Binding Targets in Vitro

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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 Arabidopsisgenome. 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.

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Authors and Affiliations

  1. Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, 100871, PR China

    Ying Gao, Zhangliang Chen, Lijia Qu & Xing Wang Deng

  2. Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA

    Ying Gao, Elizabeth Strickland & Xing Wang Deng

  3. School of Biological Sciences, Nanyang Technological University, Singapore, 637616, Singapore

    Jinming Li

  4. Bioinformatics and Computational Biology Track, Biological and Biomedical Sciences Program, Yale University, New Haven, CT, 06511, USA

    Sujun Hua

  5. Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, 06520, USA

    Hongyu Zhao

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  1. Ying Gao
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  2. Jinming Li
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Gao, Y., Li, J., Strickland, E. et al. An Arabidopsis Promoter Microarray and its Initial Usage in the Identification of HY5 Binding Targets in Vitro . Plant Mol Biol 54, 683–699 (2004). https://doi.org/10.1023/B:PLAN.0000040898.86788.59

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