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Nucleic Acids Research 2005 33(11):3479-3491; doi:10.1093/nar/gki658
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Published online 20 June 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation

Jiang Qian1,*, Noriko Esumi1, Yangjian Chen1, Qingliang Wang1, Itay Chowers3 and Donald J. Zack1,2

1Wilmer Institute, Johns Hopkins University School of Medicine Baltimore, MD 21287, USA 2Departments of Molecular Biology and Genetics, Neuroscience and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21287, USA 3Department of Ophthalmology, Hadassah University Hospital PO Box 12000, Jerusalem, 91120 Israel

*To whom correspondence should be addressed at Johns Hopkins University School of Medicine, Maumenee Bldg 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA. Tel: +1 443 287 3882; Fax: +1 410 502 5382; Email: jiang.qian{at}jhmi.edu

Received March 7, 2005. Revised April 28, 2005. Accepted May 26, 2005.

Identification of tissue-specific gene regulatory networks can yield insights into the molecular basis of a tissue's development, function and pathology. Here, we present a computational approach designed to identify potential regulatory target genes of photoreceptor cell-specific transcription factors (TFs). The approach is based on the hypothesis that genes related to the retina in terms of expression, disease and/or function are more likely to be the targets of retina-specific TFs than other genes. A list of genes that are preferentially expressed in retina was obtained by integrating expressed sequence tag, SAGE and microarray datasets. The regulatory targets of retina-specific TFs are enriched in this set of retina-related genes. A Bayesian approach was employed to integrate information about binding site location relative to a gene's transcription start site. Our method was applied to three retina-specific TFs, CRX, NRL and NR2E3, and a number of potential targets were predicted. To experimentally assess the validity of the bioinformatic predictions, mobility shift, transient transfection and chromatin immunoprecipitation assays were performed with five predicted CRX targets, and the results were suggestive of CRX regulation in 5/5, 3/5 and 4/5 cases, respectively. Together, these experiments strongly suggest that RP1, GUCY2D, ABCA4 are novel targets of CRX.


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