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Chromatin immunoprecipitation identifies photoreceptor transcription factor targets in mouse models of retinal degeneration: New findings and challenges

Published online by Cambridge University Press:  06 December 2005

GUANG-HUA PENG  and
SHIMING CHEN
GUANG-HUA PENG
Affiliation:
Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis
SHIMING CHEN
Affiliation:
Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St. Louis
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Abstract

The transcription factors, Otx2, Crx, Nrl, and Nr2e3, expressed by retinal photoreceptor cells are essential for photoreceptor gene expression, development, and maintenance. Malfunction of any of these factors due to genetic mutations causes photoreceptor disease. Protein–protein interaction studies suggest that these factors may form a regulatory network centered on Crx. To understand how these factors regulate photoreceptor gene transcription in vivo, we have employed chromatin immunoprecipitation (ChIP) assays to assess the ability of these proteins to bind to regulatory sequences of photoreceptor genes in the retina of wild-type and mutant mice with photoreceptor degeneration. This paper summarizes the advantages and limitations of ChIP, using examples from our studies to demonstrate how this technique has contributed to our understanding of the regulation of photoreceptor gene expression. We report that Crx, Otx2, Nrl, and Nr2e3 co-occupy the promoter/enhancer, but not the region 3′ of selected Crx target genes, in a retina-specific fashion. We identified Crx-dependent (Nr2e3) and Crx-independent (Otx2 and Nrl) target binding using Crx knockout mice (Crx−/−), suggesting that individual factors may use distinct mechanism(s) for binding and regulating target genes. Consistent with ChIP results, we also found that Otx2, a close family member of Crx, can activate the promoter of rod and cone genes in HEK293 cells, implicating Otx2 in regulating photoreceptor gene expression. These findings provide important information for understanding how photoreceptor transcription factors regulate photoreceptor gene expression and the mechanisms by which mutations in these factors cause transcriptional dysregulation and photoreceptor degeneration.

Keywords

Photoreceptor transcription factorsTargetsChromatin immunoprecipitationRetinal degeneration
Type
Research Article
Information
Visual Neuroscience , Volume 22 , Issue 5 , September 2005 , pp. 575 - 586
Copyright
© 2005 Cambridge University Press

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