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Timothy Joel Cherry, Marty G. Yang, David Harmin, Michael E. Greenberg; Regulation of disease gene expression in the retina and retinal pigment epithelium by tissue-specific enhancers.. Invest. Ophthalmol. Vis. Sci. 2016;57(12):4814.
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© ARVO (1962-2015); The Authors (2016-present)
Enhancers are non-coding gene regulatory elements in the genome that control organismal development through the precise coordination of genetic programs to regulate cell fate and function. Genetic mutations within enhancers can contribute to visual disorders; however identifying these mutations is difficult because the genomic location and function of enhancers that are relevant for vision are largely unknown. To define the genomic search-space for disease-causing mutations in non-coding regulatory DNA, we sought to comprehensively identify and characterize functional enhancers in the mammalian retina and retinal pigment epithelium (RPE) with a focus on enhancers that regulate the expression of genes that have been implicated in visual disorders.
We performed genome-wide, epigenetic analyses using ATAC-Seq, ChIP-Seq and total RNA-Seq to identify functional enhancers that drive gene expression in the mammalian retina and RPE. To validate enhancer activity we performed in vitro and in vivo reporter assays. We next performed transcription factor binding motif enrichment analysis, ChIP-Seq and genome-wide DNA protection assays to identify transcription factors (TFs) that bind these enhancers to drive the expression of genes implicated in visual disorders. Lastly, we compared the function of enhancer sequences across species to determine the effects of genetic variation on enhancer activity and regulation of gene expression.
We identified functional tissue-specific enhancers in a genome-wide manner in the retina and RPE, including enhancers that regulate known visual disease genes such as ABCA4, USH2A and RPE65. Within these enhancers we mapped transcription factor binding sites that are required for enhancer activity and gene expression. Finally, we identified species-specific DNA sequence changes that alter the function of enhancers between mammalian species.
This work demonstrates the nature of gene regulatory elements that control gene expression in the retina and RPE and also reveals regions of the genome that may harbor mutations that contribute to ocular diseases.
This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.
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