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Philip Andrew Ruzycki, Shiming Chen; Circularized Chromatin Conformation Capture (4C-seq) Identified Differences in Genome Organization Between Rod and Cone Photoreceptors. Invest. Ophthalmol. Vis. Sci. 2015;56(7 ):1320.
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© ARVO (1962-2015); The Authors (2016-present)
Rod and cone photoreceptors arise from common precursor cells and have similar functions, but they differ in their morphology and gene expression. Many previous studies have elucidated the network of transcription factors that controls rod vs cone fate decisions, but little is known about the importance of epigenetic modifications, particularly genome organization in these decisions and the maintenance of proper gene expression. Previous published studies from our lab used Chromatin Conformation Capture (3C) to study interactions of opsin genes with local enhancer elements. We found that such interactions were specific to the cell type in which the opsin molecule was expressed. Here we further investigate both short-range and long-range genomic interactions of 20 differentially expressed genes in rods, cones, and a control cell population.
To assay these interactions, we used Circularized Chromatin Conformation Capture with high throughput sequencing (4C-seq), as it offers the best resolution of genome-wide interactions from particular regions of interest. We have analyzed the interactions in rods and cones at two postnatal ages, and Pro-T cells as a control.
Our results first confirmed previously published data describing cell type specific interactions between local enhancers and promoters. As 4C-seq is an unbiased genome-wide analysis method, we also pinpointed novel interactions with a number of other regions on the same and on different chromosomes that could affect gene expression of tested genes. We also analyzed 4C-seq-identified interactions in the context of published datasets describing other epigenetic phenomena, such as DNase I hypersensitivity (chromatin accessibility), binding profiles of photoreceptor transcription factors and regulatory histone marks, as well as transcriptional status.
4C-seq analysis provides a new understanding of higher levels of epigenetic regulation of photoreceptor gene expression. It also reveals how active and inactive genes are dynamically organized during development in the rod and cone nuclei.
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