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Philip Andrew Ruzycki, Courtney Danielle Linne, Shiming Chen; Long Range Genomic Interactions Regulate Photoreceptor Gene Expression. Invest. Ophthalmol. Vis. Sci. 2017;58(8):4774.
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© ARVO (1962-2015); The Authors (2016-present)
Precise packaging of genomic DNA into the nucleus is critical for assuring that the cell expresses certain genes and silences others. Photoreceptors offer a powerful system to determine the role of genomic DNA packaging. We recently discovered that, in rods, some highly expressed loci on the same or different chromosomes physically interact. The Rhodopsin (Rho) locus is the most active region of the rod genome and its mutation causes blinding diseases. This study aimed to determine whether inactivation of this locus affects genomic interactions and the expression of other genes in trans.
Long-range genomic interactions of the Rho locus in mouse retinas were identified using Circularized Chromatin Conformation Capture (4C) and confirmed using 3D-Fluorescence In Situ Hybridization (3DFISH) in retinas from wild-type (WT) mice and from other species. The functional importance of the Rho interactome was investigated in strains lacking Crx, Nrl, or with a CRISPR-mediated deletion of the Rho promoter or enhancer. 3DFISH, qRT-PCR, and RNAseq were used to reveal the consequences of these genetic manipulations on 3D genomic organization and expression of Rho and other genes with which Rho physically interacts.
4C and 3DFISH assays on P14 WT (rod-dominant) mouse retinas detected several long-range interactions of actively transcribed genes. In rods, Rho interacted specifically with some active regions on the same chromosome (cis interactions) and with several other rod-expressed genes on different chromosomes (trans interactions), but at lower frequencies. Retinal 3DFISH on different species suggests that these interactions are highly conserved, although they were lost in mice lacking Crx or Nrl. Mice lacking Rho promoter, but not its enhancer, also showed decreased Rho interactions. This decrease correlated with the loss of Rho transcripts and altered expression of Rho-interacting genes as detected by quantitative RT-PCR and RNAseq.
Together, our results suggest that Rho genomic interactions in the rod nucleus are important for co-expression of a subset of rod-specific genes. These interactions depend on cell type-specific transcription factors and Rho promoter activity. Inactivation of the Rho locus can affect other genes in trans. This previously unexplored epigenetic mechanism provides a new insight into pathogenic mis-regulation of gene expression in retina development and disease.
This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.
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