Differential 3D genome topology shapes the regulatory landscapes of IRD genes in human neural retina and retinal pigment epithelium

Abstract

Purpose : Many genes involved in inherited retinal diseases (IRD) display a highly specific expression pattern within the human retina. This specificity is achieved via complex gene regulatory programs, involving thousands of cis-regulatory elements physically interacting with retinal target genes in topologically associating domains (TADs) within 3D nuclear space. In this study, we investigated the role of differential 3D genome topology in establishing tissue-specific expression patterns at IRD loci in the human neural retina, as compared to the underlying retinal pigment epithelium (RPE) and choroid.

Methods : We used in situ Hi-C to map 3D genomic interactions in the neural retina and RPE/choroid dissected from post-mortem adult donor eyes (n=4). Regions with differential 3D topology and/or differential chromatin looping in neural retina vs. RPE/choroid were identified on a genome-wide basis using, respectively, CHESS and HICCUPS. To identify chromatin loops involving active gene promoters at a high resolution (5 kb), we also performed H3K4me3 HiChIP on the same tissues (n=2) and determined both differential and stable loops using FitHiChIP.

Results : Within the genome-wide Hi-C interaction maps, we identified 535 loci with differential 3D features in neural retina vs. RPE/choroid and 740 differential chromatin loops, while HiChIP analyses greatly boosted sensitivity to identify promoter interactions, revealing over 40,000 differential loops with a resolution of 5kb. Genes within these differential loci and at differential loop anchors, were enriched for known IRD disease genes and a subset displayed specific expression in cell types of either the neural retina or the RPE/choroid. Overall, we found that almost 60% of known IRD genes were marked by differential 3D genome topology, ranging from simple increases in interaction frequency or gain of chromatin looping to rearrangements of higher-order 3D structures such as topologically associated domains.

Conclusions : In summary, with our comparative analysis of 3D genome topology in the human adult neural retina vs. RPE/choroid we demonstrate that gene regulation at key IRD loci is likely mediated by tissue-specific 3D topologies and chromatin looping.

This abstract was presented at the 2023 ARVO Annual Meeting, held in New Orleans, LA, April 23-27, 2023.