ArticleGenome biology2024
Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Revisiting retinal and macular degeneration in the genomics era.Nature reviews. Genetics · 2026Review
- Enhanced chromatin compaction is associated with de novo expression of a nuclear microprotein, global loss of H3 acetylation and local transcriptional changes in retinal rod photoreceptors.Research square · 2026Article
- 3D epigenomic landscape of the human retinal pigment epithelium.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina.Science advances · 2026Article
- Retina-specific long non-coding RNAs associated with inherited retinal disease genes.Cellular and molecular life sciences : CMLS · 2026Article
- Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment.Nature communications · 2026Article
- Paired DNA and RNA sequencing uncovers common and rare variation regulating human retinal gene expression.Nature communications · 2026Article
- Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.Cell reports · 2026Article
- De novo and inherited dominant variants in U4 and U6 snRNA genes cause retinitis pigmentosa.Nature genetics · 2026Article
- De novo and inherited dominant variants in U4 and U6 snRNAs cause retinitis pigmentosa.medRxiv : the preprint server for health sciences · 2025Article
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Authors and funding
17 authors.
Funding
Abstract
backgroundVision depends on the interplay between photoreceptor cells of the neural retina and the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases display specific spatiotemporal expression within these interconnected retinal components through the local recruitment of cis-regulatory elements (CREs) in 3D nuclear space.
resultsTo understand the role of differential chromatin architecture in establishing tissue-specific expression at inherited retinal disease loci, we mapped genome-wide chromatin interactions using in situ Hi-C and H3K4me3 HiChIP on neural retina and RPE/choroid from human adult donor eyes. We observed chromatin looping between active promoters and 32,425 and 8060 candidate CREs in the neural retina and RPE/choroid, respectively. A comparative 3D genome analysis between these two retinal tissues revealed that 56% of 290 known inherited retinal disease genes were marked by differential chromatin interactions. One of these was ABCA4, which is implicated in the most common autosomal recessive inherited retinal disease. We zoomed in on retina- and RPE-specific cis-regulatory interactions at the ABCA4 locus using high-resolution UMI-4C. Integration with bulk and single-cell epigenomic datasets and in vivo enhancer assays in zebrafish revealed tissue-specific CREs interacting with ABCA4.
conclusionsThrough comparative 3D genome mapping, based on genome-wide, promoter-centric, and locus-specific assays of human neural retina and RPE, we have shown that gene regulation at key inherited retinal disease loci is likely mediated by tissue-specific chromatin interactions. These findings do not only provide insight into tissue-specific regulatory landscapes at retinal disease loci, but also delineate the search space for non-coding genomic variation underlying unsolved inherited retinal diseases.
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