ArticleCell reports2023
Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids.
Article in Cell reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 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
- Human retinal organoid model of disease-relevant photoreceptor cell death amenable to drug screening.Cell death & disease · 2026Article
- DeepExDC interprets genomic compartmentalization changes in single-cell Hi-C data.Briefings in bioinformatics · 2025Article
- Spatiotemporally resolved transcriptomics reveals the cellular dynamics of human retinal development.Nature communications · 2025Article
- Epigenome-metabolism nexus in the retina: implications for aging and disease.Trends in genetics : TIG · 2024Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We have generated a high-resolution Hi-C map of developing human retinal organoids to elucidate spatiotemporal dynamics of genomic architecture and its relationship with gene expression patterns. We demonstrate progressive stage-specific alterations in DNA topology and correlate these changes with transcription of cell-type-restricted gene markers during retinal differentiation. Temporal Hi-C reveals a shift toward A compartment for protein-coding genes and B compartment for non-coding RNAs, displaying high and low expression, respectively. Notably, retina-enriched genes are clustered near lost boundaries of topologically associated domains (TADs), and higher-order assemblages (i.e., TAD cliques) localize in active chromatin regions with binding sites for eye-field transcription factors. These genes gain chromatin contacts at their transcription start site as organoid differentiation proceeds. Our study provides a global view of chromatin architecture dynamics associated with diversification of cell types during retinal development and serves as a foundational resource for in-depth functional investigations of retinal developmental traits.
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Registered trials
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