ArticleNature communications2022
Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 35 citations in OpenAlex.
- Linking Iris Cis-Regulatory Variants to Primary Angle-Closure Glaucoma Via Clinical Imaging and Multiomics.Investigative ophthalmology & visual science · 2024Pooled it
- Analyzing cell-type-specific isoform expression using IsoDiffR and long-read single-cell RNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- Impact of Smoking on the Efficacy of Human Autologous Oral Mucosal Epithelial Cell Sheet Transplantation for Treating Limbal Stem Cell Deficiency.Stem cells international · 2026Article
- The 3D Genome Structure of a Blcap-Linked Silencer Loop Regulates Terminal Differentiation During Lens Fiber Cell Denucleation.Investigative ophthalmology & visual science · 2025Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- Defining heterogeneity in core regulatory circuitry reveals HOXB3 condensation as a potential target in glioblastoma.Nature cell biology · 2025Article
- 3D Genome Architecture in Stem Cell Lineage Commitment: from Structural Organization to Precision Regulation.Advanced genetics (Hoboken, N.J.) · 2025Review
- CTCF-mediated 3D chromatin sets up the gene expression program in the male germline.Nature structural & molecular biology · 2025Article
- Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity.Nature communications · 2025Article
- Multiscale 3D genome rewiring during PTF1A-mediated somatic cell reprogramming into neural stem cells.Communications biology · 2024Article
- Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer.Nature cancer · 2024Article
- RAD21 deficiency drives corneal to scleral differentiation fate switching via upregulating WNT9B.iScience · 2024Article
- Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers.Epigenetics & chromatin · 2024Article
- Impact of Equine Ocular Surface Squamous Neoplasia on Interactions between Ocular Transcriptome and Microbiome.Veterinary sciences · 2024Article
- The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation.Nature communications · 2024Article
- Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome.Genome research · 2023Article
- 3D genomic organization in cancers.Quantitative biology (Beijing, China) · 2023Review
- ETS1-HMGA2 Axis Promotes Human Limbal Epithelial Stem Cell Proliferation.Investigative ophthalmology & visual science · 2023Article
- Corneal regeneration: insights in epithelial stem cell heterogeneity and dynamics.Current opinion in genetics & development · 2022Review
Corrections and comments
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Authors and funding
22 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The insights into how genome topology couples with epigenetic states to govern the function and identity of the corneal epithelium are poorly understood. Here, we generate a high-resolution Hi-C interaction map of human limbal stem/progenitor cells (LSCs) and show that chromatin multi-hierarchical organisation is coupled to gene expression. By integrating Hi-C, epigenome and transcriptome data, we characterize the comprehensive 3D epigenomic landscapes of LSCs. We find that super-silencers mediate gene repression associated with corneal development, differentiation and disease via chromatin looping and/or proximity. Super-enhancer (SE) interaction analysis identified a set of SE interactive hubs that contribute to LSC-specific gene activation. These active and inactive element-anchored loop networks occur within the cohesin-occupied CTCF-CTCF loops. We further reveal a coordinated regulatory network of core transcription factors based on SE-promoter interactions. Our results provide detailed insights into the genome organization principle for epigenetic regulation of gene expression in stratified epithelia.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.