ArticleGenome biology2022
3D genome organization in the epithelial-mesenchymal transition spectrum.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 26 citations in OpenAlex.
- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- Harmonizing single-cell 3D genome data with STARK and scNucleome.Genome biology · 2026Article
- Recent advances in single-cell bioinformatics for inferring higher-order chromatin contact maps.BMB reports · 2025Review
- Article
- Deciphering pre-existing and induced 3D genome architecture changes involved in constricted melanoma migration.iScience · 2025Article
- Rewiring cancer: 3D genome determinants of cancer hallmarks.Current opinion in genetics & development · 2025Review
- Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription.Genomics, proteomics & bioinformatics · 2024Article
- Regulating epithelial-mesenchymal plasticity from 3D genome organization.Communications biology · 2024Review
- DiffDomain enables identification of structurally reorganized topologically associating domains.Nature communications · 2024Article
- 3D genome alterations and editing in pathology.Molecular therapy : the journal of the American Society of Gene Therapy · 2023Review
- Role of epithelial-mesenchymal transition factor SNAI1 and its targets in ovarian cancer aggressiveness.Journal of cancer metastasis and treatment · 2023Article
- Novel biological insights revealed from the investigation of multiscale genome architecture.Computational and structural biotechnology journal · 2023Review
- AP-2δ Is the Most Relevant Target of AP-2 Family-Focused Cancer Therapy and Affects Genome Organization.Cells · 2022Article
- 3D genome organization in the epithelial-mesenchymal transition spectrum.Genome biology · 2022Article
- Every gene everywhere all at once: High-precision measurement of 3D chromosome architecture with single-cell Hi-C.Frontiers in molecular biosciences · 2022Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe plasticity along the epithelial-mesenchymal transition (EMT) spectrum has been shown to be regulated by various epigenetic repertoires. Emerging evidence of local chromatin conformation changes suggests that regulation of EMT may occur at a higher order of three-dimensional genome level.
resultsWe perform Hi-C analysis and combine ChIP-seq data across cancer cell lines representing different EMT states. We demonstrate that the epithelial and mesenchymal genes are regulated distinctively. We find that EMT genes are regulated within their topologically associated domains (TADs), with only a subset of mesenchymal genes being influenced by A/B compartment switches, indicating topological remodeling is required in the transcriptional regulation of these genes. At the TAD level, epithelial and mesenchymal genes are associated with different regulatory trajectories. The epithelial gene-residing TADs are enriched with H3K27me3 marks in the mesenchymal-like states. The mesenchymal gene-residing TADs, which do not show enrichment of H3K27me3 in epithelial-like states, exhibit increased interaction frequencies with regulatory elements in the mesenchymal-like states.
conclusionsWe propose a novel workflow coupling immunofluorescence and dielectrophoresis to unravel EMT heterogeneity at single-cell resolution. The predicted three-dimensional structures of chromosome 10, harboring Vimentin, identify cell clusters of different states. Our results pioneer a novel avenue to decipher the complexities underlying the regulation of EMT and may infer the barriers of plasticity in the 3D genome context.
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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.