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3D genome organization in the epithelial-mesenchymal transition spectrum

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE201919 | GEO | 2022/05/08

REPOSITORIES: GEO

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3D genome organization in the epithelial-mesenchymal transition spectrum [scHi-C_OVCA429shGRHL]

Project description:Background The 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. Results We 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 remodelling 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. Conclusions We 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.

2022-05-08 | GSE201918 | GEO

3D genome organization in the epithelial-mesenchymal transition spectrum [Hi-C]

2022-05-08 | GSE201878 | GEO

3D genome organization in the epithelial-mesenchymal transition spectrum [scHi-C_PEO1HEYA8]

2022-05-08 | GSE201917 | GEO

3D genome organization in the epithelial-mesenchymal transition spectrum

Project description:3D genome organization in the epithelial-mesenchymal transition spectrum

| PRJNA833467 | ENA

3D genome organization in the epithelial-mesenchymal transition spectrum [scHi-C_OVCA429shGRHL]

Project description:3D genome organization in the epithelial-mesenchymal transition spectrum [scHi-C_OVCA429shGRHL]

| PRJNA833468 | ENA

3D genome organization in the epithelial-mesenchymal transition spectrum [Hi-C]

Project description:3D genome organization in the epithelial-mesenchymal transition spectrum [Hi-C]

| PRJNA833402 | ENA

3D genome organization in the epithelial-mesenchymal transition spectrum [scHi-C_PEO1HEYA8]

Project description:3D genome organization in the epithelial-mesenchymal transition spectrum [scHi-C_PEO1HEYA8]

| PRJNA833470 | ENA

TET1 regulates hypoxia-induced epithelial-mesenchymal transition through DNA demethylation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-08-01 | E-GEOD-59990 | biostudies-arrayexpress

Architecture of Epigenetic Reprogramming Following Twist1 Mediated Epithelial-Mesenchymal Transition

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-12-10 | E-GEOD-53026 | biostudies-arrayexpress

Aneuploidy, oncogene amplification, and epithelial to mesenchymal transition define spontaneous transformation of murine epithelial cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-03-14 | E-GEOD-45129 | biostudies-arrayexpress

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