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

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

PROVIDER: PRJNA833468 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18982219_1.fastq.gz	Fastqsanger.gz
	SRR18982219_2.fastq.gz	Fastqsanger.gz
	SRR18982220_1.fastq.gz	Fastqsanger.gz
	SRR18982220_2.fastq.gz	Fastqsanger.gz
	SRR18982221_1.fastq.gz	Fastqsanger.gz

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3D genome organization in the epithelial-mesenchymal transition spectrum

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

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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]

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

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

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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 [scHi-C_PEO1HEYA8]

2022-05-08 | GSE201917 | 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.

Project description: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.

| S-EPMC9150291 | biostudies-literature

3D genome organization in the epithelial-mesenchymal transition spectrum

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-05-08 | GSE201919 | GEO

Transcriptional organization of autism spectrum disorder

Project description:Transcriptional organization of autism spectrum disorder

| PRJNA436104 | ENA

Shift of EMT gradient in 3D spheroid MSCs for activation of mesenchymal niche function

Project description:This project is described about the detailed characterization of 3D spheroid mesenchymal stem cells (MSCs). Specifically, authors showed the dynamic action towards EMT in 3D MSCs and the potential of EMT-enhanced “naïve” mesenchymal phenotype.

2018-06-25 | PXD006653 | Pride

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