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Consticted migration is associated with stable 3D genome structure differences in cancer cells (RNA-Seq)

ABSTRACT: Consticted migration is associated with stable 3D genome structure differences in cancer cells (RNA-Seq)

PROVIDER: PRJNA601224 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10894031_1.fastq.gz	Fastqsanger.gz
	SRR10894031_2.fastq.gz	Fastqsanger.gz
	SRR10894032_1.fastq.gz	Fastqsanger.gz
	SRR10894032_2.fastq.gz	Fastqsanger.gz
	SRR10894033_1.fastq.gz	Fastqsanger.gz

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Consticted migration is associated with stable 3D genome structure differences in cancer cells

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Consticted migration is associated with stable 3D genome structure differences in cancer cells (RNA-Seq)

Project description:We investigated the effect of constricted migration (using transwell assays with 5-μm or 12-μm in diameter) on the organization of the 3D genome in melanoma cells.

2022-06-29 | GSE143677 | GEO

Consticted migration is associated with stable 3D genome structure differences in cancer cells (ATAC-Seq)

Project description:We investigated the effect of constricted migration (using transwell assays with 5-μm or 12-μm in diameter) on the organization of the 3D genome in melanoma cells.

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Consticted migration is associated with stable 3D genome structure differences in cancer cells (Hi-C)

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RNA surveillance controls 3D genome structure via stable cohesin chromosome interaction

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Consticted migration is associated with stable 3D genome structure differences in cancer cells

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

2022-06-29 | GSE143678 | GEO

3D chromatin structure in colon cancer

Project description:We report the application of in situ Hi-C technology to 40 colorectal cancer patients and 10 paired-normal tissue to identify CRC specific changes in 3D chromatin structure. The chromatin contact matrices were generated by the sequencing data and image processing/deep learning-based algorithm was proposed to identify long-range abnormal chromatin interaction patterns in the contact matrices. The tumor specific 3D chromatin structure changes and the enhancer-promoter rewiring mediated by the identified chromatin structure changes were analyzed. The complex chromosome-wide rearrangements such as chromothripsis and its effect to 3D chromatin structure were also observed.

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Constricted migration is associated with stable 3D genome structure differences in cancer cells

Project description:To spread from a localized tumor, metastatic cancer cells squeeze through constrictions that cause major nuclear deformations. Since chromosome structure affects nucleus stiffness, gene regulation and DNA repair, here we investigate the relationship between 3D genome structure and constricted migration in cancer cells. Using melanoma (A375) cells, we identify phenotypic differences in cells that have undergone multiple rounds of constricted migration. These cells display a stably higher migration efficiency, elongated morphology, and differences in the distribution of Lamin A/C and heterochromatin. Hi-C experiments reveal differences in chromosome spatial compartmentalization specific to cells that have passed through constrictions and related alterations in expression of genes associated with migration and metastasis. Certain 3D genome structure changes, such as a loss of B compartment interaction strength, are consistently observed after constricted migration in clonal populations of A375 cells and in MDA-MB-231 breast cancer cells. Our observations suggest that consistent types of chromosome structure changes are induced or selected by passage through constrictions and that these may epigenetically encode stable differences in gene expression and cellular migration phenotype.

| S-SCDT-EMBOR-2020-52149-T | biostudies-other

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