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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE143674 | GEO | 2022/06/29

REPOSITORIES: GEO

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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 (Hi-C)

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 and breast cancer cells.

2022-06-29 | GSE143676 | GEO

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

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

Project description: Not available

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

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

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

| PRJNA601217 | ENA

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

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

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

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

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

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

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

Project description:The 3D architecture that the genome is folded into is regulated by CTCF, which determines domain borders, and cohesin, which generates interactions within domains. However, organisms lacking CTCF have been reported to still have cohesin-mediated 3D structures with strong borders. How this can be achieved and precisely regulated are yet unknown. Using in situ Hi-C, we found that 3’-end RNA processing factors coupled with proper transcription termination are a cis-acting determinant that regulates the localization and dynamics of cohesin on the chromosome arms. Loss of RNA processing factors, including nuclear exosome and Pfs2, destabilizes cohesin from the 3'-ends of convergent genes and results in decreased cohesin-mediated domain boundaries. We observed the co-localization between Rad21 and a wide range of 3'end RNA processing/termination factors. Further, deletion of Rrp6 leads to cohesin redistribution to facultative heterochromatin, resulting in improper domain boundaries. Importantly, we observed that knockdown of Rrp6Exosc10 caused a defect in cohesin binding and loss of local topologically associating domains (TADs) interactions in mouse embryonic stem cells. Based on these findings, we propose a novel function of the RNA surveillance pathway in 3D genome organization via cohesin complex, which provides the molecular basis underlying the dynamics of cohesin function.

2022-12-01 | GSE85147 | GEO

3D + LY vs. 3D culture of HUASMC

Project description:To study the impact of TGF signaling on the transcriptome of vascular smooth muscle cells, we cultured human umbilical artery smooth muscle cells as 3D aggregates in hanging drops for 48 hours. One group was treated with TGFβRI/II inhibitor LY2109761 (10 μM, additional 10 μM after 24 h), the other group with solvent (DMSO) as control. RNA was isolated from both groups after 48h

2019-12-16 | GSE133649 | GEO

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