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Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration (Hi-C)

ABSTRACT: Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration (Hi-C)

PROVIDER: PRJNA1150603 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30333182_1.fastq.gz	Fastqsanger.gz
	SRR30333182_2.fastq.gz	Fastqsanger.gz
	SRR30333183_1.fastq.gz	Fastqsanger.gz
	SRR30333183_2.fastq.gz	Fastqsanger.gz
	SRR30333184_1.fastq.gz	Fastqsanger.gz

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Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration

Project description:Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration

| PRJNA1150595 | ENA

Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration (RNA-Seq)

Project description:Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration (RNA-Seq)

| PRJNA1150602 | ENA

Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration (Hi-C)

Project description:Metastatic cancer cells traverse tight junctions that exert forces on their nucleus and the genomic contents within. Cancerous tumors are highly heterogeneous and not all cells within them can achieve such a feat. Here, we investigated what initial genome architecture characteristics favor the constricted migratory ability of cancer cells and which arise only after passage through multiple constrictions. We identified a cell surface protein (ITGB4) whose expression correlates with increased initial constricted migration ability in human melanoma A375 cells. Sorting out this subpopulation allowed us to identify cellular and nuclear features that pre-exist and favor migration, as well as alterations that only appear after cells have passed through constrictions. We identified specific genomic regions that experienced altered genome spatial compartment profiles only after constricted migration. Our study reveals 3D genome structure contributions to both selection and induction mechanisms of cell fate change during cancer metastasis.

2024-08-26 | GSE275396 | GEO

Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration (RNA-Seq)

2024-08-26 | GSE275395 | GEO

Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration

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

2024-08-26 | GSE275397 | GEO

Deciphering the role of 3D genome organization in breast cancer susceptibility (Hi-C)

Project description:Deciphering the role of 3D genome organization in breast cancer susceptibility (Hi-C)

| PRJNA763891 | ENA

Migration through a small pore disrupts inactive chromatin organisation in neutrophil-like cells [Hi-C]

Project description:Background. Mammalian cells are flexible and can rapidly change shape when they contract, adhere, or migrate. Their nucleus must be stiff enough to withstand cytoskeletal forces, but flexible enough to remodel as the cell changes shape. This is particularly important for cells migrating through constricted space, where the nuclear shape must change in order to fit through. This happens many times in the life cycle of a neutrophil, which must protect its chromatin from damage and disruption associated with migration. Results. Total RNA-sequencing identified that neutrophil migration through 5 or 14 µm pores was associated with changes in the transcript levels of inflammation and chemotaxis-related genes, when compared to unmigrated cells. Differentially expressed transcripts specific to migration with constriction were enriched for groups of genes associated with cytoskeleton remodelling. Hi-C was used to capture the genome organisation in control and migrated cells. Chromatin did not switch between the active (A) and inactive (B) compartments after migration. However, global depletion of mid- to long-range contacts was observed following active migration through the 5 µm pores. Chromatin contacts that decreased in frequency were enriched in inactive chromatin. Conclusion. Mid- to long-range contacts are preferentially lost within inactive chromatin, thus protecting transcriptionally active contacts from the disruptive effects of migration with constriction. This is consistent with current hypotheses implicating heterochromatin as the mechanoresponsive form of chromatin. Further investigation concerning the contribution of heterochromatin to stiffness, flexibility, and protection of nuclear function will be important for understanding cell migration in human health and disease.

2018-08-14 | GSE115633 | GEO

Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture.

Project description:Topological domains are key architectural building blocks of chromosomes in complex genomes. Their functional importance and evolutionary dynamics are however not well defined. Here we performed comparative Hi-C in liver cells from four mammalian species, and characterized the conservation and divergence of chromosomal contact insulation and the resulting domain architectures within distantly related genomes. We show that the modular organization of chromosomes is robustly conserved in syntenic regions. This overall conservation is compatible with conservation of the binding landscape of the insulator protein CTCF. Specifically, conserved CTCF sites are co-localized with cohesin, enriched at strong topological domain borders and bind to DNA motifs with orientations that define the directionality of CTCF’s long-range interactions. Interestingly, CTCF binding sites which are divergent between species are strongly correlated with divergence of internal domain structure. This divergence is likely driven by local CTCF binding sequence changes, demonstrating how genome evolution can be linked directly with a continuous flux of local chromosome conformation changes. Conversely, we provide evidence that large-scale domains are harder to break and that they are reorganized during genome evolution as intact modules. Hi-C and 4C-seq experiments were conducted in primary liver cells obtained from mouse, rabbit, macaque and dog

2015-02-26 | E-GEOD-65126 | biostudies-arrayexpress

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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Migration through a small pore disrupts inactive chromatin organisation in neutrophil-like cells [Hi-C]

Project description:Migration through a small pore disrupts inactive chromatin organisation in neutrophil-like cells [Hi-C]

| PRJNA475595 | ENA