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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [Hi-C]

ABSTRACT: The aim of the project was to investigate the effect of nuclear receptor activation, particularly of the vitamin D receptor, on chromatin structure, and associated functional changes in the transcriptional response of THP-1 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE190463 | GEO | 2022/04/27

REPOSITORIES: GEO

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]

Project description:The aim of the project was to investigate the effect of nuclear receptor activation, particularly of the vitamin D receptor, on CTCF-defined 3D chromatin structure, and associated functional changes in the transcriptional response of THP-1 cells.

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure

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

2022-04-27 | GSE190464 | GEO

Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [Hi-C]

Project description:Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [Hi-C]

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure

Project description:Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure

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Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]

Project description:Nuclear receptor activation leads to functional changes in CTCF-defined chromatin structure [HiChIP]

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Genome-wide analysis of vitamin D receptor (VDR) target genes in THP-1 monocytic leucemia cells

Project description:Identification of primary target genes of vitamin D receptor (VDR) in an immune-related cellular model (THP-1 cells) to study, in conjunction with VDR binding data from ChIP-seq, the genome-wide mechanisms of transcriptional regulation by VDR. THP-1 cells were treated 4 h either with 0.1% ethanol (vehicle, control) or 1?,25(OH)2D3 (1,25D)

2011-08-16 | E-GEOD-27270 | biostudies-arrayexpress

mRNA-seq in VDR knockout and control THP-1 cells

Project description:The vitamin D receptor (VDR) has been knocked out in monocytic THP-1 cells after stimulation of ko and control cells with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), quadruplicate mRNA-seq has been performed

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Genome-wide analysis of vitamin D receptor (VDR) target genes in THP-1 monocytic leucemia cells

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Transcriptomics of vitamin D treatment effects in Mycobacterium tuberculosis-infected THP-1 cells

Project description:Previous reports have shown low vitamin D serum levels and polymorphisms in the vitamin D receptor (VDR) to be associated with increased risk for TB. Given that 1?,25-dihydroxyvitamin D3 has a role in lipid metabolism control, we tested whether the link between 1?,25-dihydroxyvitamin D3 and tuberculosis involves macrophage lipid metabolism. Since formation of lipid droplets (LD) is a hallmark of lipid dysregulation in M. tuberculosis-infected macrophages, we measured LD content as a readout of altered lipid metabolism in infected THP-1 cells. Induction of LD, which peaked by 24 hours post-infection was prevented by addition of 1?,25-dihydroxyvitamin D3 at the time of infection. To investigate the mechanism of 1?,25-dihydroxyvitamin D3 modulation of LD formation, we analyzed the transcriptome of M. tuberculosis-infected THP-1 cells with and without 1?,25-dihydroxyvitamin D3 treatment. THP-1 cells were cultured in 24-well flat bottom plates, pre-treated with 20ng/ml PMA for 24 h, and incubated with M. tuberculosis H37Rv. After 4 hours of infection, cells were washed to remove extracellular bacteria and treated with 100 nM of 1?,25-dihydroxyvitamin D3. THP-1 cells were collected and analyzed at 24h. 3 biological replicates in each of the 4 groups were prepared: Infected, Infected plus 1?,25-dihydroxyvitamin D3, Non-infected, Non-infected plus 1?,25-dihydroxyvitamin D3.

2014-07-01 | E-GEOD-57028 | biostudies-arrayexpress

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

Project description:Topological domains are key architectural building blocks of chromosomes, but their functional importance and evolutionary dynamics are not well defined. We performed comparative high-throughput chromosome conformation capture (Hi-C) in four mammals 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 and that this is compatible with conservation of the binding landscape of the insulator protein CTCF. Specifically, conserved CTCF sites are co-localized with cohesin, are enriched at strong topological domain borders, and bind to DNA motifs with orientations that define the directionality of CTCF's long-range interactions. Conversely, divergent CTCF binding between species is correlated with divergence of internal domain structure, likely driven by local CTCF binding sequence changes, demonstrating how genome evolution can be linked to a continuous flux of local conformation changes. We also show that large-scale domains are reorganized during genome evolution as intact modules.

| S-EPMC4542312 | biostudies-literature

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