MRNA-seq in VDR knockout and control THP-1 cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA661550 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12594048.fastq.gz | Fastqsanger.gz | |||
| SRR12594049.fastq.gz | Fastqsanger.gz | |||
| SRR12594050.fastq.gz | Fastqsanger.gz | |||
| SRR12594051.fastq.gz | Fastqsanger.gz | |||
| SRR12594052.fastq.gz | Fastqsanger.gz |
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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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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)
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Project description:Analysis of acute effects of ligand-treatment on vitamin D receptor binding genome-wide using ChIP-seq. THP-1 monocytic leucemia cells were treated with 1?,25(OH)2D3 (1,25D) or left unstimulated to investigate the acute effects of VDR chromatin occupancy. We identified in total 2340 VDR binding sites with and without the ligand. Without the ligand, there is a considerable presence of VDR already on the chromatin. However, upon a short (40 min) ligand treatment VDR shifts from sites that rarely contain a DR3 type element to sites that frequently contain one or more DR3-type element. Genome-wide identification of VDR binding in THP-1 cells at the unstimulated state and after 40 min ligand (10 nM 1?,25(OH)2D3 (1,25D, calcitriol)) treatment.
2011-08-17 | E-GEOD-27437 | biostudies-arrayexpress
Project description:The biologically active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), is a direct regulator of gene transcription, since it is the only high affinity natural ligand of the transcription factor vitamin D receptor (VDR). Transcriptome-wide analysis of THP-1 human monocyte-like cells had indicated more than 600 genes to be significantly (p < 0.05) regulated after a 4 h stimulation with 1,25(OH)2D3. In this study, we screened of the list of primary vitamin D targets for genes encoding for transcriptional regulators and selected those of the activating transcription factor NFE2 and the transcriptional repressor BCL6. Both genes are under the control of two VDR loci and are the only 1,25(OH)2D3 targets within their respective chromosomal domain. However, NFE2 mRNA was rapidly up-regulated, while the increase of BCL6 expression showed a slower rise. After 24 h incubation of THP-1 cells with 1,25(OH)2D3 more than 1,500 genes responded significantly (p < 0.001), of which 132 where more than 2-fold induced. Public chromatin immunoprecipitation-sequencing datasets suggested that the majority of these genes could be targets of NFE2 or BCL6. In time course experiments we displayed for representative gene examples the specific delayed response of secondary 1,25(OH)2D3 targets and confirmed for the respective chromosomal domains the genomic binding of NFE2, BCL6 and VDR. In conclusion, our study indicated that the physiological response of monocytes to 1,25(OH)2D3 involves the action of NFE2 and BCL6. THP-1 cells were treated 24 h either with 0.1% ethanol (vehicle, control) or 1?,25(OH)2D3 (1,25D)
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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.
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Project description:Treatment with calcitriol, a specific VDR agonist, augmented the heterodimerization between VDR and RXR. We also wanted to investigate its impact on VDR binding to genomic regions. ChIP-seq experiments were carried out with the human monocytic THP-1 cell line under either vehicle (1:1 DMSO-ethanol) or calcitriol (100 nM) treatment conditions. Our finding is that calcitriol may have both a stimulatory or an inhibitory effect on VDR binding depending on the presence of its specific response element (VDRE), a less specific nuclear receptor (NR) half-site or absence thereof ("None"). Upon calcitriol activation, VDRE-containing genomic regions showed considerably higher occupancies on average than in the control, vehicle-treated sample. A similar induction, but to a much lesser extent, was detected for the NR half-site-containing regions. In contrast, genomic regions not containing any of these specific response elements did not show any induction upon calcitriol treatment; they rather showed a decrease of binding in promoter regions. We can conclude that ligand-induced heterodimerization and binding of the NR to its response elements are correlated events.
2020-05-16 | GSE150652 | GEO
Project description:The biologically active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), is a direct regulator of gene transcription, since it is the only high affinity natural ligand of the transcription factor vitamin D receptor (VDR). Transcriptome-wide analysis of THP-1 human monocyte-like cells had indicated more than 600 genes to be significantly (p < 0.05) regulated after a 4 h stimulation with 1,25(OH)2D3. In this study, we screened of the list of primary vitamin D targets for genes encoding for transcriptional regulators and selected those of the activating transcription factor NFE2 and the transcriptional repressor BCL6. Both genes are under the control of two VDR loci and are the only 1,25(OH)2D3 targets within their respective chromosomal domain. However, NFE2 mRNA was rapidly up-regulated, while the increase of BCL6 expression showed a slower rise. After 24 h incubation of THP-1 cells with 1,25(OH)2D3 more than 1,500 genes responded significantly (p < 0.001), of which 132 where more than 2-fold induced. Public chromatin immunoprecipitation-sequencing datasets suggested that the majority of these genes could be targets of NFE2 or BCL6. In time course experiments we displayed for representative gene examples the specific delayed response of secondary 1,25(OH)2D3 targets and confirmed for the respective chromosomal domains the genomic binding of NFE2, BCL6 and VDR. In conclusion, our study indicated that the physiological response of monocytes to 1,25(OH)2D3 involves the action of NFE2 and BCL6.
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Project description:Analysis of acute effects of ligand-treatment on vitamin D receptor binding genome-wide using ChIP-seq. THP-1 monocytic leucemia cells were treated with 1?,25(OH)2D3 (1,25D) or left unstimulated to investigate the acute effects of VDR chromatin occupancy. We identified in total 2340 VDR binding sites with and without the ligand. Without the ligand, there is a considerable presence of VDR already on the chromatin. However, upon a short (40 min) ligand treatment VDR shifts from sites that rarely contain a DR3 type element to sites that frequently contain one or more DR3-type element.
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