CTCF ChIP-seq in human monocytic THP-1 cells with replicates (4)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE69962 | GEO | 2016/01/02
SECONDARY ACCESSION(S): PRJNA287278
REPOSITORIES: GEO
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Project description:ChIP-seq for the insulator protein CTCF in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) THP-1 cells were treated for 24 h with 100 nM 1,25(OH)2D3 before ChIP assay
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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: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)
2015-04-26 | E-GEOD-60102 | 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.
2015-04-26 | GSE60102 | GEO
Project description:The nuclear hormone 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3) regulates its target genes via activation of the transcription factor vitamin D receptor (VDR) far more specifically than the chromatin modifier trichostatin A (TsA) via its inhibitory action on histone deacetylases. We selected the thrombomodulin gene locus with its complex pattern of three 1α,25(OH)2D3 target genes, five VDR binding sites and multiple histone acetylation and open chromatin regions as an example to investigate together with a number of reference genes, the primary transcriptional responses to 1α,25(OH)2D3 and TsA. Transcriptome-wide, 18.4% of all expressed genes are either up- or down-regulated already after a 90 min TsA treatment; their response pattern to 1α,25(OH)2D3 and TsA sorts them into at least six classes. TsA stimulates a far higher number of genes than 1α,25(OH)2D3 and dominates the outcome of combined treatments. However, 200 TsA target genes can be modulated by 1α,25(OH)2D3 and more than 1000 genes respond only when treated with both compounds. The genomic view on the genes suggests that the degree of acetylation at transcription start sites and VDR binding regions may determine the effect of TsA on mRNA expression and its interference with 1α,25(OH)2D3. Our findings may have implications on dual therapies using chromatin modifiers and nuclear receptor ligands. All conditions are performed in triplicate: one time point with TsA treatment and vehicle control and one time point with TsA, 1α,25-dihydroxyvitamin D3, the combination of both and vehicle
2012-10-25 | E-GEOD-36323 | biostudies-arrayexpress
Project description:Heterogeneous nuclear ribonucleoprotein (hnRNP) C1/C2 plays a pivotal role in vitamin D receptor (VDR) signaling by acting as a vitamin D response element (VDRE)-binding protein (VDRE-BP). Transcriptional regulation by active 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) involves occupancy of VDRE by VDRE-BP or 1,25(OH)2D3 bound-VDR. This relationship is disrupted by over-expression of VDRE-BP and can cause a form of human hereditary vitamin D-resistant rickets (HVDRR). DNA array analyses using B-cells from an HVDRR patient and matched control defined a sub-cluster of genes where 1,25(OH)2D3-regulated transcription was abrogated by over-expression of VDRE-BP. Amongst these, the DNA-damage-inducible transcript 4 (DDIT4), an inhibitor of mammalian target of rapamycin (mTOR) signaling, was also induced by 1,25(OH)2D3 in human osteoblasts. Chromatin immunoprecipitation using 1,25(OH)2D3-treated osteoblasts confirmed that liganded VDR and VDRE-BP compete for binding to the proximal promoter of the DDIT4 gene in a similar fashion to other known 1,25(OH)2D3-target genes. Treatment of osteoblasts with 1,25(OH)2D3 induced DDIT4 expression and suppressed phosphorylated S6K1T389 protein (a downstream target of mTOR). The functional importance of this for 1,25(OH)2D3 responses in osteoblasts was underlined by the fact that siRNA knockdown of DDIT4 expression suppressed antiproliferative and cell growth responses to 1,25(OH)2D3. These data confirm that VDRE-BP is required for normal 1,25(OH)2D3-mediated transcription and cell function in osteoblasts. Conversely over-expression of VDRE-BP exerts a dominant-negative effect on transcription of 1,25(OH)2D3-target genes. Characterization of VDRE-BP action in 1,25(OH)2D3-treated osteoblasts highlights an entirely novel role for vitamin D as a regulator of mTOR – a known ‘master regulator’ of cell function.
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