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| Status |
Public on May 16, 2020 |
| Title |
VDR ChIP-seq in human monocytic THP-1 cell line |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
ChIP-seq experiment was carried out in human monocytic THP-1 cell line under either vehicle, 1:1 DMSO-ethanol, or calcitriol (100 nM) treatment conditions.
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| Contributor(s) |
Bojcsuk D, Nagy L, Vamosi G |
| Citation(s) |
32513869 |
| BioProject |
PRJNA632899 |
| Submission date |
May 15, 2020 |
| Last update date |
Aug 17, 2020 |
| Contact name |
Laszlo Nagy |
| E-mail(s) |
lnagy@jhmi.edu
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| Organization name |
University of Debrecen
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| Street address |
Egyetem ter 1.
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| City |
Debrecen |
| ZIP/Postal code |
4032 |
| Country |
Hungary |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (4)
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| GSM4555799 |
VDR ChIP-seq in human monocytic THP-1 cell line treated with 1:1 DMSO-ethanol (1hr, rep1) |
| GSM4555800 |
VDR ChIP-seq in human monocytic THP-1 cell line treated with 1:1 DMSO-ethanol (1hr, rep2) |
| GSM4555801 |
VDR ChIP-seq in human monocytic THP-1 cell line treated with 100 nM calcitriol (D3) (1hr, rep1) |
| GSM4555802 |
VDR ChIP-seq in human monocytic THP-1 cell line treated with 100 nM calcitriol (D3) (1hr, rep2) |
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| Relations |
| SRA |
SRP261754 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150652_RAW.tar |
831.8 Mb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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