ArticleNucleic acids research2011
Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers, 1 of them a synthesis that pooled it.
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Who cites it
114 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Vitamin D-regulated Gene Expression Profiles: Species-specificity and Cell-specific Effects on Metabolism and Immunity.Endocrinology · 2021Pooled it
- The vitamin D receptor story: discovery, control, and genomic reach.The Journal of endocrinology · 2026Review
- Temporal stratification of promoter-proximal versus enhancer VDR binding directs vitamin D-responsive transcription.Epigenetics & chromatin · 2026Article
- Article
- Chromatin and transcriptional dynamics underlying the immune-modulatory effects of vitamin DScientific reports · 2025Article
- The interplay between hormonal vitamin D and lipopolysaccharide signaling on human neutrophil transcriptional responses.Frontiers in immunology · 2025Article
- EarlyFrontiers in immunology · 2025Article
- Genome-wide study identifies novel genes associated with bone toxicities in children with acute lymphoblastic leukaemia.British journal of haematology · 2024Article
- Structure and the Anticancer Activity of Vitamin D Receptor Agonists.International journal of molecular sciences · 2024Review
- Causal inference between pernicious anemia and cancers: a bidirectional two-sample mendelian randomization analysis.BMC cancer · 2024Article
- Review
- 1,25-Dihydroxyvitamin D3 regulates furin-mediated FGF23 cleavage.JCI insight · 2023Article
- Intervention Approaches in Studying the Response to Vitamin DNutrients · 2023Review
- Single-cell RNA sequencing identifiesFrontiers in physiology · 2023Article
- An Update on the Effects of Vitamin D on the Immune System and Autoimmune Diseases.International journal of molecular sciences · 2022Review
- Vitamin D in the Context of Evolution.Nutrients · 2022Review
- Vitamin D and Its Receptor from a Structural Perspective.Nutrients · 2022Review
- Vitamin D and Its Target Genes.Nutrients · 2022Review
- Time-Resolved Gene Expression Analysis Monitors the Regulation of Inflammatory Mediators and Attenuation of Adaptive Immune Response by Vitamin D.International journal of molecular sciences · 2022Article
- Vitamin D Supplementation Improves Mitochondrial Function and Reduces Inflammation in Placentae of Obese Women.Frontiers in endocrinology · 2022Article
54 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A global understanding of the actions of the nuclear hormone 1α,25-dihydroxyvitamin D(3) (1α,25(OH)(2)D(3)) and its vitamin D receptor (VDR) requires a genome-wide analysis of VDR binding sites. In THP-1 human monocytic leukemia cells we identified by ChIP-seq 2340 VDR binding locations, of which 1171 and 520 occurred uniquely with and without 1α,25(OH)(2)D(3) treatment, respectively, while 649 were common. De novo identified direct repeat spaced by 3 nucleotides (DR3)-type response elements (REs) were strongly associated with the ligand-responsiveness of VDR occupation. Only 20% of the VDR peaks diminishing most after ligand treatment have a DR3-type RE, in contrast to 90% for the most growing peaks. Ligand treatment revealed 638 1α,25(OH)(2)D(3) target genes enriched in gene ontology categories associated with immunity and signaling. From the 408 upregulated genes, 72% showed VDR binding within 400 kb of their transcription start sites (TSSs), while this applied only for 43% of the 230 downregulated genes. The VDR loci showed considerable variation in gene regulatory scenarios ranging from a single VDR location near the target gene TSS to very complex clusters of multiple VDR locations and target genes. In conclusion, ligand binding shifts the locations of VDR occupation to DR3-type REs that surround its target genes and occur in a large variety of regulatory constellations.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.