ArticlePloS one2014
Patterns of genome-wide VDR locations.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
80 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The role of vitamin D signalling in β cell apoptosis: a systematic review.Apoptosis : an international journal on programmed cell death · 2026Pooled it
- Metabolomic basis for response to high dose vitamin D in critical illness.Clinical nutrition (Edinburgh, Scotland) · 2021Trial
- No effect of 25-hydroxyvitamin D supplementation on the skeletal muscle transcriptome in vitamin D deficient frail older adults.BMC geriatrics · 2019Trial
- Vitamin D Receptor Genotype, Vitamin D3 Supplementation, and Risk of Colorectal Adenomas: A Randomized Clinical Trial.JAMA oncology · 2017Trial
- Increased chromatin accessibility following 1α,25-dihydroxyvitamin DToxicology and applied pharmacology · 2026Article
- Cooperation or Conflict? Molecular and Physiological Cross-Talk Between the Aryl Hydrocarbon and Vitamin D Receptors.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Genome-wide chromatin profiling reveals a nonlimiting role for RXR in macrophage-like cells stimulated with multiple nuclear receptor agonists.The Journal of biological chemistry · 2026Article
- Temporal stratification of promoter-proximal versus enhancer VDR binding directs vitamin D-responsive transcription.Epigenetics & chromatin · 2026Article
- Chromatin and transcriptional dynamics underlying the immune-modulatory effects of vitamin DScientific reports · 2025Article
- The Role of Vitamin D and Vitamin D Receptor in Sepsis.Current issues in molecular biology · 2025Review
- Nutri-Epigenetic Regulation of Vitamin D-Impact on Metabolism and Biological Functions: Narrative Review.Metabolites · 2025Review
- Genomic regions occupied by both RARα and VDR are involved in the convergence and cooperation of retinoid and vitamin D signaling pathways.Nucleic acids research · 2025Article
- EarlyFrontiers in immunology · 2025Article
- A comprehensive transcriptome characterization of individual nuclear receptor pathways in the human small intestine.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Lack of Association Between BsmI and FokI Polymorphisms of the VDR Gene and Sporadic Colorectal Cancer in a Romanian Cohort-A Preliminary Study.Current oncology (Toronto, Ont.) · 2024Article
- Coactivator-independent vitamin D receptor signaling causes severe rickets in mice, that is not prevented by a diet high in calcium, phosphate, and lactose.Bone research · 2024Article
- In vivo vitamin D targets reveal the upregulation of focal adhesion-related genes in primary immune cells of healthy individuals.Scientific reports · 2024Article
- Lack of vitamin D signalling in mesenchymal progenitors causes fatty infiltration in muscle.Journal of cachexia, sarcopenia and muscle · 2024Article
- Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression.Nucleic acids research · 2024Article
- Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice.Nucleic acids research · 2024Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genome-wide analysis of the binding sites of the transcription factor vitamin D receptor (VDR) is essential for a global appreciation the physiological impact of the nuclear hormone 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). Genome-wide analysis of lipopolysaccharide (LPS)-polarized THP-1 human monocytic leukemia cells via chromatin immunoprecipitation sequencing (ChIP-seq) resulted in 1,318 high-confidence VDR binding sites, of which 789 and 364 occurred uniquely with and without 1,25(OH)2D3 stimulation, while only 165 were common. We re-analyzed five public VDR ChIP-seq datasets with identical peak calling settings (MACS, version 2) and found, using a novel consensus summit identification strategy, in total 23,409 non-overlapping VDR binding sites, 75% of which are unique within the six analyzed cellular models. LPS-differentiated THP-1 cells have 22% more genomic VDR locations than undifferentiated cells and both cell types display more overlap in their VDR locations than the other investigated cell types. In general, the intersection of VDR binding profiles of ligand-stimulated cells is higher than those of unstimulated cells. De novo binding site searches and HOMER screening for binding motifs formed by direct repeats spaced by three nucleotides (DR3) suggest for all six VDR ChIP-seq datasets that these sequences are found preferentially at highly ligand responsive VDR loci. Importantly, all VDR ChIP-seq datasets display the same relationship between the VDR occupancy and the percentage of DR3-type sequences below the peak summits. The comparative analysis of six VDR ChIP-seq datasets demonstrated that the mechanistic basis for the action of the VDR is independent of the cell type. Only the minority of genome-wide VDR binding sites contains a DR3-type sequence. Moreover, the total number of identified VDR binding sites in each ligand-stimulated cell line inversely correlates with the percentage of peak summits with DR3 sites.
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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.