ArticlePloS one2014
Characterization of genomic vitamin D receptor binding sites through chromatin looping and opening.
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 17 papers.
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Who cites it
17 citing papers in PubMed.
- Trial
- The role of vitamin D receptor signaling in hair follicle health and alopecia: Current understanding and therapeutic implications.Journal of cell communication and signaling · 2026Review
- Vitamin D Reshapes Genomic Hierarchies in Skin Cells: lncRNA-Driven Responses in Carcinoma Versus Transcription Factor-Based Regulation in Healthy Skin.International journal of molecular sciences · 2025Article
- Single-cell RNA sequencing identifiesFrontiers in physiology · 2023Article
- Vitamin D and Systems Biology.Nutrients · 2022Review
- Maternal 17q21 genotype influences prenatal vitamin D effects on offspring asthma/recurrent wheeze.The European respiratory journal · 2021Article
- A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes.Scientific reports · 2021Article
- The role of the 17q21 genotype in the prevention of early childhood asthma and recurrent wheeze by vitamin D.The European respiratory journal · 2019Article
- Primary Vitamin D Target Genes of Human Monocytes.Frontiers in physiology · 2019Review
- Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes.BMC genomics · 2017Article
- Vitamin D receptor is a novel transcriptional regulator for Axin1.The Journal of steroid biochemistry and molecular biology · 2017Article
- PTH and Vitamin D.Comprehensive Physiology · 2016Review
- The multiple sclerosis susceptibility genes TAGAP and IL2RA are regulated by vitamin D in CD4+ T cells.Genes and immunity · 2016Article
- Vitamin D in Autoimmunity: Molecular Mechanisms and Therapeutic Potential.Frontiers in immunology · 2016Review
- Relevance of vitamin D receptor target genes for monitoring the vitamin D responsiveness of primary human cells.PloS one · 2015Article
- Genome-wide (over)view on the actions of vitamin D.Frontiers in physiology · 2014Review
- Nuclear Receptors in Drug Metabolism, Drug Response and Drug Interactions.Nuclear receptor researchArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The vitamin D receptor (VDR) is a transcription factor that mediates the genomic effects of 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). Genome-wide there are several thousand binding sites and hundreds of primary 1,25(OH)2D3 target genes, but their functional relation is largely elusive. In this study, we used ChIA-PET data of the transcription factor CTCF in combination with VDR ChIP-seq data, in order to map chromatin domains containing VDR binding sites. In total, we found 1,599 such VDR containing chromatin domains and studied in THP-1 human monocytic leukemia cells four representatives of them. Our combined ChIP-seq and FAIRE-seq time course data showed that each of these four domains contained a master VDR binding site, where an increase of VDR binding pairs with 1,25(OH)2D3-promoted chromatin opening and the presence of a highly significant DR3-type sequence below the peak summit. These sites differed in their relative VDR binding but not in their kinetics, while other loci either had a weaker and delayed VDR association or could not be confirmed at all. All studied chromatin domains contained at least one primary 1,25(OH)2D3 target gene demonstrating a characteristic slope of mRNA increase, while neighboring genes responded delayed, if at all. In conclusion, the observation of ligand-inducible VDR binding and chromatin opening combined with a DR3-type sequence highlighted genome-wide 160 VDR loci that have within their chromatin domain a more than 4-fold increased likelihood to identify a primary 1,25(OH)2D3 target gene than in the vicinity of other genomic VDR binding 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.