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Genome- and transcriptome-wide data has significantly increased the amount of available information about primary 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) target genes in cancer cell models, such as human THP-1 myelomonocytic leukemia cells. In this study, we investigated the genes G0S2, CDKN1A and MYC as master examples of primary vitamin D receptor (VDR) targets being involved in the control of cellular proliferation. The chromosomal domains of G0S2 and CDKN1A are 140-170 kb in size and contain one and three VDR binding sites, respectively. This is rather compact compared to the MYC locus that is 15 times larger and accommodates four VDR binding sites. All eight VDR binding sites were studied by chromatin immunoprecipitation in THP-1 cells. Interestingly, the site closest to the transcription start site of the down-regulated MYC gene showed 1,25(OH)2D3-dependent reduction of VDR binding and is not associated with open chromatin. Four of the other seven VDR binding regions contain a typical DR3-type VDR binding sequence, three of which are also occupied with VDR in macrophage-like cells. In conclusion, the three examples suggest that each VDR target gene has an individual regulatory scenario. However, some general components of these scenarios may be useful for the development of new therapy regimens [ABSTRACT FROM AUTHOR]

Abstract: The signaling cascade of the transcription factor vitamin D receptor (VDR) is triggered by its specific ligand 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3). In this study we demonstrate that in THP-1 human monocytic leukemia cells 87.4% of the 1034 most prominent genome-wide VDR binding sites co-localize with loci of open chromatin. At 165 of them 1α,25(OH)2D3 strongly increases chromatin accessibility and has at further 217 sites weaker effects. Interestingly, VDR binding sites in 1α,25(OH)2D3-responsive chromatin regions are far more often composed of direct repeats with 3 intervening nucleotides (DR3s) than those in ligand insensitive regions. DR3-containing VDR sites are enriched in the neighborhood of genes that are involved in controling cellular growth, while non-DR3 VDR binding is often found close to genes related to immunity. At the example of six early VDR target genes we show that the slope of their 1α,25(OH)2D3-induced transcription correlates with the basal chromatin accessibility of their major VDR binding regions. However, the chromatin loci controlling these genes are indistinguishable in their VDR association kinetics. Taken together, ligand responsive chromatin loci represent dynamically regulated contact points of VDR with the genome, from where it controls early 1α,25(OH)2D3 target genes. [Copyright &y& Elsevier]

Vitamin D deficiency has been associated with an increased risk of developing a number of diseases. Here we investigated samples from 71 pre-diabetic individuals of the VitDmet study, a 5-month high dose vitamin D3 intervention trial during Finnish winter, for their changes in serum 25-hydroxyvitamin D3 (25(OH)D3) concentrations and the expression of primary vitamin D target genes in peripheral blood mononuclear cells and adipose tissue. A negative correlation between serum concentrations of parathyroid hormone and 25(OH)D3 suggested an overall normal physiological vitamin D response among the participants. The genes CD14 and thrombomodulin (THBD) are up-regulated primary vitamin D targets and showed to be suitable gene expression markers for vitamin D signaling in both primary tissues. However, in a ranking of the samples concerning their expected response to vitamin D only the top half showed a positive correlation between the changes of CD14 or THBD mRNA and serum 25(OH)D3 concentrations. Interestingly, this categorization allows unmasking a negative correlation between changes in serum concentrations of 25(OH)D3 and the inflammation marker interleukin 6. We propose the genes CD14 and THBD as transcriptomic biomarkers, from which the effects of a vitamin D3 supplementation can be evaluated. These biomarkers allow the classification of subjects into those, who might benefit from a vitamin D3 supplementation, and others who do not. [ABSTRACT FROM AUTHOR]

The transcription factor vitamin D receptor (VDR) is the nuclear sensor for the biologically most active metabolite of vitamin D, 1α,25-dihydroxyvitamin D(3) (1α,25(OH)(2)D(3)). The physiological actions of the VDR and its ligand are not only the well-known regulation of calcium and phosphorus uptake and transport controlling bone formation, but also their significant involvement in the control of immune functions and of cellular growth and differentiation. For a general understanding of the mechanisms of 1α,25(OH)(2)D(3) signaling, it is essential to monitor the genome-wide location of VDR in relation to primary 1α,25(OH)(2)D(3) target genes. Within the last months, two chromatin immunoprecipitation sequencing (ChIP-Seq) studies using cells of the hematopoietic system, lymphoblastoids and monocytes, were published. The reports indicated the existence of 2776 and 1820 1α,25(OH)(2)D(3)-stimulated VDR-binding sites, comparable numbers, of which, however, only 18.2% overlapped. The two studies were very different in their 1α,25(OH)(2)D(3) treatment times (36 h versus 40 min), but showed consensus in identifying response elements formed by a direct repeat of two hexameric binding sites with three intervening nucleotide (DR3) as major DNA contact sites of the VDR. Interestingly, when analyzed in the same way, both reports indicated that within 100 bp of their VDR ChIP-Seq peak summits only fewer than 40% contain a DR3-type response element. This review provides a detailed comparison of the insights obtained from both ChIP-Seq studies.

The vitamin D receptor (VDR) is a ligand-inducible transcription factor whose target genes play key roles in cellular metabolism, bone formation, cellular growth, differentiation and in controlling inflammation. Many of these VDR target genes are also involved in dysregulated pathways leading to common human diseases, such as cancer. The activation of VDR by natural and synthetic ligands may improve such pathological conditions. On a genomic level, these pathways converge on regulatory modules, some of which contain VDR-binding sites, so-called vitamin D response elements (VDREs). Transcriptome analysis, chromatin immunoprecipitation scans and in silico screening approaches have already identified many genomic targets of the VDR. Important cancer regulatory modules with VDREs should have a major impact on understanding the role and potential therapeutic value of VDR in cancer.