Genome-wide (over)view on the actions of vitamin D

Abstract

For a global understanding of the physiological impact of the nuclear hormone 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) the analysis of the genome-wide locations of its high affinity receptor, the transcription factor vitamin D receptor (VDR), is essential. Chromatin immunoprecipitation sequencing (ChIP-seq) in GM10855 and GM10861 lymphoblastoid cells, undifferentiated and lipopolysaccharide-differentiated THP-1 monocytes, LS180 colorectal cancer cells and LX2 hepatic stellate cells revealed between 1000 and 13,000 VDR-specific genomic binding sites. The harmonized analysis of these ChIP-seq datasets indicates that the mechanistic basis for the action of the VDR is independent of the cell type. Formaldehyde-assisted isolation of regulatory elements sequencing (FAIRE-seq) data highlight accessible chromatin regions, which are under control of 1,25(OH)2D3. In addition, public data, such as from the ENCODE project, allow to relate the genome-wide actions of VDR and 1,25(OH)2D3 to those of other proteins within the nucleus. For example, locations of the insulator protein CTCF suggest a segregation of the human genome into chromatin domains, of which more than 1000 contain at least one VDR binding site. The integration of all these genome-wide data facilitates the identification of the most important VDR binding sites and associated primary 1,25(OH)2D3 target genes. Expression changes of these key genes can serve as biomarkers for the actions of vitamin D3 and its metabolites in different tissues and cell types of human individuals. Analysis of primary tissues obtained from vitamin D3 intervention studies using such markers indicated a large inter-individual variation for the efficiency of vitamin D3 supplementation. In conclusion, a genome-wide (over)view on the genomic locations of VDR provides a broader basis for addressing vitamin D's role in health and disease.

Keywords: chromatin; epigenomics; gene regulation; genomics; vitamin D; vitamin D receptor.

Figure 1

Conserved genomic VDR binding in six cellular models. The Integrative Genomics Viewer (IGV) browser (Robinson et al., 2011) was used to visualize the VDR binding site 15.3 kb downstream of the ZMIZ1 TSS. The peak tracks display data from VDR ChIP-seq datasets from two B cell-like cells (dark and light blue), monocyte-like cells (red), macrophage-like cells (orange), colon cells (gray) and liver cells (violet). The cells were either unstimulated (−) or treated with VDR ligand (+). The gene structures are shown in blue and the sequence of the DR3-type element below the summit of the VDR peak is indicated.

Figure 2

Genomic view of 1,25(OH)₂D₃-dependent chromatin opening. The IGV browser visualizes the loci of a VDR locus 225 kb downstream of the CHD7 gene (±40 kb of the peak summit). The peak tracks display data from THP-1 cells: a time course of FAIRE-seq data [gray for EtOH-treated controls and turquoise for 1,25(OH)₂D₃ (1,25D) treatments for the indicated time periods] and a VDR ChIP-seq data [red, from unstimulated cells and after 40 min 1,25(OH)₂D₃ treatment]. The gene structures are shown in blue and the sequence of the DR3-type element below the summit of the VDR peak is indicated.

Figure 3

Chromatin domain containing VDR binding sites. The IGV browser was used to display the chromatin domain around the CD14 gene. VDR ChIP-seq data from THP-1 cells [unstimulated (−) and treated for 40 min with 1,25(OH)₂D₃ (+), red] are shown in comparison with CTCF ChIP-seq data from the ENCODE cell lines NHEK, HUVEC and K562 (orange) and CTCF ChIA-PET data from K562 cells in the track view (light blue). The gene structures are shown in blue and the sequence of the DR3-type elements below the summits of the VDR peaks are indicated.