Genome‐wide identification of vitamin D receptor (VDR) binding sites in DNA from prostate epithelial cells (PEC) by chromatin immunoprecipitation‐sequencing (ChIP‐seq)

Abstract

The 1,25 dihydroxyvitamin D (1,25D) activates the VDR to bind DNA and initiate gene transcription. While microarray studies show 1,25D regulates expression of many transcripts, few of these genes have been examined for VDR binding. Using ChIP‐seq, we mapped VDR binding sites in DNA from the human PEC line, RWPE1. Cells were treated with vehicle or 1,25D (10 nM, 3 h) and subjected to ChIP using either VDR antibody or IgG. Using IgG as the reference, 1236 and 1175 VDR binding peaks were found in 1,25D and vehicle‐treated cells, respectively (0.1 FDR, 200 bp window, Cisgenome). Genes with known VDREs were confirmed e.g. CYP24 and IGFBP3. Correlation between ChIP‐seq peaks and a previous microarray study found that only 39% were associated with 1,25D‐regulated transcripts, including novel peaks close to the transcription factors (TF) JunB, FOS and TBP. Also only 5% of VDR peaks were found within 5 kb of the transcription start site of a gene and the known DR3 VDR binding motif was found in just 15% of the peaks. However, several other DNA‐binding motifs were enriched under the peaks suggesting indirect DNA association of VDR through other TF. Our data suggest the relationship between VDR binding and transcription is more complex that previously reported.Grant Funding Source: Showalter Trust to JCF