1,25-Dihydroxyvitamin D3 induced histone profiles guide discovery of VDR action sites

Abstract

The chromatin environment dictates activity throughout the genome. Post-translational modification of the N-terminal tails of histone proteins allow nucleosomes to shift, the chromatin to relax and genes to become activated. Histone modification events and markers will change in response to environmental stimuli; therefore they present a method for identification of sites of transcription factor activity. 1,25-Dihydroxyvitamin D3 induces the vitamin D receptor (VDR) to bind to DNA and activate transcription. These actions alter the chromatin environment and can be detected by increases or decreases in the histone modifications. In fact, in genomic loci with multiple enhancers, selective modulation of those enhancers after vitamin D3 stimulation can be readily detected by histone modifications. We provide an example of these actions on the Mmp13 gene locus where VDR binds selectively to an enhancer 10kb upstream of the transcriptional start site. This binding event is accompanied by an enhancer-selective increase in histone 3 lysine 9 acetylation (H3K9Ac). ChIP-seq analysis of histone modifications requires less genomic material than transcription factor ChIP-seq, thus proving advantageous to in vivo assays with limited cellular material. Therefore, histone modification activity alone may be used as a guide for discovering sites of VDR action for further biochemical analysis. This article is part of a Special Issue entitled '16th Vitamin D Workshop'.

Keywords: ChIP-seq; H3K9Ac; Histone modification; Mmp13; VDR.

Figure 1

The Mmp13 gene locus contains three distinct enhancer regions. ChIP-seq tag density profiles (normalized to 10⁷ tags) for the Mmp13 gene locus for VDR and H3K9Ac. The vehicle treated cell tracks (red) are overlaid on the 1,25(OH)₂D₃ cell tracks (blue). Increased binding due to 1,25(OH)₂D₃ treatment will appear as blue, vehicle enriched as red and the overlapping regions purple. Genomic location (mouse mm9 genome) and scale are indicated in each track, max height of tag sequence density for the data track is indicated on Y-axis. Gene transcriptional direction is indicated by an arrow and exons by boxes.