Chromosome Conformation Capture Reveals Two Elements That Interact with the () Transcription Start Site

The long-range control of gene expression is facilitated by chromatin looping and can be detected using chromosome conformation capture-3C. Here we focus on the chromatin architecture of the (Polypyrimidine tract binding protein 3) locus to evaluate its potential role in regulating expression of the gene. expression in prostate cancer cell lines is found significantly higher compared to skin fibroblasts using real-time PCR ( < 0.05) and digital droplet PCR ( < 0.01). Exploration of the chromatin spatial architecture of a nearly 200-kb fragment of chromosome 9 encompassing the gene identified two elements located 63 kb upstream and 48 kb downstream of , which looped specifically to the promoter. These elements contain histone acetylation patterns characteristic of open chromatin regions with active enhancers. Our results reveal for the first time that long-range chromatin interactions between the -63 kb and +48 kb loci and the promoter regulate the expression of this gene in prostate cancer cells. These interactions support an open chromatin form for the locus in cancer cells and the three-dimensional structural model proposed in this paper.