Evaluating Chromatin Interactions in Prostate Cancer

To evaluate functional relevance of the chromatin interactions, we aligned our interaction peaks with the genomic locations of GENCODE genes (v19; http://www.gencodegenes.org), and histone modifications including active enhancers (H3K27ac, H3K4me1), active promoters (H3K4me3) and (H3K4me2), which usually overlapped with transcription factor binding regions51 (link)52 (link)53 (link)54 (link). For the most significant interactions, we examined the binding of genome organizer proteins CTCF, RAD21 and prostate specific transcription factors: AR, FOXA1, HOXB13 in prostate specific cell lines LNCaP, VCaP and NCIH660. eQTL analysis was performed using RNA-seq data and SNP genotyping data (Illumina HumanOmni2.5–8 Beadchip) derived from 476 normal prostate tissues in our laboratory. Linear regression was used to correlate genotypes of selected SNPs and expression level (RPKM) of candidate genes.