A prostate cancer chromatin interaction map

A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome Prostate cancer (PCa) is the leading cancer among men in the United States. To understand gene regulation in 3D, chromatin interactions in prostate cancer cell is measured using in situ Hi-C. To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we developed high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and transcriptome profiling, we identified topologically associating domains that changed in size and epigenetic states between normal and prostate cancer cells. Moreover, we identified normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. This creation of 3D epigenomic maps will enable a better understanding of prostate cancer biology and mechanisms of gene regulation. Overall design: Examination of prostate cancer epithelial cell 22Rv1 chromatin interactions using Hi-C In situ Hi-C, ChIP-seq using active and repressive histone marks and CTCF binding sites, NOMe-seq for nucleosome-depleted regions, and RNA-seq for transcriptome profiling in prostate epithelial cells to characterize prostate cancer epigenomic transcriptome. Please note that processed data was generated from all replicates and is linked to the corresponding rep1 sample records (or to Series records).