Emerging evidence suggests that chromatin adopts a nonrandom 3D topology and that the organization of genes into structural hubs and domains affects their transcriptional status. How chromatin conformation changes in diseases such as cancer is poorly understood. Moreover, how oncogenic transcription factors, which bind to thousands of sites across the genome, influence gene regulation by globally altering the topology of chromatin requires further investigation. To address these questions, we performed unbiased high-resolution mapping of intra-and interchromosome interactions upon overexpression of ERG, an oncogenic transcription factor frequently overexpressed in prostate cancer as a result of a gene fusion. By integrating data from genome-wide chromosome conformation capture (Hi-C), ERG binding, and gene expression, we demonstrate that oncogenic transcription factor overexpression is associated with global, reproducible, and functionally coherent changes in chromatin organization. The results presented here have broader implications, as genomic alterations in other cancer types frequently give rise to aberrant transcription factor expression, e.g., EWS-FLI1, c-Myc, n-Myc, and PML-RARα.M ounting evidence suggests that many genes dynamically colocalize to shared nuclear compartments that favor gene activation or silencing (1-3). As demonstrated by chromosome conformation capture (3C) (4), ligand-bound androgen receptors (AR) and estrogen receptors mediate looped chromatin structures resulting in coordinated transcription of target genes (5, 6). In embryonic carcinoma cells, the PolyComb complex subunit EZH2 represses some of its target genes via the formation of similar looped chromatin structures (7). Trans-interactions that regulate gene expression have also been reported (8-10). These data suggest that oncogenic transcriptional regulators are capable of inducing changes in chromatin structures. These studies have mainly focused on local chromatin structures, and it is still unclear whether more global changes occur in the process of oncogene-mediated transformation. A broader implication of these observations is that global chromatin organization changes could impact functional and phenotypic aspects of cancer.To globally investigate oncogene-mediated chromatin structure changes we focused on ERG, the ETS-family transcription factor most frequently rearranged and overexpressed in prostate cancer through the TMPRSS2-ERG and other gene fusions involving androgen-responsive promoters (11-13). ERG interacts with several cofactors (14) and other transcription factors including AR to regulate the expression of thousands of genes that favor dedifferentiation, cell invasion, and neoplastic transformation of prostate epithelium when overexpressed (15-20). We therefore hypothesized that changes in global gene expression induced by ERG overexpression could be associated with global changes in the 3D structure of chromosomes.Results ERG Overexpression Is Associated with Chromatin Topology. To test our hypothesis, we used...