Genome wide enhancer loops (HiChIP) and 3-D high order chromatin features associated with EWS-FLI1 in Ewing Sarcoma. [ChIP-seq]

Tumor cell identity is the product of complex interactions between oncogenic drivers and mechanisms regulating normal differentiation pathways. Cell fate transitions observed in embryonic development involve structural changes in genomic organization that provide proper lineage specification, however, whether similar events also occur within tumor cells and contribute to cancer evolution remains largely unexplored. Here we modeled this process in the pediatric bone cancer Ewing sarcoma and investigated high resolution looping and large-scale 3D nuclear conformation changes associated with EWS-FLI1, the oncogenic fusion protein that drives this tumor. We find that chromatin interactions in Ewing sarcoma cells are dominated by highly connected looping hubs centered on EWS-FLI1 binding sites, which directly control the activity of linked enhancers and promoters to establish oncogenic expression programs. Depletion of EWS-FLI1 leads to the loss of looping networks associated with the fusion protein and, strikingly, also results in widespread nuclear reorganization through the establishment of new patterns of looping and large-scale inter-compartment connectivity that resemble the chromatin configuration of mesenchymal stem cells, a candidate cell of origin of this tumor. Our data thus demonstrate that major architectural features of nuclear organization in cancer cells can be linked to a single oncogenic event and readily reversed to re-establish latent differentiation programs. H3K27ac ChIP is carried out to identify the all active chromatin regions marked by the H3K27ac histone modifications. NOTE FROM SUBMITTER: Since the MSC samples (HiC, HiChIP and ChIP-seq) are from patients, we did not include the raw data due to privacy concern.