EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma

The aberrant transcription factor EWS-FLI1 drives Ewing sarcoma, but its molecular function is not completely understood. We find that EWS-FLI1 reprograms gene regulatory circuits in Ewing sarcoma by directly inducing or repressing enhancers. At GGAA repeat elements, which lack evolutionary conservation and regulatory potential in other cell types, EWS-FLI1 multimers induce chromatin opening and create de novo enhancers that physically interact with target promoters. Conversely, EWS-FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild-type ETS transcription factors. These divergent chromatin-remodeling patterns repress tumor suppressors and mesenchymal lineage regulators while activating oncogenes and potential therapeutic targets, such as the kinase VRK1. Our findings demonstrate how EWS-FLI1 establishes an oncogenic regulatory program governing both tumor survival and differentiation. [Display omitted] •A single aberrant transcription factor directly activates or represses enhancers•Chromatin remodeling at enhancer elements is dictated by the underlying DNA sequence•EWS-FLI1 displays divergent patterns of chromatin remodeler recruitment•De novo enhancers mediate tumor dependencies Using integrated analyses of chromatin states in human Ewing sarcoma, Riggi et al. find that the EWS-FLI1 fusion protein drives an oncogenic regulatory program governing both survival and differentiation by either creating enhancers de novo or competing with endogenous ETS to repress conserved enhancers.