Disordered domains in oncogenic gene regulation

Intrinsically disordered regions (IDRs) in DNA-associated proteins play important roles in oncogenic gene regulation but their overall genomic distribution and cooperative functions remain incompletely understood. In particular, EWS fusion proteins, which are formed by the combination of the EWS IDR and the DNA-binding domains of various transcription factors, serve as paradigms for IDR function in cancer. Our laboratory has shown that the addition of the EWS IDR to the ETS transcription factor FLI1 in Ewing sarcoma has profound functional consequences, leading to the formation of an oncogene that operates as a pioneer factor at new genomic locations that are not accessible to wildtype FLI1. Furthermore, our data shows that EWS-FLI1 bound enhancers reconfigure the 3D nuclear architecture of Ewing sarcoma cells to establish an oncogenic gene regulation program that is critical for cell survival and proliferation. In order to identify other critical IDR containing proteins and characterize their roles in gene regulation programs, we set out to develop methodologies to map the localization of DNA bound disordered proteins genome-wide. We recently reported a new antibody-independent chemical precipitation assay that can simultaneously map endogenous DNA-associated disordered proteins through a combination of biotinylated isoxazole precipitation and next-generation sequencing (DisP-seq, disordered protein precipitation followed by DNA sequencing). DisP-seq profiles are composed of thousands of peaks that are associated with diverse chromatin states, are enriched for disordered transcription factors (TFs) and are often arranged in large lineage-specific clusters with high local concentrations of disordered proteins and different combinations of histone modifications linked to regulatory potential. DisP-seq analysis of Ewing sarcoma cells revealed how disordered protein clusters containing EWS-FLI1 enable IDR-dependent mechanisms that control the binding and function of other disordered TFs, including oncogene-dependent sequestration through long-range interactions and the reactivation of differentiation pathways upon loss of oncogenic stimuli.