ZFTA fusion oncoproteins drive tumorigenesis through transcriptional condensates

Over 95% of ependymomas (EPNs) that arise in the cortex are driven by a gene fusion involving the zinc finger translocation associated (ZFTA) protein. Using super-resolution and lattice light sheet microscopy, we demonstrate that the most frequent fusion variant, ZFTA-RELA (ZR), forms dynamic nuclear condensates that are required for oncogene expression and tumorigenesis. Mutagenesis of ZR reveals a key intrinsically disordered region (IDR) that governs condensate formation. Condensate-modulating ZR IDR mutations impaired genomic occupancy at oncogenic loci, and inhibited the recruitment of transcriptional effector proteins, such as MED1, BRD4 and RNA polymerase II. Using nuclear magnetic resonance spectroscopy, we examined the protein structure of the critical zinc finger found in ZR, and characterized its significance for condensate formation, genomic binding, and oncogene activation. Our data leverages microscopy, genomics, cell biology, animal modeling, structural biology, and machine learning approaches to provide mechanistic insights into the processes that govern oncogene expression in ZFTA FO-driven tumors.