Hypertrophic chromatin condensates govern oncogene control in cancer

Summary: This study shows that hypertrophic transcriptional condensates are the defining regulatory architecture for oncogenes in diverse cancers, describes mechanisms that lead to their assembly and regulation, and suggests therapeutic concepts that may be broadly applicable to cancers with dysregulated transcription. Pertinent experimental procedures: We investigate oncogenic transcriptional condensates using an integrated cell-biological, genomic, and biochemical framework. Alterations of protein, DNA, and RNA constituents of transcriptional condensates and dependencies on these components are analyzed in public and experimentally generated datasets. Condensate dynamics are quantified using microscopy approaches, such as fluorescence recovery after photobleaching (FRAP) and single particle tracking (SPT) with acute genetic and pharmacologic perturbations of condensate constituents. Interactions between oncogenic transcription factors (TFs) and cis-regulatory elements are assessed by chromatin immunoprecipitation and complementary methods and combined with chromatin-accessibility mapping. Key molecular interactions are identified by approaches including co-immunoprecipitation, proximity labeling, and mass spectrometry. Description of the new, unpublished data: Hypertrophic transcriptional condensates, defined as exceptionally large pathogenic assemblies of transcription apparatus with specialized physicochemical properties, are assembled at driver oncogenes in a broad spectrum of cancers. These transcriptional condensates differ from those in most normal cells in their exceptional size, the genetic and biochemical mechanisms involved in their assembly, and their components' dynamics. Some hypertrophic transcriptional condensates incorporate a disproportionately large portion of the transcription apparatus, encompass nearly a megabase of DNA, remain assembled longer than typical transcriptional condensates, and arrest the properties that produce condensate dissolution in normal cells. Some of the properties of the hypertrophic condensates are amenable to new approaches that concentrate drugs within the pathological assembly. Conclusions: Driver oncogenes in cancers share a unifying theme: their transcription is controlled by hypertrophic transcriptional condensates, which differ from normal transcriptional condensates in terms of their exceptional size, the genetic and biochemical mechanisms involved in their assembly, and their components' dynamics. We present common features to this condensate architecture and describe mechanisms that lead to their assembly and unusual regulatory behaviors. The concept that hypertrophic transcriptional condensates evolve to serve oncogenic drivers, and evidence of their specialized physicochemical environments, offers new opportunities for antineoplastic drug discovery.