Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription

• Published in: Molecular cell 2022-06, Vol.82 (11), p.2084-2097.e5
• Main Authors: Chong, Shasha, Graham, Thomas G.W., Dugast-Darzacq, Claire, Dailey, Gina M., Darzacq, Xavier, Tjian, Robert
• Format: Article
• Language: English
• Subjects: cell nucleolus; Ewing sarcoma; EWS::FLI1; gene activation; humans; intrinsically disordered regions; liquid-liquid phase separation; low-complexity domains; microsatellite repeats; multivalent interactions; nucleolus; separation; single-cell and single-molecule imaging; therapeutics; transcription (genetics); transcription factor; transcriptional activation; transcriptional control
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2022.04.007

Gene activation by mammalian transcription factors (TFs) requires multivalent interactions of their low-complexity domains (LCDs), but how such interactions regulate transcription remains unclear. It has been proposed that extensive LCD-LCD interactions culminating in liquid-liquid phase separation (LLPS) of TFs is the dominant mechanism underlying transactivation. Here, we investigated how tuning the amount and localization of LCD-LCD interactions in vivo affects transcription of endogenous human genes. Quantitative single-cell and single-molecule imaging reveals that the oncogenic TF EWS::FLI1 requires a narrow optimum of LCD-LCD interactions to activate its target genes associated with GGAA microsatellites. Increasing LCD-LCD interactions toward putative LLPS represses transcription of these genes in patient-derived cells. Likewise, ectopically creating LCD-LCD interactions to sequester EWS::FLI1 into a well-documented LLPS compartment, the nucleolus, inhibits EWS::FLI1-driven transcription and oncogenic transformation. Our findings show how altering the balance of LCD-LCD interactions can influence transcriptional regulation and suggest a potential therapeutic strategy for targeting disease-causing TFs. [Display omitted] •EWS::FLI1 requires a narrow optimum of LCD-LCD interactions to activate transcription•Boosting LCD-LCD interactions toward phase separation represses transcription•Sequestering EWS::FLI1 into the nucleolus inhibits its transcription functions•EWS::FLI1 diffuses more slowly within the phase-separated nucleolus It has been proposed that mammalian TFs require phase separation to activate transcription. Using EWS::FLI1 as a model system, Chong et al. show that a TF requires a narrow optimum of LCD-LCD interactions to activate transcription in vivo, and phase separation of TFs represses transcription of its endogenous target genes.