Dynamic regulation of endogenous transcription factor hubs at single-molecule resolution

Eukaryotic transcription factors (TFs) form local, high-concentration hubs at specific genomic loci through dynamic, multivalent protein-protein interactions mediated by their low-complexity domains. The hub formation behavior plays an essential role in TFs' transcriptional activation activities. Characterizing the dimensions, dynamics, and regulation of TF hubs requires high-resolution imaging of TFs in their native cellular environment, but much of such biophysical characterization remains missing. Here, we combined CRISPR/Cas9-mediated genome editing and advanced quantitative cell imaging, including single-molecule microscopy, to investigate the dynamic behaviors of the endogenous oncogenic fusion TF EWS::FLI1 in Ewing sarcoma cells. We found that endogenous EWS::FLI1 forms dynamic, sub-diffraction-limit hubs with mechanisms of dissolution that prevent the hubs from achieving macroscopic liquid-liquid phase separation. Hub formation is a neomorphic behavior of EWS::FLI1 that is not directly conferred by its parental proteins, EWSR1 and FLI1. We found that during mitosis, EWS::FLI1 hubs dissolve, but EWS::FLI1 molecules continue to dynamically bind and unbind mitotic chromosomes, revealing a role of EWS::FLI1 in mitotic bookmarking. Nascent RNA destabilizes EWS::FLI1 hubs on chromatin, but it does not affect the dimensions of the hubs. Finally, we visualized endogenous EWS::FLI1 hubs upon treatment with various compounds that were previously indicated to affect EWS::FLI1 function. We found that LY2835219 and trabectedin significantly alter the nuclear distribution of endogenous EWS::FLI1, disrupting and mislocalizing EWS::FLI1 hubs, respectively. This finding highlights the therapeutic potential of both compounds for Ewing sarcoma. Together, our results reveal new insights into the assembly and regulation of endogenous EWS::FLI1 hubs at an unprecedented resolution. The methodology developed here will be useful for characterizing the functional hubs of many regular and pathological TFs in the future.