Shawn Yoshida

Eukaryotic transcription factors (TFs) form local, high‐concentration hubs at specific genomic loci through dynamic, multivalent interactions mediated by their low‐complexity domains, a behavior essential for transcriptional activation. Characterizing the dynamics and regulation of TF hubs requires high‐resolution imaging of TFs in their native cellular environment; however, such biophysical characterization remains limited. Here, we combine CRISPR/Cas9‐mediated genome editing and single‐molecule microscopy to investigate the behaviors of endogenous oncogenic fusion TF EWS::FLI1 in Ewing sarcoma cells. EWS::FLI1 forms sub‐diffraction‐limit hubs with dissolution mechanisms that prevent macroscopic liquid‐liquid phase separation. Hub formation is a neomorphic behavior of EWS::FLI1 not conferred by its parental proteins, EWSR1 and FLI1. During mitosis, EWS::FLI1 hubs dissolve, but EWS::FLI1 molecules continue to dynamically associate with mitotic chromosomes, consistent with a mitotic bookmarking role. Nascent RNA destabilizes EWS::FLI1 hubs without affecting their dimensions. Finally, LY2835219 and trabectedin, compounds previously reported to affect EWS::FLI1 function, disrupt and mislocalize endogenous EWS::FLI1 hubs, respectively, highlighting their therapeutic potential for treating Ewing sarcoma. Together, our results reveal new insights into the assembly and regulation of endogenous EWS::FLI1 hubs at an unprecedented resolution and establish a framework for biophysical and functional characterization of other TF hubs in the future.

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.

Fluorescence microscopy techniques have been widely adopted in biology for their ability to visualize the structure and dynamics of a wide range of cellular and subcellular processes. The specificity and sensitivity that these techniques afford have made them primary tools in the characterization of protein localizations within cells. Many of the fluorescence microscopy techniques require cells to be fixed via chemical or alternative methods before being imaged. However, some fixation methods have been found to induce the redistribution of particular proteins in the cell, resulting in artifacts in the characterization of protein localizations and functions under physiological conditions. Here, we review the ability of commonly used cell fixation methods to faithfully preserve the localizations of proteins that bind to chromatin, undergo liquid-liquid phase separation (LLPS), and are involved in the formation of various membrane-bound organelles. We also review the mechanisms underlying various fixation artifacts and discuss potential alternative fixation methods to minimize the artifacts while investigating different proteins and cellular structures. Overall, fixed-cell fluorescence microscopy is a very powerful tool in biomedical research; however, each experiment demands the careful selection of an appropriate fixation method to avoid potential artifacts and may benefit from live-cell imaging validation.

Fixing cells with paraformaldehyde (PFA) is an essential step in numerous biological techniques as it is thought to preserve a snapshot of biomolecular transactions in living cells. Fixed-cell imaging techniques such as immunofluorescence have been widely used to detect liquid–liquid phase separation (LLPS) in vivo. Here, we compared images, before and after fixation, of cells expressing intrinsically disordered proteins that are able to undergo LLPS. Surprisingly, we found that PFA fixation can both enhance and diminish putative LLPS behaviors. For specific proteins, fixation can even cause their droplet-like puncta to artificially appear in cells that do not have any detectable puncta in the live condition. Fixing cells in the presence of glycine, a molecule that modulates fixation rates, can reverse the fixation effect from enhancing to diminishing LLPS appearance. We further established a kinetic model of fixation in the context of dynamic protein–protein interactions. Simulations based on the model suggest that protein localization in fixed cells depends on an intricate balance of protein–protein interaction dynamics, the overall rate of fixation, and notably, the difference between fixation rates of different proteins. Consistent with simulations, live-cell single-molecule imaging experiments showed that a fast overall rate of fixation relative to protein–protein interaction dynamics can minimize fixation artifacts. Our work reveals that PFA fixation changes the appearance of LLPS from living cells, presents a caveat in studying LLPS using fixation-based methods, and suggests a mechanism underlying the fixation artifact.

The serial nature of reactions involved in the RNA life-cycle motivates the incorporation of delays in models of transcriptional dynamics. The models couple a bursty or switching promoter to a fairly general set of Markovian or deterministically delayed monomolecular RNA interconversion reactions with no feedback. We provide numerical solutions for the RNA copy number distributions the models induce, and solve several systems with splicing and degradation. An analysis of single-cell and single-nucleus RNA sequencing data using these models reveals that the kinetics of nuclear export do not appear to require invocation of a non-Markovian waiting time.

Fixing cells with paraformaldehyde (PFA) is an essential step in numerous biological techniques as it is thought to preserve a snapshot of biomolecular transactions in living cells. Fixed cell imaging techniques such as immunofluorescence have been widely used to detect liquid-liquid phase separation (LLPS) in vivo . Here, we compared images, before and after fixation, of cells expressing intrinsically disordered proteins that are able to undergo LLPS. Surprisingly, we found that PFA fixation can both enhance and diminish putative LLPS behaviors. For specific proteins, fixation can even cause their droplet-like puncta to artificially appear in cells that do not have any detectable puncta in the live condition. Fixing cells in the presence of glycine, a molecule that modulates fixation rates, can reverse the fixation effect from enhancing to diminishing LLPS appearance. We further established a kinetic model of fixation in the context of dynamic protein-protein interactions. Simulations based on the model suggest that protein localization in fixed cells depends on an intricate balance of protein-protein interaction dynamics, the overall rate of fixation, and notably, the difference between fixation rates of different proteins. Consistent with simulations, live-cell single-molecule imaging experiments showed that a fast overall rate of fixation relative to protein-protein interaction dynamics can minimize fixation artifacts. Our work reveals that PFA fixation changes the appearance of LLPS from living cells, presents a caveat in studying LLPS using fixation-based methods, and suggests a mechanism underlying the fixation artifact.

Anomalous diffusion dynamics in confined nanoenvironments govern the macroscale properties and interactions of many biophysical and material systems. Currently, it is difficult to quantitatively link the nanoscale structure of porous media to anomalous diffusion within them. Fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) has been shown to extract nanoscale structure and Brownian diffusion dynamics within gels, liquid crystals, and polymers, but has limitations which hinder its wider application to more diverse, biophysically-relevant datasets. Here, we parallelize the least-squares curve fitting step on a GPU improving computation times by up to a factor of 40, implement anomalous diffusion and two-component Brownian diffusion models, and make fcsSOFI more accessible by packaging it in a user-friendly GUI. We apply fcsSOFI to simulations of the protein fibrinogen diffusing in polyacrylamide of varying matrix densities and super-resolve locations where slower, anomalous diffusion occurs within smaller, confined pores. The improvements to fcsSOFI in speed, scope, and usability will allow for the wider adoption of super-resolution correlation analysis to diverse research topics.