Structural and functional determinants of biomolecular condensates in transcription organization

Many cellular processes use phase separation to sequesters biomolecules into membraneless organelles or condensates. This concept is of particular importance in the cell nucleus. Most nuclear condensates are associated with specific chromatin loci. Thus, chromatin organization and biomolecular condensate formation are closely related. Topology, epigenetic modification, or enzymatic activity are possible links between the chromatin scaffold and protein condensation. We have previously described condensates that concentrate transcription machinery at super-enhancers but understanding of cell-to-cell variability and locus specific features that nucleate condensates is missing. Preliminary data indicates that active chromatin decorates the surface of transcription condensates below the resolution limit of conventional microscopy. Making use of recent developments in multiplexed super-resolution microscopy of both chromatin elements and protein factors, we will characterize the nature of the chromatin enrichment layer and determine if it reflects the condensate surface as an active interface that regulates transcription. We will for the first time directly observe the interplay of local chromatin topology, epigenetic signatures, and condensate formation in a specific model locus in mouse embryonic stem cells. By scrutinizing with genomic resolution how each of the regulatory elements in the locus interacts with the condensate we will determine if chromatin structures such as enhancer hubs nucleate condensates, or if condensates induce specific chromatin topologies by connecting active elements. Finally, we will investigate at the molecular level how condensate constituents interact with the microenvironment and associated chromatin elements, and test the hypothesis that retention of transcription factors boosts binding site occupancy and stabilizes condensates at regulatory chromatin. Targeted perturbation and locus-specific observation will allow us to answer this question and begin to identify genome-wide rules that predict where precisely chromatin-supported condensates form. The overall vision for this research program is to develop an integrated view of chromatin organization and condensate formation. Experimental data will inspire new conceptual frameworks and help us integrate the full complexity of condensates into paradigms of biological function such as transcription regulation. We expect that new biophysical models of self-organization and self-regulation will emerge from our studies of intracellular condensates.