Droplet-assisted folding of long regulatory RNAs

Long regulatory RNA regions orchestrate complex cellular processes, including gene expression and epigenetic modifications. How these RNAs dynamically fold and refold in response to cellular signals remains poorly understood. Given that RNAs interact with ubiquitous RNA-binding proteins (RBPs) prone to form biomolecular condensates, we explore how protein droplets interacting along an RNA impact its folding process. Attached droplets prevent premature folding by competing with RNA:RNA interactions. When droplets dissolve due to cellular signals, capillary effects cause the RNA to collapse while refolding. We test this process of condensate-guided RNA folding by adapting established RNA secondary structure predictors to mimic various folding pathways and supplement this with coarse-grained simulations. We find that interactions with transient droplets robustly leads to the formation of long-range RNA contacts, which are otherwise hard to achieve. Our results compare favorably with available experimental data. We propose that this strategy, which we call droplet-assisted RNA folding, represents a previously unexplored mechanism for shaping RNA structures. Given the widespread propensity of RBPs to form condensates, this process could play a fundamental role in the structural organization, conditional reshaping, and functional regulation of long regulatory RNAs.