Linking molecular-level RNA-protein interactions with mesoscale properties of the nucleolus.

Abstract

The nucleolus is the most prominent nuclear body, and represents a condensate comprising the machinery of ribosome biogenesis, including multi-step transcription, processing, and assembly of ribosomal RNA (rRNA). These intricate steps are organized in well-characterized nucleolar substructures, with a host of RNA and proteins components that have been described in detail. However, the role of specific molecular-level interactions, such as RNA-RNA and RNA-protein, in governing nucleolar morphology and its material properties is unknown. Towards addressing this problem, we have deployed a suite of chemical biology, quantitative cellular microscopy and in vitro biophysical methods. Specifically, we use chemical perturbations to selectively and transiently inhibit distinct steps of ribosome biogenesis in cells. We then visualize and classify changes in nucleolar morphology as well as profile thermodynamics of nucleolar RNA-binding proteins (RBPs) upon treating cells with these inhibitors. Preliminary results indicate that the RBP thermodynamic profiles and morphologies are dependent on the presence or absence of specific RNA and/or RBP species in the nucleolus, suggesting that select RBP-RNA interactions may differentially contribute to nucleolar structure and function. To test this hypothesis, we are investigating material properties, dynamics, and RNA structural landscapes of in vitro nucleolar condensates with varying RNA and RBP compositions. Given that aberrant ribosome production is a hallmark of cancer and other diseases, our findings on the molecular thermodynamics of the nucleolus will pave the way towards rational therapeutic targeting.