mRNA structure determines specificity of a polyQ-driven phase separation

TLDR

RNA drives liquid‑liquid phase separation to form membraneless compartments, yet the mechanisms that establish and maintain distinct compositions within these compartments remain unknown. We show that mRNA secondary structure drives self‑association and determines recruitment to or exclusion from liquid compartments, with the polyQ protein Whi3 altering RNA conformation to generate sequence‑dependent fluctuations, thereby promoting distinct droplet assembly and maintaining compartment identity through structure‑based RNA‑RNA interactions and protein‑driven dynamics.

Abstract

RNA promotes liquid-liquid phase separation (LLPS) to build membraneless compartments in cells. How distinct molecular compositions are established and maintained in these liquid compartments is unknown. Here, we report that secondary structure allows messenger RNAs (mRNAs) to self-associate and determines whether an mRNA is recruited to or excluded from liquid compartments. The polyQ-protein Whi3 induces conformational changes in RNA structure and generates distinct molecular fluctuations depending on the RNA sequence. These data support a model in which structure-based, RNA-RNA interactions promote assembly of distinct droplets and protein-driven, conformational dynamics of the RNA maintain this identity. Thus, the shape of RNA can promote the formation and coexistence of the diverse array of RNA-rich liquid compartments found in a single cell.