Immiscible proteins compete for RNA binding to order condensate layers

Area of Science:

• Cell Biology
• Molecular Biology
• Biophysics

Background:

• Biomolecular condensates compartmentalize cellular functions.
• Many condensates feature distinct internal subdomains.
• Understanding the relationship between molecular features and condensate organization is challenging.

Purpose of the Study:

• To investigate the assembly logic of multi-domain nuclear paraspeckles.
• To determine how lncRNA NEAT1 influences paraspeckle organization.
• To explore the roles of core (FUS, NONO) and shell (TDP-43) proteins in paraspeckle layer formation.

Main Methods:

• Bioinformatics analysis of RNA-protein interactions.
• Biochemical experiments to assess protein binding preferences.
• Physics-based simulations of condensate assembly.
• In vitro studies of paraspeckle component interactions.

Main Results:

• Core proteins FUS and NONO preferentially bind shell-associated NEAT1 RNA domains, contrary to prevailing models.
• The shell protein TDP-43 also shows preference for shell-associated NEAT1 domains.
• TDP-43 forms surfactant-like shell layers around core protein condensates.
• Competitive RNA binding and protein immiscibility drive paraspeckle layer organization.

Conclusions:

• Paraspeckle layer formation is driven by competitive binding of core and shell proteins to specific NEAT1 RNA domains.
• Sub-condensate organization can emerge from the interplay of collaborative and competitive interactions.
• This study provides a new model for understanding the self-assembly of multi-domain biomolecular condensates.