Liquid-liquid phase separation driven compartmentalization of reactive nucleoplasm

Organization and regulation of intracellular biochemistry are achieved by compartmentalizing biomolecules through the liquid-liquid phase separation process (LLPS) and its associated chemical reactions into membrane-bound and membrane-less organelles. The LLPS of proteins/RNA within the nucleus plays a crucial role in the gene regulation of eukaryotic cells. Here, we present a reaction-diffusion model of transcription which connects the phase separation of proteins-RNA mixture inside nucleoplasm with transcriptional and catalytic reactions. Our model shows the existence of a variety of complex protein-RNA patterns that arise from the competition between different mechanisms including LLPS, biomolecular interactions, and biochemical reactions. The protein-RNA pattern formation is strongly dependent on the interplay of time-scales for diffusion, transcription, and translation. Under appropriate kinetic regimes, we can dramatically accelerate or slow down the phase-separation process, thereby leading to arrested phases.