RNA transcription modulates phase transition-driven nuclear body assembly

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 112; no. 38; pp. E5237 - E5245
• Main Authors: Berry, Joel, Weber, Stephanie C., Vaidya, Nilesh, Haataja, Mikko, Brangwynne, Clifford P.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 22-09-2015; National Acad Sciences
• Series: PNAS Plus
• Subjects: Animals; Biological Sciences; Caenorhabditis elegans; Cell growth; Cell Nucleolus - metabolism; Cell Nucleus - metabolism; Cells; Cytoplasm - metabolism; Embryos; Green Fluorescent Proteins - metabolism; Homeostasis; Intranuclear Inclusion Bodies - metabolism; Microscopy, Fluorescence; Nematodes; Physical Sciences; PNAS Plus; Ribonucleic acid; RNA; RNA, Ribosomal - chemistry; Simulation; Thermodynamics; Transcription, Genetic; Flory–Huggins regular solution theory; RNA/protein droplets; Brownian coalescence; Ostwald ripening; intracellular phase separation
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1509317112

Nuclear bodies are RNA and protein-rich, membraneless organelles that play important roles in gene regulation. The largest and most well-known nuclear body is the nucleolus, an organelle whose primary function in ribosome biogenesis makes it key for cell growth and size homeostasis. The nucleolus and other nuclear bodies behave like liquid-phase droplets and appear to condense from the nucleoplasm by concentration-dependent phase separation. However, nucleoli actively consume chemical energy, and it is unclear how such nonequilibrium activity might impact classical liquid–liquid phase separation. Here, we combine in vivo and in vitro experiments with theory and simulation to characterize the assembly and disassembly dynamics of nucleoli in earlyCaenorhabditis elegansembryos. In addition to classical nucleoli that assemble at the transcriptionally active nucleolar organizing regions, we observe dozens of “extranucleolar droplets” (ENDs) that condense in the nucleoplasm in a transcription-independent manner. We show that growth of nucleoli and ENDs is consistent with a first-order phase transition in which late-stage coarsening dynamics are mediated by Brownian coalescence and, to a lesser degree, Ostwald ripening. By manipulatingC. eleganscell size, we change nucleolar component concentration and confirm several key model predictions. Our results show that rRNA transcription and other nonequilibrium biological activity can modulate the effective thermodynamic parameters governing nucleolar and END assembly, but do not appear to fundamentally alter the passive phase separation mechanism.