Nuclear bodies: the emerging biophysics of nucleoplasmic phases

Zhu, Lian; Brangwynne, Clifford P.

doi:10.1016/j.ceb.2015.04.003

Cited by 233 publications

(235 citation statements)

References 57 publications

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“…A growing body of evidence points to phase separation as a general mechanism for the assembly of nuclear bodies and other membraneless organelles (5,6,39). Living cells appear to use several different strategies to control these physicochemical processes.…”

Section: Discussionmentioning

confidence: 99%

RNA transcription modulates phase transition-driven nuclear body assembly

Berry

Weber

Vaidya

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

449

426

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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 early Caenorhabditis elegans embryos. 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 manipulating C. elegans cell 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.RNA/protein droplets | intracellular phase separation | Brownian coalescence | Ostwald ripening | Flory-Huggins regular solution theory L iving cells are composed of complex and spatially heterogeneous materials that partition into functional compartments called organelles. Many organelles are vesicle-like structures with an enclosing membrane. However, a large number of RNA and protein-rich bodies maintain a dynamic but coherent structure even in the absence of a membrane. These so-called RNA/ protein granules are found in the cytoplasm and in the nucleus, where they are referred to as nuclear bodies. The mechanisms by which such structures form and stably persist are not well understood. However, recent evidence suggests that these membraneless organelles, such as P granules (1, 2), nucleoli (3), and stress granules (4), are liquid-phase droplets that may assemble by intracellular phase separation (5, 6). This concept is supported by work on synthetic systems, including repetitive protein domains that form droplets in vitro and in the cytoplasm (7) and intrinsically disordered protein domains that show signatures of liquid-liquid phase separation when expressed in the cell nucleus (8).By examining the cell size-dependent assembly of nucleoli in early Caenorhabditis elegans embryos, we previously showed that nucleolar assembly is controlled by a concentration-dependent phase transition (9). Using a simple model based on the de...

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Section: Discussionmentioning

confidence: 99%

RNA transcription modulates phase transition-driven nuclear body assembly

Berry

Weber

Vaidya

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

449

426

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“…In these studies, the components that are internalised within NBs are referred to as 'seed' molecules, e.g. RNA and chromatin, and are thought to aid regulation of stress responses and coordinate cellular dynamics in changing environments [1][2][3]41].…”

Section: Discussionmentioning

confidence: 99%

“…On a cellular level such dynamic and stimulus-dependent localization patterns involve and comprise distinct but connected compartments like the cytosol and nucleus. In some prominent cases, sub-compartmental pools of proteins, both within the cytosol and nucleus, can be distinguished and addressed visually by microscopic techniques (for example, see figures 1(A) and (B) or the examples within [1,2]). The formation of so-called nuclear bodies (NBs), in particular, is thought to be crucial for transcriptional regulation and chromatin dynamics, as has been observed in both mammalian and plant cells [1,3].…”

Section: Introductionmentioning

confidence: 99%

“…In some prominent cases, sub-compartmental pools of proteins, both within the cytosol and nucleus, can be distinguished and addressed visually by microscopic techniques (for example, see figures 1(A) and (B) or the examples within [1,2]). The formation of so-called nuclear bodies (NBs), in particular, is thought to be crucial for transcriptional regulation and chromatin dynamics, as has been observed in both mammalian and plant cells [1,3]. However, how such large structures within the nuclei of cells (in some cases observed to be between 1 and 2 μm [4]) form spontaneously is currently an open question, particularly in plants.…”

Section: Introductionmentioning

confidence: 99%

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Insight into nuclear body formation of phytochromes through stochastic modelling and experiment

et al. 2018

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Spatial relocalization of proteins is crucial for the correct functioning of living cells. An interesting example of spatial ordering is the light-induced clustering of plant photoreceptor proteins. Upon irradiation by white or red light, the red light-active phytochrome, phytochrome B, enters the nucleus and accumulates in large nuclear bodies (NBs). The underlying physical process of nuclear body formation remains unclear, but phytochrome B is thought to coagulate via a simple protein-protein binding process. We measure, for the first time, the distribution of the number of phytochrome B-containing NBs as well as their volume distribution. We show that the experimental data cannot be explained by a stochastic model of nuclear body formation via simple protein-protein binding processes using physically meaningful parameter values. Rather modelling suggests that the data is consistent with a two step process: a fast nucleation step leading to macroparticles followed by a subsequent slow step in which the macroparticles bind to form the nuclear body. An alternative explanation for the observed nuclear body distribution is that the phytochromes bind to a so far unknown molecular structure. We believe it is likely this result holds more generally for other nuclear body-forming plant photoreceptors and proteins. PAPEROriginal content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence.

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“…They play important roles in regulating transcription and RNA processing. NB formation is driven by nonspecific inter-molecular interactions, which are modulated by posttranslational modifications and ions, as well as by macromolecular crowding (Richter et al 2008;Zhu and Brangwynne 2015;Banani et al 2017;Staněk and Fox 2017).…”

Section: Computational Models Of the Genetic Materialsmentioning

confidence: 99%

Molecular simulations of cellular processes

Trovato

Fumagalli

2017

Biophys Rev

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It is, nowadays, possible to simulate biological processes in conditions that mimic the different cellular compartments. Several groups have performed these calculations using molecular models that vary in performance and accuracy. In many cases, the atomistic degrees of freedom have been eliminated, sacrificing both structural complexity and chemical specificity to be able to explore slow processes. In this review, we will discuss the insights gained from computer simulations on macromolecule diffusion, nuclear body formation, and processes involving the genetic material inside cell-mimicking spaces. We will also discuss the challenges to generate new models suitable for the simulations of biological processes on a cell scale and for cellcycle-long times, including non-equilibrium events such as the co-translational folding, misfolding, and aggregation of proteins. A prominent role will be played by the wise choice of the structural simplifications and, simultaneously, of a relatively complex energetic description. These challenging tasks will rely on the integration of experimental and computational methods, achieved through the application of efficient algorithms.

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Nuclear bodies: the emerging biophysics of nucleoplasmic phases

Cited by 233 publications

References 57 publications

RNA transcription modulates phase transition-driven nuclear body assembly

RNA transcription modulates phase transition-driven nuclear body assembly

Insight into nuclear body formation of phytochromes through stochastic modelling and experiment

Molecular simulations of cellular processes

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