The nucleolus is the most prominent nuclear body and serves a fundamentally important biological role as a site of ribonucleoprotein particle assembly, primarily dedicated to ribosome biogenesis. Despite being one of the first intracellular structures visualized historically, the biophysical rules governing its assembly and function are only starting to become clear. Recent studies have provided increasing support for the concept that the nucleolus represents a multilayered biomolecular condensate, whose formation by liquid–liquid phase separation (LLPS) facilitates the initial steps of ribosome biogenesis and other functions. Here, we review these biophysical insights in the context of the molecular and cell biology of the nucleolus. We discuss how nucleolar function is linked to its organization as a multiphase condensate and how dysregulation of this organization could provide insights into still poorly understood aspects of nucleolus-associated diseases, including cancer, ribosomopathies and neurodegeneration as well as ageing. We suggest that the LLPS model provides the starting point for a unifying quantitative framework for the assembly, structural maintenance and function of the nucleolus, with implications for gene regulation and ribonucleoprotein particle assembly throughout the nucleus. The LLPS concept is also likely useful in designing new therapeutic strategies to target nucleolar dysfunction.
This is a preview of subscription content, access via your institution
Open Access articles citing this article.
RNA-mediated demixing transition of low-density condensates
Nature Communications Open Access 27 April 2023
Cell surface-localized CsgF condensate is a gatekeeper in bacterial curli subunit secretion
Nature Communications Open Access 26 April 2023
Spatially non-uniform condensates emerge from dynamically arrested phase separation
Nature Communications Open Access 08 February 2023
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Get just this article for as long as you need it
Prices may be subject to local taxes which are calculated during checkout
Pederson, T. The plurifunctional nucleolus. Nucleic Acids Res. 26, 3871–3876 (1998).
Boisvert, F. M., van Koningsbruggen, S., Navascues, J. & Lamond, A. I. The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 8, 574–585 (2007).
Lafontaine, D. L. J. Noncoding RNAs in eukaryotic ribosome synthesis and function. Nat. Struct. Mol. Biol. 22, 11–19 (2015).
Iarovaia, O. V. et al. Nucleolus: a central hub for nuclear functions. Trends Cell Biol. 29, 647–659 (2019).
Amon, A. A decade of Cdc14 — a personal perspective. Delivered on 9 July 2007 at the 32nd FEBS Congress in Vienna, Austria. FEBS J. 275, 5774–5784 (2008).
Boulon, S., Westman, B. J., Hutten, S., Boisvert, F. M. & Lamond, A. I. The nucleolus under stress. Mol. Cell 40, 216–227 (2010).
Andersen, J. S. et al. Directed proteomic analysis of the human nucleolus. Curr. Biol. 12, 1–11 (2002).
Scherl, A. et al. Functional proteomic analysis of human nucleolus. Mol. Biol. Cell 13, 4100–4109 (2002).
Salvetti, A. & Greco, A. Viruses and the nucleolus: the fatal attraction. Biochim. Biophys. Acta 1842, 840–847 (2014).
Hetman, M. & Slomnicki, L. P. Ribosomal biogenesis as an emerging target of neurodevelopmental pathologies. J. Neurochem. 148, 325–347 (2019).
Calle, A. et al. Nucleolin is required for an efficient herpes simplex virus type 1 infection. J. Virol. 82, 4762–4773 (2008).
Zink, D., Fischer, A. H. & Nickerson, J. A. Nuclear structure in cancer cells. Nat. Rev. Cancer 4, 677–687 (2004).
Stamatopoulou, V., Parisot, P., De Vleeschouwer, C. & Lafontaine, D. L. J. Use of the iNo score to discriminate normal from altered nucleolar morphology, with applications in basic cell biology and potential in human disease diagnostics. Nat. Protoc. 13, 2387–2406 (2018).
Frankowski, K. J. et al. Metarrestin, a perinucleolar compartment inhibitor, effectively suppresses metastasis. Sci. Transl Med. 10, eaap8307 (2018).
Brangwynne, C. P., Mitchison, T. J. & Hyman, A. A. Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proc. Natl Acad. Sci. USA 108, 4334–4339 (2011). This paper shows that X. laevis nucleoli are highly spherical, and when pushed together with microneedles readily coalesce into a large sphere; the fusion dynamics can be used to determine the apparent viscosity, which is dependent on the ATP concentration.
Feric, M. et al. Coexisting liquid phases underlie nucleolar subcompartments. Cell 165, 1686–1697 (2016). This paper shows that X. laevis nucleolar subcompartments (DFC and GC) readily fuse with one another, whereas in vitro reconstitution of the DFC/GC core–shell architecture supports the concept that nucleolar subcompartments are immiscible liquids arranged by their relative surface tensions.
Mitrea, D. M. et al. Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation. Nat. Commun. 9, 842 (2018).
Mitrea, D. M. et al. Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA. eLife 5, e13571 (2016). This paper demonstrates that the GC meshwork protein nucleophosmin undergoes heterotypic LLPS in vitro with proteins containing Arg-rich tracts or rRNA, thus providing critical insight into the underlying biophysics driving nucleolar assembly and biomolecule localization to the nucleolus.
Falahati, H. & Wieschaus, E. Independent active and thermodynamic processes govern the nucleolus assembly in vivo. Proc. Natl Acad. Sci. USA 114, 1335–1340 (2017). This paper uses a microfluidic system to reveal that the tendency of nucleolar proteins to condense in living cells exhibits differential sensitivity to imposed temperature changes, suggesting that active, non-equilibrium processes contribute to nucleolar phase separation in living cells.
Weber, S. C. & Brangwynne, C. P. Inverse size scaling of the nucleolus by a concentration-dependent phase transition. Curr. Biol. 25, 641–646 (2015).
Caragine, C. M., Haley, S. C. & Zidovska, A. Nucleolar dynamics and interactions with nucleoplasm in living cells. eLife 8, e47533 (2019).
Frottin, F. et al. The nucleolus functions as a phase-separated protein quality control compartment. Science 365, 342–347 (2019). This paper demonstrates that the GC phase of the nucleolus plays a role in protein homeostasis by transiently storing metastable and potentially misfolded nuclear proteins during heat stress in order to prevent their aggregation.
Yao, R. W. et al. Nascent pre-rRNA sorting via phase separation drives the assembly of dense fibrillar components in the human nucleolus. Mol. Cell (2019). This paper demonstrates that the box C/D-associated methyltransferase fibrillarin plays an essential role in initial pre-rRNA sorting and cleavage through establishment by phase separation of the DFC subcompartment of the nucleolus.
Ferrolino, M. C., Mitrea, D. M., Michael, J. R. & Kriwacki, R. W. Compositional adaptability in NPM1–SURF6 scaffolding networks enabled by dynamic switching of phase separation mechanisms. Nat. Commun. 9, 5064 (2018).
Shin, Y. & Brangwynne, C. P. Liquid phase condensation in cell physiology and disease. Science 357, eaaf4382 (2017).
Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K. Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285–298 (2017).
Ehrenberg, L. Influence of temperature on the nucleolus and its coacervate nature. Hereditas 32, 407–418 (1946).
Phair, R. D. & Misteli, T. High mobility of proteins in the mammalian cell nucleus. Nature 404, 604–609 (2000).
Handwerger, K. E., Cordero, J. A. & Gall, J. G. Cajal bodies, nucleoli, and speckles in the Xenopus oocyte nucleus have a low-density, sponge-like structure. Mol. Biol. Cell 16, 202–211 (2005).
Houtsmuller, A. B. et al. Action of DNA repair endonuclease ERCC1/XPF in living cells. Science 284, 958–961 (1999).
Lee, C. F. Formation of liquid-like cellular organelles depends on their composition. Nature 581, 144–145 (2020).
Thiry, M. & Lafontaine, D. L. J. Birth of a nucleolus: the evolution of nucleolar compartments. Trends Cell Biol. 15, 194–199 (2005).
Lamaye, F., Galliot, S., Alibardi, L., Lafontaine, D. L. J. & Thiry, M. Nucleolar structure across evolution: the transition between bi- and tri-compartmentalized nucleoli lies within the class Reptilia. J. Struct. Biol. 174, 352–359 (2011).
Bartholome, O. et al. Relationships between the structural and functional organization of the turtle cell nucleolus. J. Struct. Biol. 208, 107398 (2019).
Stenström, L. et al. Mapping of the nucleolar proteome reveals spatiotemporal organization related to intrinsic protein disorder. Preprint at bioRxiv https://doi.org/10.1101/2020.01.30.923003 (2020).
Nemeth, A. et al. Initial genomics of the human nucleolus. PLoS Genet. 6, e1000889 (2010).
Lafontaine, D. L. J. Birth of nucleolar compartments: phase separation-driven ribosomal RNA sorting and processing. Mol. Cell 76, 694–696 (2019).
Xing, Y. H. et al. SLERT regulates DDX21 rings associated with Pol I transcription. Cell 169, 664–678.e16 (2017).
Girard, J. P. et al. GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J. 11, 673–682 (1992).
Scott, M. S., Boisvert, F. M., McDowall, M. D., Lamond, A. I. & Barton, G. J. Characterization and prediction of protein nucleolar localization sequences. Nucleic Acids Res. 38, 7388–7399 (2010).
Colau, G., Thiry, M., Leduc, V., Bordonne, R. & Lafontaine, D. L. J. The small nucle(ol)ar RNA cap trimethyltransferase is required for ribosome synthesis and intact nucleolar morphology. Mol. Cell. Biol. 24, 7976–7986 (2004).
Elbaum-Garfinkle, S. et al. The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics. Proc. Natl Acad. Sci. USA 112, 7189–7194 (2015).
Chong, P. A., Vernon, R. M. & Forman-Kay, J. D. RGG/RG motif regions in RNA binding and phase separation. J. Mol. Biol. 430, 4650–4665 (2018).
Berry, J., Weber, S. C., Vaidya, N., Haataja, M. & Brangwynne, C. P. RNA transcription modulates phase transition-driven nuclear body assembly. Proc. Natl Acad. Sci. USA 112, E5237–E5245 (2015). This paper shows that the dynamics of nucleolar assembly behaviour is consistent with the classical dynamics of coarsening liquid droplets, albeit in which classical phase separation behaviour is locally amplified by transcription of rRNA at nucleolar organizer regions.
Taylor, N. et al. Biophysical characterization of organelle-based RNA/protein liquid phases using microfluidics. Soft Matter 12, 9142–9150 (2016).
Lee, D. S. W., Wingreen, N. S. & Brangwynne, C. Chromatin mechanics dictates subdiffusion and coarsening dynamics of embedded condensates. Preprint at bioRxiv https://doi.org/10.1101/2020.06.03.128561 (2020).
Amin, M. A., Matsunaga, S., Uchiyama, S. & Fukui, K. Depletion of nucleophosmin leads to distortion of nucleolar and nuclear structures in HeLa cells. Biochem. J. 415, 345–351 (2008).
Grisendi, S., Mecucci, C., Falini, B. & Pandolfi, P. P. Nucleophosmin and cancer. Nat. Rev. Cancer 6, 493–505 (2006).
Mitrea, D. M. et al. Structural polymorphism in the N-terminal oligomerization domain of NPM1. Proc. Natl Acad. Sci. USA 111, 4466–4471 (2014).
Feric, M. & Brangwynne, C. P. A nuclear F-actin scaffold stabilizes ribonucleoprotein droplets against gravity in large cells. Nat. Cell Biol. 15, 1253–1259 (2013).
Feric, M., Broedersz, C. P. & Brangwynne, C. P. Soft viscoelastic properties of nuclear actin age oocytes due to gravitational creep. Sci. Rep. 5, 16607 (2015).
Mao, S., Kuldinow, D., Haataja, M. P. & Kosmrlj, A. Phase behavior and morphology of multicomponent liquid mixtures. Soft Matter 15, 1297–1311 (2019).
Sanders, D. W. et al. Competing protein–RNA interaction networks control multiphase intracellular organization. Cell 181, 306–324 (2020).
Rubinstein, M. & Colby, R. Polymer Physics 199–305 (Oxford Univ. Press, 2003).
Molliex, A. et al. Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization. Cell 163, 123–133 (2015).
Patel, A. et al. A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation. Cell 162, 1066–1077 (2015).
Zhang, H. et al. RNA controls PolyQ protein phase transitions. Mol. Cell 60, 220–230 (2015).
Murakami, T. et al. ALS/FTD mutation-induced phase transition of FUS liquid droplets and reversible hydrogels into irreversible hydrogels impairs RNP granule function. Neuron 88, 678–690 (2015).
Eggers, J., Lister, J. R. & Stone, H. A. Coalescence of liquid drops. J. fluid Mech. 401, 293–310 (1999).
Andersen, J. S. et al. Nucleolar proteome dynamics. Nature 433, 77–83 (2005).
Lam, Y. W., Evans, V. C., Heesom, K. J., Lamond, A. I. & Matthews, D. A. Proteomics analysis of the nucleolus in adenovirus-infected cells. Mol. Cell. Proteomics 9, 117–130 (2010).
Moore, H. M. et al. Quantitative proteomics and dynamic imaging of the nucleolus reveal distinct responses to UV and ionizing radiation. Mol. Cell. Proteomics 10, M111 009241 (2011).
Dundr, M., Misteli, T. & Olson, M. O. The dynamics of postmitotic reassembly of the nucleolus. J. Cell Biol. 150, 433–446 (2000).
Leung, A. K. et al. Quantitative kinetic analysis of nucleolar breakdown and reassembly during mitosis in live human cells. J. Cell Biol. 166, 787–800 (2004).
Hernandez-Verdun, D. Assembly and disassembly of the nucleolus during the cell cycle. Nucleus 2, 189–194 (2011).
Rai, A. K., Chen, J. X., Selbach, M. & Pelkmans, L. Kinase-controlled phase transition of membraneless organelles in mitosis. Nature 559, 211–216 (2018).
Kashchiev, D. Nucleation 17–42 (Elsevier, 2020).
Sirri, V., Hernandez-Verdun, D. & Roussel, P. Cyclin-dependent kinases govern formation and maintenance of the nucleolus. J. Cell Biol. 156, 969–981 (2002).
Booth, D. G. et al. Ki-67 is a PP1-interacting protein that organises the mitotic chromosome periphery. eLife 3, e01641 (2014).
Sobecki, M. et al. The cell proliferation antigen Ki-67 organises heterochromatin. eLife 5, e13722 (2016).
Cuylen, S. et al. Ki-67 acts as a biological surfactant to disperse mitotic chromosomes. Nature 535, 308–312 (2016).
Falahati, H., Pelham-Webb, B., Blythe, S. & Wieschaus, E. Nucleation by rRNA dictates the precision of nucleolus assembly. Curr. Biol. 26, 277–285 (2016).
Caudron-Herger, M. et al. Alu element-containing RNAs maintain nucleolar structure and function. EMBO J. 34, 2758–2774 (2015).
Thiry, M., Cheutin, T., O’Donohue, M. F., Kaplan, H. & Ploton, D. Dynamics and three-dimensional localization of ribosomal RNA within the nucleolus. RNA 6, 1750–1761 (2000).
Riback, J. A. et al. Composition-dependent thermodynamics of intracellular phase separation. Nature 581, 209–214 (2020). This paper establishes that most intracellular condensates have a non-fixed saturation concentration stabilized by heterotypic biomolecular interactions, which provides a thermodynamic basis for ‘on-demand’ nucleolar assembly in the presence of nascent rRNA, whereas assembled ribosomal subunits are expelled into the nucleoplasm.
Bohnsack, K. E. & Bohnsack, M. T. Uncovering the assembly pathway of human ribosomes and its emerging links to disease. EMBO J. 38, e100278 (2019).
Dez, C., Houseley, J. & Tollervey, D. Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae. EMBO J. 25, 1534–1546 (2006).
Lafontaine, D. L. J. A ‘garbage can’ for ribosomes: how eukaryotes degrade their ribosomes. Trends Biochem. Sci. 35, 267–277 (2010).
Hernandez-Verdun, D., Roussel, P., Thiry, M., Sirri, V. & Lafontaine, D. L. J. The nucleolus: structure/function relationship in RNA metabolism. Wiley Interdiscip. Rev. RNA 1, 415–431 (2010).
Burger, K. et al. Chemotherapeutic drugs inhibit ribosome biogenesis at various levels. J. Biol. Chem. 285, 12416–12425 (2010).
Nicolas, E. et al. Involvement of human ribosomal proteins in nucleolar structure and p53-dependent nucleolar stress. Nat. Commun. 7, 11390 (2016). This paper is a systematic investigation of the role of the 80 human ribosomal proteins in nucleolar structure, pre-rRNA processing, mature rRNA production and p53 homeostasis, revealing the importance of the central protuberance assembly in nucleolar phase establishment (see companion www.ribosomalproteins.com).
Donati, G., Peddigari, S., Mercer, C. A. & Thomas, G. 5S ribosomal RNA is an essential component of a nascent ribosomal precursor complex that regulates the Hdm2–p53 checkpoint. Cell Rep. 4, 87–98 (2013).
Sloan, K. E., Bohnsack, M. T. & Watkins, N. J. The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress. Cell Rep. 5, 237–247 (2013).
Shin, Y. et al. Spatiotemporal control of intracellular phase transitions using light-activated optodroplets. Cell 168, 159–171.e14 (2017).
Zhu, L. et al. Controlling the material properties and rRNA processing function of the nucleolus using light. Proc. Natl Acad. Sci. USA 116, 17330–17335 (2019).
Mann, J. R. et al. RNA binding antagonizes neurotoxic phase transitions of TDP-43. Neuron 102, 321–338.e8 (2019).
Kilic, S. et al. Phase separation of 53BP1 determines liquid-like behavior of DNA repair compartments. EMBO J. 38, e101379 (2019).
Wei, M.-T., Chang, Y.-C., Shimobayashi, S. F., Shin, Y. & Brangwynne, C. P. Nucleated transcriptional condensates amplify gene expression. Preprint at bioRxiv https://doi.org/10.1101/737387 (2020).
Galea, C. A. et al. Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. J. Proteome Res. 8, 211–226 (2009).
Derenzini, M., Montanaro, L. & Trere, D. What the nucleolus says to a tumour pathologist. Histopathology 54, 753–762 (2009).
Farley-Barnes, K. I., Ogawa, L. M. & Baserga, S. J. Ribosomopathies: old concepts, new controversies. Trends Genet. 35, 754–767 (2019).
Kwon, I. et al. Poly-dipeptides encoded by the C9orf72 repeats bind nucleoli, impede RNA biogenesis, and kill cells. Science 345, 1139–1145 (2014).
Wen, X. et al. Antisense proline–arginine RAN dipeptides linked to C9ORF72-ALS/FTD form toxic nuclear aggregates that initiate in vitro and in vivo neuronal death. Neuron 84, 1213–1225 (2014).
Lee, K. H. et al. C9orf72 dipeptide repeats impair the assembly, dynamics, and function of membrane-less organelles. Cell 167, 774–788.e17 (2016). This paper shows that dipeptide repeat polypeptides produced by non-ATG templated translation from the neurodegenerative disease-causing gene C9ORF72 penetrate the nucleolus, where they interfere with establishment of multivalent weak interactions important for its phase behaviour, leading to loss of function and cell death.
White, M. R. et al. C9orf72 poly(PR) dipeptide repeats disturb biomolecular phase separation and disrupt nucleolar function. Mol. Cell 74, 713–728.e6 (2019).
Boeynaems, S. et al. Spontaneous driving forces give rise to protein–RNA condensates with coexisting phases and complex material properties. Proc. Natl Acad. Sci. USA 116, 7889–7898 (2019).
Tiku, V. et al. Small nucleoli are a cellular hallmark of longevity. Nat. Commun. 8, 16083 (2017).
Sinclair, D. A. & Guarente, L. Extrachromosomal rDNA circles — a cause of aging in yeast. Cell 91, 1033–1042 (1997).
Sinclair, D. A., Mills, K. & Guarente, L. Accelerated aging and nucleolar fragmentation in yeast sgs1 mutants. Science 277, 1313–1316 (1997).
Houston, R. et al. Acetylation-mediated phase control of the nucleolus regulates cellular acetyl-CoA responses. Preprint at bioRxiv https://doi.org/10.1101/2020.01.24.918706 (2019).
Jain, S. et al. ATPase-modulated stress granules contain a diverse proteome and substructure. Cell 164, 487–498 (2016).
Putnam, A., Cassani, M., Smith, J. & Seydoux, G. A gel phase promotes condensation of liquid P granules in Caenorhabditis elegans embryos. Nat. Struct. Mol. Biol. 26, 220–226 (2019).
Taylor, N. O., Wei, M. T., Stone, H. A. & Brangwynne, C. P. Quantifying dynamics in phase-separated condensates using fluorescence recovery after photobleaching. Biophys. J. 117, 1285–1300 (2019).
Gardel, M. L. & Weitz, D. A. Microrheology 1–50 (Springer, 2005).
Roussel, P., Andre, C., Comai, L. & Hernandez-Verdun, D. The rDNA transcription machinery is assembled during mitosis in active NORs and absent in inactive NORs. J. Cell Biol. 133, 235–246 (1996).
Farley, K. I., Surovtseva, Y., Merkel, J. & Baserga, S. J. Determinants of mammalian nucleolar architecture. Chromosoma 124, 323–331 (2015).
Caragine, C. M., Haley, S. C. & Zidovska, A. Surface fluctuations and coalescence of nucleolar droplets in the human cell nucleus. Phys. Rev. Lett. 121, 148101 (2018).
Huang, S. Building an efficient factory: where is pre-rRNA synthesized in the nucleolus? J. Cell Biol. 157, 739–741 (2002).
Lewis, J. D. & Tollervey, D. Like attracts like: getting RNA processing together in the nucleus. Science 288, 1385–1389 (2000).
Warner, J. R. The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24, 437–440 (1999).
Duncan, R. & Hershey, J. W. Identification and quantitation of levels of protein synthesis initiation factors in crude HeLa cell lysates by two-dimensional polyacrylamide gel electrophoresis. J. Biol. Chem. 258, 7228–7235 (1983).
Nott, T. J. et al. Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol. Cell 57, 936–947 (2015).
Brangwynne, C., Tompa, P. & Pappu, R. V. Polymer physics of intracellular phase transitions. Nat. Phys. 11, 899–904 (2015).
van der Lee, R. et al. Classification of intrinsically disordered regions and proteins. Chem. Rev. 114, 6589–6631 (2014).
Choi, J. M., Holehouse, A. S. & Pappu, R. V. Physical principles underlying the complex biology of intracellular phase transitions. Annu. Rev. Biophys. 49, 107–133 (2020).
Research in the Lafontaine laboratory is supported by the Belgian Fonds de la Recherche Scientifique (F.R.S./FNRS) (‘RiboEurope’ European Joint Programme on Rare Diseases (EJP RD/JTC2019/PINT-MULTI) grant n°R.8015.19 and PDR grant n°T.0144.20), the Université Libre de Bruxelles (ULB), the Région Wallonne (SPW EER) (‘RIBOcancer’ FSO grant n°1810070), the Fonds Jean Brachet, the Internationale Brachet Stiftung and the Epitran COST action (CA16120). The Brangwynne laboratory is supported by the Howard Hughes Medical Institute, the St. Jude Research Collaborative on Membrane-less Organelles and the National Institutes of Health (NIH) (U01 DA040601).
The authors declare no competing interests.
Peer review information
Nature Reviews Molecular Cell Biology thanks T. Pederson, R. Kriwacki and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
- Protein trans-acting factors
Proteins important for ribosomal subunit biogenesis that interact only transiently with maturing ribosomal subunits; they are not found on mature ribosomes.
- Small nucleolar RNAs
Antisense small RNAs involved in RNA modification, pre-rRNA folding and processing.
- Phase behaviour
The collection of biophysical features exhibited by materials capable of undergoing phase transitions, including the conditions under which phase separation occurs and the interfacial properties (for example, surface tension) defining wetting and coarsening behaviour.
- Liquid–liquid phase separation
(LLPS). The process by which a single, uniform liquid phase demixes into two compositionally distinct liquid phases. Oil and water mixtures are an everyday example of phase-separated mixtures.
A term often used in the chemistry field to describe a condensed phase arising from a type of polymeric phase transition.
- Fluorescence recovery after photobleaching
(FRAP). A technique that utilizes intense laser illumination to irreversibly deactivate fluorescent molecules locally, after which the return of a fluorescence signal within that region is indicative of biomolecular exchange with non-bleached fluorescent molecules from the surrounding areas of the sample.
- Ribosomal proteins
Proteins that are structurally integrated into the ribosome. The fully assembled human ribosome contains 80 ribosomal proteins, most of which are assembled together with the four ribosomal RNAs within the nucleolus, with a notable exception of the acidic proteins forming the P stalk, which are assembled in the cytoplasm.
A system that is not within a global thermodynamic free-energy minimum. Although equilibrium approaches may be applicable in some cases, biological systems are fundamentally out of equilibrium, due to their continuous consumption of energy and production and degradation of molecules.
A ‘surface-acting’ molecule that tends to localize at the interface of two phases, reducing surface tension; amphiphilic molecules are classic surfactants, due to their ability to simultaneously interact with both water and relatively hydrophobic structures. Ki-67 protein has been proposed to act as a surfactant in the context of the perichromosomal region.
- Perinucleolar chromatin
Condensed chromatin lining the nucleolus during interphase and enriched in specific genes to react to the environment and others (stress, sensory and so on).
- Intrinsically disordered regions
(IDRs). Protein regions that exhibit considerable conformational heterogeneity. The biased amino acid sequences of IDRs encode an intrinsic preference for conformational disorder and an inability to fold into singular well-defined 3D structures under physiological conditions.
The preference of a component for one of two distinct phases, quantified as the ratio of concentrations in the two phases (defining the partition coefficient, for example K = Cnucleolus / Cnucleoplasm) or as the free energy of transfer (ΔGtransfer = –RTlog(K)).
- P granule
A perinuclear condensate implicated in germ cell lineage maintenance in Caenorhabditis elegans. P granules may serve similar functions to polar granules or nuage, which regulate germ cell biology across animal cells.
Liquid–liquid phase-separated solutions in which droplets of one liquid phase are dispersed throughout another immiscible continuous liquid phase; for example, droplets of vinegar in oil.
- Ostwald ripening
The process by which larger droplets grow at the expense of smaller droplets, as a result of droplet surface tension (Laplace pressure) causing a higher chemical potential within the smaller droplet.
A viscoelastic material is one whose response to applied stresses is intermediate between that of a purely elastic solid and that of a purely viscous liquid; striking but common examples include silly putty and corn starch/water mixtures.
- Saturation concentration
The concentration of a structurally key biomolecule above which liquid–liquid phase separation occurs. Note that for multicomponent systems governed by heterotypic interactions, the saturation concentration may not be identical to the concentration outside the condensate.
- Cajal bodies
(Also known as coiled bodies). Nuclear condensates containing coilin and survival of motor neuron protein (SMN). Cajal bodies are enriched in U snRNAs and share some protein components with the nucleolus, such as fibrillarin.
- Stress granule
Cytoplasmic condensates that form in response to stress (for example, oxidative stress and heat stress).
- P body
Cytoplasmic condensates involved in mRNA degradation.
- Surface tension
A material parameter characterizing the energy per unit area associated with an interface between two distinct phases. Liquids tend to round up into spheres as spheres minimize the surface area and thus minimize the interfacial energy imposed by surface tension. As nucleoli exhibit multiple subphases, each interface between them will have its own surface tension.
- Complex fluids
Typically soft, liquid-like materials that often contain multiple macromolecular components such as polymers or colloidal particles and that usually exhibit viscoelastic properties; an emulsion is a type of complex fluid.
A physical system may be said to be metastable if it resides in a local thermodynamic minimum, which over longer periods may begin transitioning into a different state associated with an even lower (global) energy minimum.
A technique used to measure the rheological properties of a microscopic material. Passive microrheology consists of tracking Brownian motions/thermal fluctuations of probe particles embedded within soft materials to determine viscoelasticity. Active microrheology utilizes externally applied stresses (for example, through optical or magnetic tweezers) and is particularly attractive for studying non-equilibrium systems where fluctuating motion may not be purely thermal (for example, ATP-dependent fluctuations).
- Nucleolar breakdown
The process of nucleolar disassembly at the onset of mitosis.
- Nucleolar genesis
The process of nucleolar (re)assembly at the end of mitosis.
- Spinodal decomposition
The process by which phase separation occurs spontaneously without any nucleation barriers, due to the negative curvature of the free-energy landscape.
- Heterogeneous nucleation
A process by which nucleation and growth of one phase within another is facilitated by nucleation on a favourable pre-existing surface (such as nascent pre-ribosomal RNAs in the case of nucleolar genesis).
- Precursor–product relationship
A relationship between A and B if the production of B depends upon the disappearance of A. This applies, for example, to RNA processing (between upstream and downstream intermediates) and to the successive intermediate condensates formed during nucleolar genesis.
- Perichromosomal region
Liquid-like condensate made of nucleolar proteins forming a ‘sheath’ around the compacted mitotic chromosomes (absent at the centromeres).
- Nucleolar-derived foci
Condensates consisting of nucleolar proteins and formed during mitosis after nuclear envelope breakdown.
- Prenucleolar bodies
Nuclear condensates consisting of nucleolar protein formed during mitosis at the time of nuclear membrane reassembly.
- Alu RNAs
RNAs encoded in Alu repeats, which are the most abundant repetitive genetic elements found in primates, representing up to 10% of the human genome.
- RNA exosome
A 3′–5′ exoribonucleolytic and endonucleolytic multi-protein complex involved in RNA 3′ end formation, RNA turnover and RNA surveillance (quality control).
- Nucleolar surveillance
A p53-dependent antitumoural surveillance pathway triggered upon ribosomal assembly dysfunction and involving the sequestration of Hdm2 by a complex consisting of ribosomal proteins uL5, uL18 and the 5S ribosomal RNA.
- Central protuberance
A major architectural landmark of the large ribosomal subunit (60S) essential for ribosomal function; it promotes transmission of allosteric information between the functional centres of the large ribosomal subunit, and between the small and large subunits during translation.
Congenital or somatic tissue-specific diseases resulting from mutations in ribosomal proteins or ribosome biogenesis factors and leading to the shortage of mature ribosomes and, generally, to a hypo-proliferation phenotype. The blood and the brain are prime targets of ribosomopathies. Ribosomopathies often lead to cancer owing to secondary mutations.
- Amyotrophic lateral sclerosis
A disease that causes the death of neurons controlling voluntary muscles.
- Frontotemporal dementia
Diseases that affect mostly the frontal and temporal lobes of the brain associated with personality, behaviour and language.
Rights and permissions
About this article
Cite this article
Lafontaine, D.L.J., Riback, J.A., Bascetin, R. et al. The nucleolus as a multiphase liquid condensate. Nat Rev Mol Cell Biol 22, 165–182 (2021). https://doi.org/10.1038/s41580-020-0272-6
This article is cited by
Spatially non-uniform condensates emerge from dynamically arrested phase separation
Nature Communications (2023)
In phase with the nucleolus
Cell Research (2023)
Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes
Nature Reviews Molecular Cell Biology (2023)
Engineering synthetic biomolecular condensates
Nature Reviews Bioengineering (2023)
A guide to membraneless organelles and their various roles in gene regulation
Nature Reviews Molecular Cell Biology (2023)