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The Nucleolus As a Multiphase Liquid Condensate

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The Nucleolus As a Multiphase Liquid Condensate REVIEWS The nucleolus as a multiphase liquid condensate Denis L. J. Lafontaine 1 ✉ , Joshua A. Riback 2, Rümeyza Bascetin 1 and Clifford P. Brangwynne 2,3 ✉ Abstract | 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. Protein trans-acting factors Among numerous microscopically visible nuclear sub- at the inner core where rRNA transcription occurs and Proteins important for structures, the nucleolus is the most prominent and proceeding towards the periphery (Fig. 1). ribosomal subunit biogenesis represents a functionally and biophysically distinct body In addition to the ribosome, other ribonucleoprotein that interact only transiently or compartment. The nucleolus is, in fact, so promi- particles are assembled, at least in part, in the nucleolus2. with maturing ribosomal subunits; they are not found nent that it drew the attention of early biologists over This is notably the case for the signal recognition par- on mature ribosomes. 200 years ago, in light microscopy studies by Fontana, ticle, involved in protein secretion and targeting to the Valentin and Wagner1. Following these early descriptions endoplasmic reticulum of transmembrane proteins, and 1 came the understanding of the functional importance for telomerase, required for the maintenance of chromo- RNA Molecular Biology, 4 Fonds de la Recherche of the nucleolus, including its primary role as the site for some ends . There have also been reports of precur- Scientifique (F.R.S./FNRS), the initial steps of ribosome biogenesis, including RNA sors of tRNAs, and even of mRNAs, transiting through Université Libre de Bruxelles polymerase I (Pol I)-driven transcription, processing and the nucleolus1. Although it is not entirely clear why Cancer Research Center modification of ribosomal RNA (rRNA) and the assem- non-rRNAs transit through the nucleolus during their life (ULB-CRC), Center for bly of rRNA-containing complexes2 (FIG. 1). These pro- cycle, it is largely assumed that they do so to benefit from Microscopy and Molecular Imaging (CMMI), Gosselies, cesses involve several hundred protein trans-acting factors the abundant assembly and modification machineries Belgium. and small nucleolar RNAs3, which serve to guide the speci- present there. 2Department of Chemical ficity of rRNA chemical modifications, pre-rRNA folding The nucleolus is physically separated from the and Biological Engineering, and cleavage. Once precursor subunits are released from rest of the nuclear space, yet is accessible for dynamic Princeton University, the nucleolar structure, they undergo further maturation exchange due to the absence of a delimiting membrane. Princeton, NJ, USA. in the nucleoplasm and cytoplasm prior to becoming Hence, it is an ideal locale for fine regulation of cell home- 3 HHMI, Princeton University, fully functional ribosomal subunits, ready to engage in ostasis, for example, through the transient sequestration Princeton, NJ, USA. translating mRNA into protein. This nucleolar function of key regulators of the cell cycle5. The nucleolus also ✉e-mail: denis.lafontaine@ ulb.ac.be; cbrangwy@ is accompanied by organization of the nucleolus into plays important roles in sensing diverse stresses, includ- princeton.edu distinct subcompartments. In mammalian cells, nucleoli ing genotoxic and oxidative stress, heat shock, nutrient 6 https://doi.org/10.1038/ display three layers, nested like Russian dolls, where suc- deprivation, oncogene activation and viral infection . s41580-020-0272-6 cessive steps of ribosome production take place, starting Although these diverse nucleolar functions have been NATURE REVIEWS | MOLECULAR CELL BIOLOGY REVIEWS Nucleolar interstice a b Nucleolar functions in ribosome biogenesis FC Nuclear envelope DFC rRNA synthesis rDNA RNA Pol I Paraspeckle Nuclear pore Nascent pre-rRNA FBL complex 5′ ETS P granule Gem GC Phase separation and DFC phase GAR (IDRs) RBD establishment Cajal α-Helix Processing body 1 rRNA sorting body FC into DFC phase DFC ITS1 ITS2 Nuclear 5′ ETS 3′ ETS spleckles Stress 18S 5.8S 28S granule PC rRNA processing Nucleolus: rRNA modification FC DFC GC PC c FC (RPA194) DFC (FBL) GC (PES1) Overlay rRNP assembly GC uL18 2 uL5 2.5 m rRNP transport Central μ protuberance assembly Pre-40S 5S rRNA (small subunit) Mathematical modelling d SIM of FC–DFC core of FBL 'beads' Central protuberance FBL rRNP surveillance Pre-60S DFC (large subunit) 20 nm DFC (FBL) PC FC (Pol I) Fig. 1 | Nucleolar organization and its role in ribosome biogenesis. central protuberance assembly by depletion of uL5, uL18 or factors a | Schematic of a eukaryotic cell with representative cytoplasmic and important for their assembly severely disrupts the nucleolar phase nuclear condensates important for gene expression regulation. (see FIg. 6a). Interestingly, depletion of the vast majority of the other The nucleolus is represented with its three subcompartments: the fibrillar 78 ribosomal proteins, in particular those belonging to the small ribosomal centre (FC), the dense fibrillar component (DFC) and the granular subunit, has no, or little, effect on nucleolar phase behaviour. c | The three component (GC). b | Coordination of the nucleolar substructure with its subnucleolar compartments detected by immunofluorescence in roles in ribosome biogenesis. The main functions of the nucleolus in confocal microscopy: the FC detected with RNA polymerase I (Pol I) ribosome biogenesis are indicated in boxes. In cells, these steps are subunit RPA194, the DFC with FBL and the GC with the protein Pescadillo largely concomitant. The importance of the liquid–liquid phase ribosomal biogenesis factor 1 (PES1). d | Each human nucleolus consists separation model in understanding the connections between nucleolar of several dozen FC–DFC modules. Interestingly, the number of these functions and phase behaviour is illustrated with two examples: modules is relatively constant within a particular cell type but varies nascent pre-ribosomal rRNA (pre-rRNA) sorting (step 1)23 and central considerably between cell types, making it a powerful biomarker for protuberance assembly (step 2)81. (1) As nascent transcripts emerge from cell classification. Each FC–DFC module contains two or three the FC–DFC interface where they are synthesized, they are bound by the transcriptionally active ribosomal DNAs (rDNAs) at the FC–DFC interface RNA binding domain (RBD) of fibrillarin (FBL). FBL self-associates through where Pol I complexes are enriched and where transcription occurs its Gly–Arg-rich domain (GAR domain), which consists of intrinsically (left panel; image of FC–DFC interface in a HeLa cell obtained with disordered regions (IDRs). This promotes establishment of the DFC phase, structured illumination microscopy (SIM)). Ribosome assembly factors, sorting of the nascent transcript from the FC–DFC interface to the DFC such as FBL (present at roughly 3,600 copies per FC–DFC unit), form a and initial pre-rRNA processing. Note that whereas the RBD of FBL is spherical network of 18–24 regularly spaced ‘beads’ ~130 nm in diameter located in its methyltransferase domain, this methylation function is not that assemble into the DFC around the FC (right panel; 3D in silico model required either for rRNA sorting or for processing. (2) A complex of the clustered FBL distribution in the DFC). ETS, external transcribed consisting of the ribosomal proteins uL5 and uL18 and the 5S rRNA spacer; ITS, internal transcribed spacer; PC, perinucleolar chromatin; (produced in the nucleoplasm by RNA polymerase III, not shown) is rRNP, ribosomal ribonucleoprotein. Images in part c are unpublished and assembled late on the maturing pre-60S subunits to form the central a courtesy of D.L.J.L. and R.B. Part d adapted with permission from protuberance, a structure essential for ribosome function. Inhibition of REF. 23, Elsevier. www.nature.com/nrm REVIEWS Small nucleolar RNAs largely perceived as uncoupled from biophysical mod- yet coherent shape — are reconciled by the LLPS model, Antisense small RNAs involved els of nucleolar assembly, they are increasingly being which provides a predictive biophysical framework in RNA modification, pre-rRNA revisited through the lens of nucleolar
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