Lafontaine, D. L. J., Riback, J. A., Bascetin, R. & Brangwynne, C. P. The nucleolus as a multiphase liquid condensate. Nat. Rev. Mol. Cell Bio. 22, 165–182 (2021).
Thul, P. J. et al. A subcellular map of the human proteome. Science 356, eaal3321 (2017).
Huh, W. K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003).
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 76, 767–783.e711 (2019).
Wu, M. et al. lncRNA SLERT controls phase separation of FC/DFCs to facilitate Pol I transcription. Science 373, 547–555 (2021).
Boisvert, F. M., van Koningsbruggen, S., Navascues, J. & Lamond, A. I. The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 8, 574–585 (2007).
Andersen, J. S. et al. Nucleolar proteome dynamics. Nature 433, 77–83 (2005).
Andersen, J. S. et al. Directed proteomic analysis of the human nucleolus. Curr. Biol. 12, 1–11 (2002).
Frottin, F. et al. The nucleolus functions as a phase-separated protein quality control compartment. Science 365, 342–347 (2019).
Scherl, A. et al. Functional proteomic analysis of human nucleolus. Mol. Biol. Cell 13, 4100–4109 (2002).
Hu, R. et al. ZNF668 functions as a tumor suppressor by regulating p53 stability and function in breast cancer. Cancer Res. 71, 6524–6534 (2011).
Guo, D. C. et al. Loss-of-function mutations in YY1AP1 lead to grange syndrome and a fibromuscular dysplasia-like vascular disease. Am. J. Hum. Genet. 100, 21–30 (2017).
Stenstrom, L. et al. Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. Mol. Syst. Biol. 16, e9469 (2020).
Cuylen, S. et al. Ki-67 acts as a biological surfactant to disperse mitotic chromosomes. Nature 535, 308–312 (2016).
Meszaros, B., Erdos, G. & Dosztanyi, Z. IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res. 46, W329–W337 (2018).
Feric, M. et al. Coexisting liquid phases underlie nucleolar subcompartments. Cell 165, 1686–1697 (2016).
Grob, A., Colleran, C. & McStay, B. Construction of synthetic nucleoli in human cells reveals how a major functional nuclear domain is formed and propagated through cell division. Genes Dev. 28, 220–230 (2014).
Drygin, D. et al. Anticancer activity of CX-3543: a direct inhibitor of rRNA biogenesis. Cancer Res. 69, 7653–7661 (2009).
Granick, D. Nucleolar necklaces in chick embryo fibroblast cells. I. Formation of necklaces by dichlororibobenzimidazole and other adenosine analogues that decrease RNA synthesis and degrade preribosomes. J. Cell Biol. 65, 398–417 (1975).
Mnaimneh, S. et al. Exploration of essential gene functions via titratable promoter alleles. Cell 118, 31–44 (2004).
Dez, C. et al. Npa1p, a component of very early pre-60S ribosomal particles, associates with a subset of small nucleolar RNPs required for peptidyl transferase center modification. Mol. Cell. Biol. 24, 6324–6337 (2004).
Narla, A. & Ebert, B. L. Ribosomopathies: human disorders of ribosome dysfunction. Blood 115, 3196–3205 (2010).
Tafforeau, L. et al. The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of Pre-rRNA processing factors. Mol. Cell 51, 539–551 (2013).
Zubradt, M. et al. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat. Methods 14, 75–82 (2017).
Peculis, B. A. & Steitz, J. A. Sequence and structural elements critical for U8 snRNP function in Xenopus oocytes are evolutionarily conserved. Genes Dev. 8, 2241–2255 (1994).
Badrock, A. P. et al. Analysis of U8 snoRNA variants in zebrafish reveals how bi-allelic variants cause leukoencephalopathy with calcifications and cysts. Am. J. Hum. Genet. 106, 694–706 (2020).
Leone, S., Bar, D., Slabber, C. F., Dalcher, D. & Santoro, R. The RNA helicase DHX9 establishes nucleolar heterochromatin, and this activity is required for embryonic stem cell differentiation. EMBO Rep. 18, 1248–1262 (2017).
Calo, E. et al. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature 518, 249–253 (2015).
Bond, A. T., Mangus, D. A., He, F. & Jacobson, A. Absence of Dbp2p alters both nonsense-mediated mRNA decay and rRNA processing. Mol. Cell. Biol. 21, 7366–7379 (2001).
Martin, R., Straub, A. U., Doebele, C. & Bohnsack, M. T. DExD/H-box RNA helicases in ribosome biogenesis. RNA Biol. 10, 4–18 (2013).
Thomson, E., Ferreira-Cerca, S. & Hurt, E. Eukaryotic ribosome biogenesis at a glance. J. Cell Sci. 126, 4815–4821 (2013).
Farley-Barnes, K. I. et al. Diverse regulators of human ribosome biogenesis discovered by changes in nucleolar number. Cell Rep. 22, 1923–1934 (2018).
Schmid, M. & Jensen, T. H. The nuclear RNA exosome and its cofactors. Adv. Exp. Med. Biol. 1203, 113–132 (2019).
Wasmuth, E. V., Januszyk, K. & Lima, C. D. Structure of an Rrp6–RNA exosome complex bound to poly(A) RNA. Nature 511, 435–439 (2014).
Dez, C., Houseley, J. & Tollervey, D. Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae. EMBO J. 25, 2662–2662 (2006).
Lafontaine, D. L. J. A. ‘Garbage can’ for ribosomes: how eukaryotes degrade their ribosomes. Trends Biochem. Sci 35, 267–277 (2010).
Lu, Z. et al. RNA duplex map in living cells reveals higher-order transcriptome structure. Cell 165, 1267–1279 (2016).
Dunn, K. W., Kamocka, M. M. & McDonald, J. H. A practical guide to evaluating colocalization in biological microscopy. Am. J. Physiol. Cell Physiol. 300, C723–C742 (2011).
Liu, C. X. et al. Structure and degradation of circular RNAs regulate PKR activation in innate immunity. Cell 177, 865–880.e821 (2019).
Walker, M. B. & Kimmel, C. B. A two-color acid-free cartilage and bone stain for zebrafish larvae. Biotech. Histochem. 82, 23–28 (2007).
Shen, B. et al. Efficient genome modification by CRISPR–Cas9 nickase with minimal off-target effects. Nat. Methods 11, 399–402 (2014).
Thisse, C. & Thisse, B. High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat. Protoc. 3, 59–69 (2008).
Oka, Y. & Sato, T. N. Whole-mount single molecule FISH method for zebrafish embryo. Sci. Rep. 5, 8571 (2015).
Cordero, P., Kladwang, W., VanLang, C. C. & Das, R. Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. Biochemistry 51, 7037–7039 (2012).
Deigan, K. E., Li, T. W., Mathews, D. H. & Weeks, K. M. Accurate SHAPE-directed RNA structure determination. Proc. Natl Acad. Sci. USA 106, 97–102 (2009).
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