Abdelmohsen, K., Gorospe, M., 2012. RNA-binding protein nucleolin in disease. RNA Biol. 9, 799-808.
|
Ahmad, Y., Boisvert, F.M., Gregor, P., Cobley, A., Lamond, A.I., 2009. NOPdb:nucleolar proteome database-2008 update. Nucleic Acids Res. 37, D181-D184.
|
Andersen, J.S., Lam, Y.W., Leung, A.K., Ong, S.E., Lyon, C.E., Lamond, A.I., Mann, M., 2005. Nucleolar proteome dynamics. Nature 433, 77-83.
|
Barnum, K.J., O'Connell, M.J., 2014. Cell cycle regulation by checkpoints. Methods Mol. Biol. 1170, 29-40.
|
Baserga, S.J., Agentis, T.M., Wormsley, S., Dunbar, D.A., Lee, S., 1997. Mpp10p, a new protein component of the U3 snoRNP required for processing of 18S rRNA precursors. Nucleic Acids Symp. Ser. 64-67.
|
Bassler, J., Hurt, E., 2019. Eukaryotic ribosome assembly. Annu. Rev. Biochem. 88, 281-306.
|
Boisvert, F.M., van Koningsbruggen, S., Navascues, J., Lamond, A.I., 2007. The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 8, 574-585.
|
Charette, J.M., Baserga, S.J., 2010. The DEAD-box RNA helicase-like Utp25 is an SSU processome component. RNA 16, 2156-2169.
|
Charton, K., Sarparanta, J., Vihola, A., Milic, A., Jonson, P.H., Suel, L., Luque, H., Boumela, I., Richard, I., Udd, B., 2015. CAPN3-mediated processing of C-terminal titin replaced by pathological cleavage in titinopathy. Hum. Mol. Genet. 24, 3718-3731.
|
Chen, F., Huang, D., Shi, H., Gao, C., Wang, Y., Peng, J., 2020. Capn3 depletion causes Chk1 and Wee1 accumulation and disrupts synchronization of cell cycle reentry during liver regeneration after partial hepatectomy. Cell Regen. 9, 8.
|
Chen, J., Ng, S.M., Chang, C., Zhang, Z., Bourdon, J.C., Lane, D.P., Peng, J., 2009a. p53 isoform Δ113p53 is a p53 target gene that antagonizes p53 apoptotic activity via BclxL activation in zebrafish. Genes Dev. 23, 278-290.
|
Chen, J., Ruan, H., Ng, S.M., Gao, C., Soo, H.M., Wu, W., Zhang, Z., Wen, Z., Lane, D.P., Peng, J., 2005. Loss of function of def selectively up-regulates Δ113p53 expression to arrest expansion growth of digestive organs in zebrafish. Genes Dev. 19, 2900-2911.
|
Chen, Y.H., Lu, Y.F., Ko, T.Y., Tsai, M.Y., Lin, C.Y., Lin, C.C., Hwang, S.P., 2009b. Zebrafish cdx1b regulates differentiation of various intestinal cell lineages. Dev. Dynam. 238, 1021-1032.
|
Colombo, E., Alcalay, M., Pelicci, P.G., 2011. Nucleophosmin and its complex network:a possible therapeutic target in hematological diseases. Oncogene 30, 2595-2609.
|
Coute, Y., Burgess, J.A., Diaz, J.J., Chichester, C., Lisacek, F., Greco, A., Sanchez, J.C., 2006. Deciphering the human nucleolar proteome. Mass Spectrom. Rev. 25, 215-234.
|
de Morree, A., Lutje Hulsik, D., Impagliazzo, A., van Haagen, H.H., de Galan, P., van Remoortere, A., t Hoen, P.A., van Ommen, G.B., Frants, R.R., van der Maarel, S.M., 2010. Calpain 3 is a rapid-action, unidirectional proteolytic switch central to muscle remodeling. PLoS One 5, e11940.
|
den Brave, F., Cairo, L.V., Jagadeesan, C., Ruger-Herreros, C., Mogk, A., Bukau, B., Jentsch, S., 2020. Chaperone-mediated protein disaggregation triggers proteolytic clearance of intra-nuclear protein inclusions. Cell Rep. 31, 107680.
|
Enam, C., Geffen, Y., Ravid, T., Gardner, R.G., 2018. Protein quality control degradation in the nucleus. Annu. Rev. Biochem. 87, 725-749.
|
Farley-Barnes, K.I., Ogawa, L.M., Baserga, S.J., 2019. Ribosomopathies:old concepts, new controversies. Trends Genet. 35, 754-767.
|
Feng, G., Long, Y., Peng, J., Li, Q., Cui, Z., 2015. Transcriptomic characterization of the dorsal lobes after hepatectomy of the ventral lobe in zebrafish. BMC Genom. 16, 979.
|
Franic, D., Zubcic, K., Boban, M., 2021. Nuclear ubiquitin-proteasome pathways in proteostasis maintenance. Biomolecules 11, 54.
|
Fredrickson, E.K., Gallagher, P.S., Clowes Candadai, S.V., Gardner, R.G., 2013. Substrate recognition in nuclear protein quality control degradation is governed by exposed hydrophobicity that correlates with aggregation and insolubility. J. Biol. Chem. 288, 6130-6139.
|
Fredrickson, E.K., Rosenbaum, J.C., Locke, M.N., Milac, T.I., Gardner, R.G., 2011. Exposed hydrophobicity is a key determinant of nuclear quality control degradation. Mol. Biol. Cell 22, 2384-2395.
|
Frottin, F., Schueder, F., Tiwary, S., Gupta, R., Korner, R., Schlichthaerle, T., Cox, J., Jungmann, R., Hartl, F.U., Hipp, M.S., 2019. The nucleolus functions as a phaseseparated protein quality control compartment. Science 365, 342-347.
|
Goldfeder, M.B., Oliveira, C.C., 2010. Utp25p, a nucleolar Saccharomyces cerevisiae protein, interacts with U3 snoRNP subunits and affects processing of the 35S pre-rRNA. FEBS J. 277, 2838-2852.
|
Gong, L., Gong, H., Pan, X., Chang, C., Ou, Z., Ye, S., Yin, L., Yang, L., Tao, T., Zhang, Z., Liu, C., Lane, D.P., Peng, J., Chen, J., 2015. p53 isoform Δ113p53/Δ133p53 promotes DNA double-strand break repair to protect cell from death and senescence in response to DNA damage. Cell Res. 25, 351-369.
|
Granneman, S., Gallagher, J.E., Vogelzangs, J., Horstman, W., van Venrooij, W.J., Baserga, S.J., Pruijn, G.J., 2003. The human Imp3 and Imp4 proteins form a ternary complex with hMpp10, which only interacts with the U3 snoRNA in 60-80S ribonucleoprotein complexes. Nucleic Acids Res. 31, 1877-1887.
|
Guan, Y., Huang, D., Chen, F., Gao, C., Tao, T., Shi, H., Zhao, S., Liao, Z., Lo, L.J., Wang, Y., Chen, J., Peng, J., 2016. Phosphorylation of def regulates nucleolar p53 turnover and cell cycle progression through def recruitment of Calpain3. PLoS Biol. 14, e1002555.
|
Harscoet, E., Dubreucq, B., Palauqui, J.C., Lepiniec, L., 2010. NOF1 encodes an Arabidopsis protein involved in the control of rRNA expression. PLoS One 5, e12829.
|
Henras, A.K., Plisson-Chastang, C., O'Donohue, M.F., Chakraborty, A., Gleizes, P.E., 2015. An overview of pre-ribosomal RNA processing in eukaryotes. Wiley Interdis. Rev. RNA 6, 225-242.
|
Huang, W., Chen, F., Ma, Q., Xin, J., Li, J., Chen, J., Zhou, B., Chen, M., Li, J., Peng, J., 2020. Ribosome biogenesis gene DEF/UTP25 is essential for liver homeostasis and regeneration. Sci. China Life Sci. 63, 1651-1664.
|
Iarovaia, O.V., Minina, E.P., Sheval, E.V., Onichtchouk, D., Dokudovskaya, S., Razin, S.V., Vassetzky, Y.S., 2019. Nucleolus:a central hub for nuclear functions. Trends Cell Biol. 29, 647-659.
|
Kamakaka, R.T., Rine, J., 1998. Sir- and silencer-independent disruption of silencing in Saccharomyces by Sas10p. Genetics 149, 903-914.
|
Khmelinskii, A., Blaszczak, E., Pantazopoulou, M., Fischer, B., Omnus, D.J., Le Dez, G., Brossard, A., Gunnarsson, A., Barry, J.D., Meurer, M., et al., 2014. Protein quality control at the inner nuclear membrane. Nature 516, 410-413.
|
Koch, B.A., Jin, H., Tomko Jr., R.J., Yu, H.G., 2019. The anaphase-promoting complex regulates the degradation of the inner nuclear membrane protein Mps3. J. Cell Biol. 218, 839-854.
|
Lafontaine, D.L.J., Riback, J.A., Bascetin, R., Brangwynne, C.P., 2021. The nucleolus as a multiphase liquid condensate. Nat. Rev. Mol. Cell Biol. 22, 165-182.
|
Latonen, L., 2011. Nucleolar aggresomes as counterparts of cytoplasmic aggresomes in proteotoxic stress. Proteasome inhibitors induce nuclear ribonucleoprotein inclusions that accumulate several key factors of neurodegenerative diseases and cancer. Bioessays 33, 386-395.
|
Lee, S.J., Baserga, S.J., 1999. Imp3p and Imp4p, two specific components of the U3 small nucleolar ribonucleoprotein that are essential for pre-18S rRNA processing. Mol. Cell Biol. 19, 5441-5452.
|
Lerch-Gaggl, A., Haque, J., Li, J., Ning, G., Traktman, P., Duncan, S.A., 2002. Pescadillo is essential for nucleolar assembly, ribosome biogenesis, and mammalian cell proliferation. J. Biol. Chem. 277, 45347-45355.
|
Lopez, D.J., Rodriguez, J.A., Banuelos, S., 2020. Nucleophosmin, a multifunctional nucleolar organizer with a role in DNA repair. Biochim. Biophys. Acta. Protein Proteonomics 1868, 140532.
|
Ma, Z., Zhu, P., Shi, H., Guo, L., Zhang, Q., Chen, Y., Chen, S., Zhang, Z., Peng, J., Chen, J., 2019. PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components. Nature 568, 259-263.
|
Marcel, V., Vijayakumar, V., Fernandez-Cuesta, L., Hafsi, H., Sagne, C., Hautefeuille, A., Olivier, M., Hainaut, P., 2010. p53 regulates the transcription of its D133p53 isoform through specific response elements contained within the TP53 P2 internal promoter. Oncogene 29, 2691-2700.
|
Matsumoto-Taniura, N., Pirollet, F., Monroe, R., Gerace, L., Westendorf, J.M., 1996. Identification of novel M phase phosphoproteins by expression cloning. Mol. Biol. Cell 7, 1455-1469.
|
Mijaljica, D., Prescott, M., Devenish, R.J., 2012. A late form of nucleophagy in Saccharomyces cerevisiae. PLoS One 7, e40013.
|
Miller, S.B., Mogk, A., Bukau, B., 2015. Spatially organized aggregation of misfolded proteins as cellular stress defense strategy. J. Mol. Biol. 427, 1564-1574.
|
Mitchell, P., 2010. Rrp47 and the function of the Sas10/C1D domain. Biochem. Soc. Trans. 38, 1088-1092.
|
Moretti, D., Del Bello, B., Cosci, E., Biagioli, M., Miracco, C., Maellaro, E., 2009. Novel variants of muscle calpain 3 identified in human melanoma cells:cisplatininduced changes in vitro and differential expression in melanocytic lesions. Carcinogenesis 30, 960-967.
|
Okuda, M., 2002. The role of nucleophosmin in centrosome duplication. Oncogene 21, 6170-6174.
|
Ono, Y., Ojima, K., Shinkai-Ouchi, F., Hata, S., Sorimachi, H., 2016. An eccentric calpain, CAPN3/p94/calpain-3. Biochimie 122, 169-187.
|
Ono, Y., Ojima, K., Torii, F., Takaya, E., Doi, N., Nakagawa, K., Hata, S., Abe, K., Sorimachi, H., 2010. Skeletal muscle-specific calpain is an intracellular Na+-dependent protease. J. Biol. Chem. 285, 22986-22998.
|
Ono, Y., Torii, F., Ojima, K., Doi, N., Yoshioka, K., Kawabata, Y., Labeit, D., Labeit, S., Suzuki, K., Abe, K., Maeda, T., Sorimachi, H., 2006. Suppressed disassembly of autolyzing p94/CAPN3 by N2A connectin/titin in a genetic reporter system. J. Biol. Chem. 281, 18519-18531.
|
Papandreou, M.E., Tavernarakis, N., 2019. Nucleophagy:from homeostasis to disease. Cell Death Differ. 26, 630-639.
|
Roberts, P., Moshitch-Moshkovitz, S., Kvam, E., O'Toole, E., Winey, M., Goldfarb, D.S., 2003. Piecemeal microautophagy of nucleus in Saccharomyces cerevisiae. Mol. Biol. Cell 14, 129-141.
|
Sa-Moura, B., Kornprobst, M., Kharde, S., Ahmed, Y.L., Stier, G., Kunze, R., Sinning, I., Hurt, E., 2017. Mpp10 represents a platform for the interaction of multiple factors within the 90S pre-ribosome. PLoS One 12, e0183272.
|
Scott, D.D., Oeffinger, M., 2016. Nucleolin and nucleophosmin:nucleolar proteins with multiple functions in DNA repair. Biochem. Cell. Biol. 94, 419-432.
|
Smoyer, C.J., Smith, S.E., Gardner, J.M., McCroskey, S., Unruh, J.R., Jaspersen, S.L., 2019. Distribution of proteins atthe inner nuclearmembrane is regulated bythe Asi1 E3 ligase in Saccharomyces cerevisiae. Genetics 211, 1269-1282.
|
Sorimachi, H., Imajoh-Ohmi, S., Emori, Y., Kawasaki, H., Ohno, S., Minami, Y., Suzuki, K., 1989. Molecular cloning of a novel mammalian calcium-dependent protease distinct from both m- and mu-types. Specific expression of the mRNA in skeletal muscle. J. Biol. Chem. 264, 20106-20111.
|
Tai, E., Benchimol, S., 2009. TRIMming p53 for ubiquitination. Proc. Natl. Acad. Sci. U. S. A. 106, 11431-11432.
|
Tao, B., Lo, L.J., Peng, J., He, J., 2020. rDNA subtypes and their transcriptional expression in zebrafish at different developmental stages. Biochem. Biophys. Res. Commun. 529, 819-825.
|
Tao, T., Shi, H., Guan, Y., Huang, D., Chen, Y., Lane, D.P., Chen, J., Peng, J., 2013. Def defines a conserved nucleolar pathway that leads p53 to proteasomeindependent degradation. Cell Res. 23, 620-634.
|
Varshavsky, A., 2005. Regulated protein degradation. Trends Biochem. Sci. 30, 283-286.
|
Wang, Y., Luo, Y., Hong, Y., Peng, J., Lo, L., 2012. Ribosome biogenesis factor Bms1-like is essential for liver development in zebrafish. J. Genet. Genom. 39, 451-462.
|
Watanabe, N., Arai, H., Nishihara, Y., Taniguchi, M., Watanabe, N., Hunter, T., Osada, H., 2004. M-phase kinases induce phospho-dependent ubiquitination of somatic Wee1 by SCFβ-TrCP. Proc. Natl. Acad. Sci. U. S. A. 101, 4419-4424.
|
Woolford Jr., J.L., Baserga, S.J., 2013. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 195, 643-681.
|
Zhang, Y.W., Otterness, D.M., Chiang, G.G., Xie, W., Liu, Y.C., Mercurio, F., Abraham, R.T., 2005. Genotoxic stress targets human Chk1 for degradation by the ubiquitin-proteasome pathway. Mol. Cell. 19, 607-618.
|
Zhao, S., Chen, Y., Chen, F., Huang, D., Shi, H., Lo, L.J., Chen, J., Peng, J., 2019. Sas10 controls ribosome biogenesis by stabilizing Mpp10 and delivering the Mpp10-Imp3-Imp4 complex to nucleolus. Nucleic Acids Res. 47, 2996-3012.
|
Zhu, Z., Chen, J., Xiong, J.W., Peng, J., 2014. Haploinsufficiency of Def activates p53-dependent TGFβ signalling and causes scar formation after partial hepatectomy. PLoS One 9, e96576.
|