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Xie W, Sun H, Li X, Lin F, Wang Z, Wang X. Ovarian cancer: epigenetics, drug resistance, and progression. Cancer Cell Int 2021; 21:434. [PMID: 34404407 PMCID: PMC8369623 DOI: 10.1186/s12935-021-02136-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/03/2021] [Indexed: 03/05/2023] Open
Abstract
Ovarian cancer (OC) is one of the most common malignant tumors in women. OC is associated with the activation of oncogenes, the inactivation of tumor suppressor genes, and the activation of abnormal cell signaling pathways. Moreover, epigenetic processes have been found to play an important role in OC tumorigenesis. Epigenetic processes do not change DNA sequences but regulate gene expression through DNA methylation, histone modification, and non-coding RNA. This review comprehensively considers the importance of epigenetics in OC, with a focus on microRNA and long non-coding RNA. These types of RNA are promising molecular markers and therapeutic targets that may support precision medicine in OC. DNA methylation inhibitors and histone deacetylase inhibitors may be useful for such targeting, with a possible novel approach combining these two therapies. Currently, the clinical application of such epigenetic approaches is limited by multiple obstacles, including the heterogeneity of OC, insufficient sample sizes in reported studies, and non-optimized methods for detecting potential tumor markers. Nonetheless, the application of epigenetic approaches to OC patient diagnosis, treatment, and prognosis is a promising area for future clinical investigation.
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Affiliation(s)
- Weiwei Xie
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China
| | - Huizhen Sun
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China
| | - Xiaoduan Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feikai Lin
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China
| | - Ziliang Wang
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China.
| | - Xipeng Wang
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University School of Medicine Xinhua Hospital, 1665 Kongjiang Road, Yangpu District, Shanghai, China.
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2
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Chatzileontiadou DSM, Samiotaki M, Alexopoulou AN, Cotsiki M, Panayotou G, Stamatiadi M, Balatsos NAA, Leonidas DD, Kontou M. Proteomic Analysis of Human Angiogenin Interactions Reveals Cytoplasmic PCNA as a Putative Binding Partner. J Proteome Res 2017; 16:3606-3622. [PMID: 28777577 DOI: 10.1021/acs.jproteome.7b00335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human Angiogenin (hAng) is a member of the ribonuclease A superfamily and a potent inducer of neovascularization. Protein interactions of hAng in the nucleus and cytoplasm of the human umbilical vein cell line EA.hy926 have been investigated by mass spectroscopy. Data are available via ProteomeXchange with identifiers PXD006583 and PXD006584. The first gel-free analysis of hAng immunoprecipitates revealed many statistically significant potential hAng-interacting proteins involved in crucial biological pathways. Surprisingly, proliferating cell nuclear antigen (PCNA), was found to be immunoprecipitated with hAng only in the cytoplasm. The hAng-PCNA interaction and colocalization in the specific cellular compartment was validated with immunoprecipitation, immunoblotting, and immunocytochemistry. The results revealed that PCNA is predominantly localized in the cytoplasm, while hAng is distributed both in the nucleus and in the cytoplasm. hAng and PCNA colocalize in the cytoplasm, suggesting that they may interact in this compartment.
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Affiliation(s)
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming" , Vari 16672, Greece
| | | | - Marina Cotsiki
- Biomedical Sciences Research Center "Alexander Fleming" , Vari 16672, Greece
| | - George Panayotou
- Biomedical Sciences Research Center "Alexander Fleming" , Vari 16672, Greece
| | - Melina Stamatiadi
- Department of Biochemistry and Biotechnology, University of Thessaly , Biopolis, 41500 Larissa, Greece
| | - Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly , Biopolis, 41500 Larissa, Greece
| | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly , Biopolis, 41500 Larissa, Greece
| | - Maria Kontou
- Department of Biochemistry and Biotechnology, University of Thessaly , Biopolis, 41500 Larissa, Greece
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3
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Mazaira GI, Lagadari M, Erlejman AG, Galigniana MD. The Emerging Role of TPR-Domain Immunophilins in the Mechanism of Action of Steroid Receptors. NUCLEAR RECEPTOR RESEARCH 2014. [DOI: 10.11131/2014/101094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- G. I. Mazaira
- Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. Lagadari
- Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - A. G. Erlejman
- Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. D. Galigniana
- Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
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Miranda TB, Morris SA, Hager GL. Complex genomic interactions in the dynamic regulation of transcription by the glucocorticoid receptor. Mol Cell Endocrinol 2013; 380:16-24. [PMID: 23499945 PMCID: PMC3724757 DOI: 10.1016/j.mce.2013.03.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/26/2013] [Accepted: 03/03/2013] [Indexed: 12/13/2022]
Abstract
The glucocorticoid receptor regulates transcriptional output through complex interactions with the genome. These events require continuous remodeling of chromatin, interactions of the glucocorticoid receptor with chaperones and other accessory factors, and recycling of the receptor by the proteasome. Therefore, the cohort of factors expressed in a particular cell type can determine the physiological outcome upon treatment with glucocorticoid hormones. In addition, circadian and ultradian cycling of hormones can also affect GR response. Here we will discuss revision of the classical static model of GR binding to response elements to incorporate recent findings from single cell and genome-wide analyses of GR regulation. We will highlight how these studies have changed our views on the dynamics of GR recruitment and its modulation of gene expression.
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5
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Cardoso J, Lima CDP, Leal T, Gradia DF, Fragoso SP, Goldenberg S, De Sá RG, Krieger MA. Analysis of proteasomal proteolysis during the in vitro metacyclogenesis of Trypanosoma cruzi. PLoS One 2011; 6:e21027. [PMID: 21698116 PMCID: PMC3117861 DOI: 10.1371/journal.pone.0021027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 05/18/2011] [Indexed: 12/15/2022] Open
Abstract
Proteasomes are large protein complexes, whose main function is to degrade unnecessary or damaged proteins. The inhibition of proteasome activity in Trypanosoma cruzi blocks parasite replication and cellular differentiation. We demonstrate that proteasome-dependent proteolysis occurs during the cellular differentiation of T. cruzi from replicative non-infectious epimastigotes to non-replicative and infectious trypomastigotes (metacyclogenesis). No peaks of ubiquitin-mediated degradation were observed and the profile of ubiquitinated conjugates was similar at all stages of differentiation. However, an analysis of carbonylated proteins showed significant variation in oxidized protein levels at the various stages of differentiation and the proteasome inhibition also increased oxidized protein levels. Our data suggest that different proteasome complexes coexist during metacyclogenesis. The 20S proteasome may be free or linked to regulatory particles (PA700, PA26 and PA200), at specific cell sites and the coordinated action of these complexes would make it possible for proteolysis of ubiquitin-tagged proteins and oxidized proteins, to coexist in the cell.
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Affiliation(s)
| | | | - Tiago Leal
- Universidade Federal de Ouro Preto/UFOP, Ouro Preto, Minas Gerais, Brazil
| | | | | | | | | | - Marco A. Krieger
- Instituto Carlos Chagas/FIOCRUZ, Curitiba, Parana, Brazil
- * E-mail:
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Structure characterization of the 26S proteasome. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1809:67-79. [PMID: 20800708 DOI: 10.1016/j.bbagrm.2010.08.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Revised: 08/17/2010] [Accepted: 08/19/2010] [Indexed: 01/27/2023]
Abstract
In all eukaryotic cells, 26S proteasome plays an essential role in the process of ATP-dependent protein degradation. In this review, we focus on structure characterization of the 26S proteasome. Although the progress towards a high-resolution structure of the 26S proteasome has been slow, the recently solved structures of various proteasomal subcomplexes have greatly enhanced our understanding of this large machinery. In addition to having an ATP-dependent proteolytic function, the 26S proteasome is also involved in many non-proteolytic cellular activities, which are often mediated by subunits in its 19S regulatory complex. Thus, we include a detailed discussion of the structures of 19S subunits, including proteasomal ATPases, ubiquitin receptors, deubiquitinating enzymes and subunits that contain PCI domain. This article is part of a Special Issue entitled The 26S Proteasome: When degradation is just not enough!
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Keppler BR, Archer TK, Kinyamu HK. Emerging roles of the 26S proteasome in nuclear hormone receptor-regulated transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1809:109-18. [PMID: 20728592 DOI: 10.1016/j.bbagrm.2010.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 08/10/2010] [Accepted: 08/16/2010] [Indexed: 02/07/2023]
Abstract
The mechanisms by which nuclear hormone receptors (NHRs) regulate transcription are highly dynamic and require interplay between a myriad of regulatory protein complexes including the 26S proteasome. Protein degradation is the most well-established role of the proteasome; however, an increasing body of evidence suggests that the 26S proteasome may regulate transcription in proteolytic and nonproteolytic mechanisms. Here we review how these mechanisms may apply to NHR-mediated transcriptional regulation. This article is part of a Special Issue entitled The 26S Proteasome: When degradation is just not enough!
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Affiliation(s)
- Brian R Keppler
- Chromatin and Gene Expression Section, Laboratory of Molecular Carcinogenesis, NIEHS/NIH, Research Triangle Park, NC 27709, USA
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Abstract
The glucocorticoid receptor regulates the expression of a large number of genes in mammalian cells. The interaction of this receptor with regulatory elements has been discovered to be highly dynamic, with occupancy states measured in seconds, rather than minutes or hours. This finding has led to a paradigm shift in our understanding of receptor function throughout the genome. The mechanisms involved in these rapid exchange events, as well as the implications for receptor function, are discussed.
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Affiliation(s)
- Simon C Biddie
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892-5055, USA
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9
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Honys D, Rĕnák D, Feciková J, Jedelský PL, Nebesárová J, Dobrev P, Capková V. Cytoskeleton-associated large RNP complexes in tobacco male gametophyte (EPPs) are associated with ribosomes and are involved in protein synthesis, processing, and localization. J Proteome Res 2009; 8:2015-31. [PMID: 19714881 DOI: 10.1021/pr8009897] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The progamic phase of male gametophyte development involves activation of synthetic and catabolic processes required for the rapid growth of the pollen tube. It is well-established that both transcription and translation play an important role in global and specific gene expression patterns during pollen maturation. On the contrary, germination of many pollen species has been shown to be largely independent of transcription but vitally dependent on translation of stored mRNAs. Here, we report the first structural and proteomic data about large ribonucleoprotein particles (EPPs) in tobacco male gametophyte. These complexes are formed in immature pollen where they contain translationally silent mRNAs. Although massively activated at the early progamic phase, they also serve as a long-term storage of mRNA transported along with the translational machinery to the tip region. Moreover, EPPs were shown to contain ribosomal subunits, rRNAs and a set of mRNAs. Presented results extend our view of EPP complexes from mere RNA storage and transport compartment in particular stages of pollen development to the complex and well-organized machinery devoted to mRNA storage, transport and subsequent controlled activation resulting in protein synthesis, processing and precise localization. Such an organization is extremely useful in fast tip-growing pollen tube. There, massive and orchestrated protein synthesis, processing, and transport must take place in accurately localized regions. Moreover, presented complex role of EPPs in tobacco cytoplasmic mRNA and protein metabolism makes them likely to be active in another plant species too. Expression of vast majority of the closest orthologues of EPP proteins also in Arabidopsis male gametophyte further extends this concept from tobacco to Arabidopsis, the model species with advanced tricellular pollen.
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Affiliation(s)
- David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, v. v. i., Rozvojová 263, 165 02 Prague 6, Czech Republic.
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Abstract
Alcohol ingestion causes alteration in several cellular mechanisms, and leads to inflammation, apoptosis, immunological response defects, and fibrosis. These phenomena are associated with significant changes in the epigenetic mechanisms, and subsequently, to liver cell memory. The ubiquitin-proteasome pathway is one of the vital pathways in the cell that becomes dysfunctionial as a result of chronic ethanol consumption. Inhibition of the proteasome activity in the nucleus causes changes in the turnover of transcriptional factors, histone modifying enzymes, and therefore, affects epigenetic mechanisms. Alcohol consumption has been associated with an increase in histone acetylation and a decrease in histone methylation, which leads to gene expression changes. DNA and histone modifications that result from ethanol-induced proteasome inhibition are key players in regulating gene expression, especially genes involved in the cell cycle, immunological responses, and metabolism of ethanol. The present review highlights the consequences of ethanol-induced proteasome inhibition in the nucleus of liver cells that are chronically exposed to ethanol.
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Kinyamu HK, Collins JB, Grissom SF, Hebbar PB, Archer TK. Genome wide transcriptional profiling in breast cancer cells reveals distinct changes in hormone receptor target genes and chromatin modifying enzymes after proteasome inhibition. Mol Carcinog 2008; 47:845-85. [PMID: 18381591 DOI: 10.1002/mc.20440] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Steroid hormone receptors, like glucocorticoid (GR) and estrogen receptors (ER), are master regulators of genes that control many biological processes implicated in health and disease. Gene expression is dependent on receptor levels which are tightly regulated by the ubiquitin-proteasome system. Previous studies have shown that proteasome inhibition increases GR, but decreases ER-mediated gene expression. At the gene expression level this divergent role of the proteasome in receptor-dependent transcriptional regulation is not well understood. We have used a genomic approach to examine the impact of proteasome activity on GR- and ER-mediated gene expression in MCF-7 breast cancer cells treated with dexamethasone (DEX) or 17beta-estradiol (E2), the proteasome inhibitor MG132 (MG) or MG132 and either hormone (MD or ME2) for 24 h. Transcript profiling reveals that inhibiting proteasome activity modulates gene expression by GR and ER in a similar manner in that several GR and ER target genes are upregulated and downregulated after proteasome inhibition. In addition, proteasome inhibition modulates receptor-dependent genes involved in the etiology of a number of human pathological states, including multiple myeloma, leukemia, breast/prostate cancer, HIV/AIDS, and neurodegenerative disorders. Importantly, our analysis reveals that a number of transcripts encoding histone and DNA modifying enzymes, prominently histone/DNA methyltransferases and demethylases, are altered after proteasome inhibition. As proteasome inhibitors are currently in clinical trials as therapy for multiple myeloma, HIV/AIDS and leukemia, the possibility that some of the target molecules are hormone regulated and chromatin modifying enzymes is intriguing in this era of epigenetic therapy.
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Affiliation(s)
- H Karimi Kinyamu
- Chromatin and Gene Expression Section, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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12
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Rousseau E, Kojima R, Hoffner G, Djian P, Bertolotti A. Misfolding of proteins with a polyglutamine expansion is facilitated by proteasomal chaperones. J Biol Chem 2008; 284:1917-29. [PMID: 18986984 PMCID: PMC2615503 DOI: 10.1074/jbc.m806256200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Deposition of misfolded proteins with a polyglutamine expansion is a hallmark of Huntington disease and other neurodegenerative disorders. Impairment of the proteolytic function of the proteasome has been reported to be both a cause and a consequence of polyglutamine accumulation. Here we found that the proteasomal chaperones that unfold proteins to be degraded by the proteasome but also have non-proteolytic functions co-localized with huntingtin inclusions both in primary neurons and in Huntington disease patients and formed a complex independently of the proteolytic particle. Overexpression of Rpt4 or Rpt6 facilitated aggregation of mutant huntingtin and ataxin-3 without affecting proteasomal degradation. Conversely, reducing Rpt6 or Rpt4 levels decreased the number of inclusions in primary neurons, indicating that endogenous Rpt4 and Rpt6 facilitate inclusion formation. In vitro reconstitution experiments revealed that purified 19S particles promote mutant huntingtin aggregation. When fused to the ornithine decarboxylase destabilizing sequence, proteins with expanded polyglutamine were efficiently degraded and did not aggregate. We propose that aggregation of proteins with expanded polyglutamine is not a consequence of a proteolytic failure of the 20S proteasome. Rather, aggregation is elicited by chaperone subunits of the 19S particle independently of proteolysis.
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Affiliation(s)
- Erwann Rousseau
- MRC Laboratory of Molecular Biology, Hills Rd., Cambridge CB2 0QH, United Kingdom
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13
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Abstract
In this issue of Molecular Cell, Conaway and colleagues (Yao et al., 2008) provide a glimpse into an interesting mechanism to control a deubiquitylating enzyme via interaction of two complexes-the 19S proteasome regulatory particle and an ATP-dependent nucleosome remodeling complex.
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Fátyol K, Grummt I. Proteasomal ATPases are associated with rDNA: the ubiquitin proteasome system plays a direct role in RNA polymerase I transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:850-9. [PMID: 18804559 DOI: 10.1016/j.bbagrm.2008.08.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2008] [Revised: 07/29/2008] [Accepted: 08/20/2008] [Indexed: 12/23/2022]
Abstract
Significant amount of data have accumulated in the last several years pointing to the essential role of the ubiquitin proteasome system in the regulation of RNA polymerase II transcription; however, its involvement in RNA polymerase I transcription has remained largely unexplored. In this study, we demonstrate that proteasome activity is required for pre-rRNA synthesis. We can detect the association of proteasomal ATPases with both the rDNA promoter and coding region. Additionally, we show that the RNA polymerase I associated transcription factor, TIF-IA interacts with proteasomal ATPases, representing a potential link via which proteasomes and/or proteasome related complexes are recruited to rRNA genes. In summary, our findings suggest that the ubiquitin proteasome system is directly involved in RNA polymerase I transcription in analogy to the RNA polymerase II system.
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Affiliation(s)
- Károly Fátyol
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120, Heidelberg, Germany.
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15
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Wehenkel M, Hong JT, Kim KB. Proteasome modulators: essential chemical genetic tools for understanding human diseases. MOLECULAR BIOSYSTEMS 2008; 4:280-6. [DOI: 10.1039/b716221a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Girard C, Verheggen C, Neel H, Cammas A, Vagner S, Soret J, Bertrand E, Bordonné R. Characterization of a short isoform of human Tgs1 hypermethylase associating with small nucleolar ribonucleoprotein core proteins and produced by limited proteolytic processing. J Biol Chem 2007; 283:2060-9. [PMID: 18039666 DOI: 10.1074/jbc.m704209200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tgs1 is the hypermethylase responsible for m(3)G cap formation of U small nuclear RNAs (U snRNAs) and small nucleolar RNAs (snoRNAs). In vertebrates, hypermethylation of snRNAs occurs in the cytoplasm, whereas this process takes place in the nucleus for snoRNAs. Accordingly, the hypermethylase is found in both compartments with a diffuse localization in the cytoplasm and a concentration in Cajal bodies in the nucleoplasm. In this study, we report that the Tgs1 hypermethylase exists as two species, a full-length cytoplasmic isoform and a shorter nuclear isoform of 65-70 kDa. The short isoform exhibits methyltransferase activity and associates with components of box C/D and H/ACA snoRNPs, pointing to a role of this isoform in hypermethylation of snoRNAs. We also show that production of the short Tgs1 isoform is inhibited by MG132, suggesting that it results from proteasomal limited processing of the full-length Tgs1 protein. Together, our results suggest that proteasome maturation constitutes a mechanism regulating Tgs1 function by generating Tgs1 species with different substrate specificities, subcellular localizations, and functions.
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Affiliation(s)
- Cyrille Girard
- Institut de Génétique Moléculaire de Montpellier, UMR 5535, IFR 122, CNRS et Université de Montpellier, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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Baker SP, Grant PA. The SAGA continues: expanding the cellular role of a transcriptional co-activator complex. Oncogene 2007; 26:5329-40. [PMID: 17694076 PMCID: PMC2746020 DOI: 10.1038/sj.onc.1210603] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Throughout the last decade, great advances have been made in our understanding of how DNA-templated cellular processes occur in the native chromatin environment. Proteins that regulate transcription, replication, DNA repair, mitosis and other processes must be targeted to specific regions of the genome and granted access to DNA, which is normally tightly packaged in the higher-order chromatin structure of eukaryotic nuclei. Massive multiprotein complexes have been discovered, which facilitate access to DNA and recruitment of downstream effectors through three distinct mechanisms: chemical modification of histone amino-acid residues, ATP-dependent chromatin remodeling and histone exchange. The yeast Spt-Ada-Gcn5-Acetyl transferase (SAGA) transcriptional co-activator complex regulates numerous cellular processes through coordination of multiple histone post-translational modifications. SAGA is known to generate and interact with a number of histone modifications, including acetylation, methylation, ubiquitylation and phosphorylation. Although best characterized for its role in regulating transcriptional activation, SAGA is also required for optimal transcription elongation, mRNA export and perhaps nucleotide excision repair. Here, we discuss findings from recent years that have elucidated the function of this 1.8-MDa complex in multiple cellular processes, and how misregulation of the homologous complexes in humans may ultimately play a role in development of disease.
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Affiliation(s)
- S P Baker
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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Kinyamu HK, Archer TK. Proteasome activity modulates chromatin modifications and RNA polymerase II phosphorylation to enhance glucocorticoid receptor-mediated transcription. Mol Cell Biol 2007; 27:4891-904. [PMID: 17438138 PMCID: PMC1951501 DOI: 10.1128/mcb.02162-06] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The 26S proteasome modulates steroid hormone receptor-dependent gene transcription at least in part by regulating turnover and recycling of receptor/transcriptional DNA complexes, thereby ensuring continued hormone response. For the glucocorticoid receptor (GR), inhibition of proteasome-mediated proteolysis or RNA interference-mediated depletion of specific proteasome subunits results in an increase in gene expression. To facilitate transcription, proteasome inhibition alters at least two features associated with modification of chromatin architecture and gene transcription. First, proteasome inhibition increases trimethyl histone H3K4 levels with a corresponding accumulation of this modification on GR-regulated promoters in vivo. Secondly, global levels of phosphorylated RNA polymerase II (Pol II) increase, together with hormone-dependent association of the phosphorylated Pol II, with the promoter and the body of the activated gene. We propose that apart from modulating receptor turnover, the proteasome directly influences both the transcription machinery and chromatin structure, factors integral to nuclear receptor-regulated gene transcription.
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Affiliation(s)
- H Karimi Kinyamu
- Chromatin and Gene Expression Section, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, 111 Alexander Drive, P.O. Box 12233 (MD C4-01), Research Triangle Park, NC 27709, USA
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Zhang H, Sun L, Liang J, Yu W, Zhang Y, Wang Y, Chen Y, Li R, Sun X, Shang Y. The catalytic subunit of the proteasome is engaged in the entire process of estrogen receptor-regulated transcription. EMBO J 2006; 25:4223-33. [PMID: 16957778 PMCID: PMC1570434 DOI: 10.1038/sj.emboj.7601306] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Accepted: 08/01/2006] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin-proteasome system plays an important role in a variety of cellular functions by means of its proteolytic activity. Interestingly, recent studies have indicated that the proteasome components are also integral parts of transcription complexes. In genome-wide screening for steroid receptor coactivator (SRC)-interacting proteins using yeast two-hybrid system, we found that the 20S proteasome beta subunit LMP2 (Low Molecular mass Polypeptide 2) interacts directly with the SRC coactivators. We showed that LMP2 is required for estrogen receptor (ER)-mediated gene transcription and for estrogen-stimulated cell cycle progression. We found that LMP2-associated proteasome is recruited to the entire sequence of ER target genes, implicating a role for the proteasome in both transcription initiation and elongation. We demonstrated that the recruitment of LMP2 by SRC coactivators is necessary for cyclic association of ER-regulated transcription complexes on ER targets. These results revealed a mechanism by which the proteasome machinery is recruited in ER-mediated gene transcription. Our experiments also provided evidence implicating SRC coactivators in gene transcription elongation.
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Affiliation(s)
- Hua Zhang
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Luyang Sun
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Jing Liang
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Wenhua Yu
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Yan Wang
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Yupeng Chen
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Ruifang Li
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Xiaojing Sun
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 38 Xue Yuan Road, Beijing 100083, China. Tel.: +86 10 82805118; Fax: +86 10 82801355. E-mail:
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Marx C, Berger C, Xu F, Amend C, Scott GK, Hann B, Park JW, Benz CC. Validated high-throughput screening of drug-like small molecules for inhibitors of ErbB2 transcription. Assay Drug Dev Technol 2006; 4:273-84. [PMID: 16834533 DOI: 10.1089/adt.2006.4.273] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A whole cell high-throughput screening assay was developed and tested against > 2,000 structurally and functionally diverse drug-like small molecules to identify lead compounds capable of cell permeability and selective silencing of ErbB2 transcription. Screening employed reporter sublines clonally selected from ErbB2-negative MCF7 breast cancer cells after stable genomic integration of the ErbB2 proximal promoter driving a luciferase reporter; anti-ErbB2 activities (50% inhibitory concentration values) were compared to inhibition of control MCF7 sublines bearing integrated reporters driven by either a mutated ErbB2 promoter or the cyclin D1 promoter. Of the seven resulting lead compounds, four emerged from the National Cancer Institute (NCI)/ Developmental Therapeutics Program (DTP) Structural Diversity Set (NSC-131547, NSC-176328, NSC-259968, and NSC-321237); three others emerged from a panel of anticancer compounds with known mechanistic actions and included a minor groove DNA-binding antibiotic (NSC-58514, chromomycin A3), a hydroxamic acid inhibitor of histone deacetylases (NSC-709238, trichostatin A), and a tripeptide aldehyde proteasome inhibitor (MG-132). For optimization, 58 scaffold analogs of the four NCI/DTP structural leads and nine functional analogs of the mechanistic leads were secondarily screened to identify seven compounds with comparable or superior activity relative to the leads, including an approved anticancer drug, PS-341 (bortezomib). PS-341 activity was validated against cultured ErbB2-positive breast cancer cell lines (SKBr3 and BT474) and a trastuzumab-resistant ErbB2-positive breast cancer xenograft model (B585), in which PS-341 antitumor activity correlated with selective down-regulation of ErbB2 mRNA and protein levels, confirming the ErbB2- silencing potential of proteasome inhibitors.
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Affiliation(s)
- Corina Marx
- Program of Cancer and Development Therapeutics, Buck Institute for Age Research, Novato, CA 94945, USA
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Abstract
In eukaryotes, thousands of genes have to be organized and expressed in the cell nucleus. Conformational and kinetic instability of nuclear structure and components appear to enable cells to use the encoded information selectively. The ubiquitin-proteasome system is active in distinct nuclear domains and plays a major role controlling the initial steps of gene expression, DNA repair and nuclear quality-control mechanisms. Recent work indicates that a tuned balance of ubiquitylation and proteasome-dependent protein degradation of nuclear proteins is instrumental in nuclear function and, when deregulated, leads to the development of diseases such as polyQ disorders and other neurodegenerative conditions.
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Affiliation(s)
- Anna von Mikecz
- Institut für umweltmedizinische Forschung, Heinrich-Heine-Universität Düsseldorf, Auf'm Hennekamp 50, 40225 Düsseldorf, Germany.
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Schmitt HP. Protein ubiquitination, degradation and the proteasome in neuro-degenerative disorders: no clear evidence for a significant pathogenetic role of proteasome failure in Alzheimer disease and related disorders. Med Hypotheses 2006; 67:311-7. [PMID: 16580788 DOI: 10.1016/j.mehy.2006.02.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2006] [Revised: 02/16/2006] [Accepted: 02/17/2006] [Indexed: 11/20/2022]
Abstract
It has recently been proposed that Alzheimer disease (AD) might be initiated by a molecular 'hit' into a regulatory protein, e.g. a cell surface receptor [Schmitt HP. Neuro-modulation, aminergic neuro-disinhibition and neuro-degeneration: draft of a comprehensive theory for Alzheimer disease. Med Hypoth 2005;65:1106-19]. However, other substrates, in particular intra-cellular protein complexes such as the ubiquitin/proteasome system (UPS) could as well serve as a targets for such a 'hit' which might insert a mutation or induce conformational changes resulting in functional failure of protein degradation along the ubiquitin/proteasome proteolytic pathway. It has been claimed that impairment of the large multi-catalytic protease complex, the 20S/26S proteasome, might represent a key factor in the early pathogenesis of neuro-degenerative disorders characterized by the formation of abnormal protein aggregates such as neuronal cytoplasmic or nuclear inclusion bodies and fibrillary deposits. This article aims to review critically whether current information really supports the idea that impairment of the UPS might play a significant role in the early pathogenesis of neuro-degenerative disorders, with special emphasis on AD. The data provided in favour of proteasome impairment were, as a rule, revealed in in vitro experiments which cannot be unequivocally transferred to the in vivo conditions in neuro-degeneration. The author concludes that there is yet no clear evidence of a pivotal role of proteasome failure in the early pathogenesis of AD.
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Affiliation(s)
- H Peter Schmitt
- Institute of Pathology, Department for Neuropathology, University of Heidelberg, Im Neuernheimer Feld 220-221, 69120 Heidelberg, Germany.
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Ulvila J, Parikka M, Kleino A, Sormunen R, Ezekowitz RA, Kocks C, Rämet M. Double-stranded RNA is internalized by scavenger receptor-mediated endocytosis in Drosophila S2 cells. J Biol Chem 2006; 281:14370-5. [PMID: 16531407 DOI: 10.1074/jbc.m513868200] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Double-stranded RNA (dsRNA) fragments are readily internalized and processed by Drosophila S2 cells, making these cells a widely used tool for the analysis of gene function by gene silencing through RNA interference (RNAi). The underlying mechanisms are insufficiently understood. To identify components of the RNAi pathway in S2 cells, we developed a screen based on rescue from RNAi-induced lethality. We identified Argonaute 2, a core component of the RNAi machinery, and three gene products previously unknown to be involved in RNAi in Drosophila: DEAD-box RNA helicase Belle, 26 S proteasome regulatory subunit 8 (Pros45), and clathrin heavy chain, a component of the endocytic machinery. Blocking endocytosis in S2 cells impaired RNAi, suggesting that dsRNA fragments are internalized by receptor-mediated endocytosis. Indeed, using a candidate gene approach, we identified two Drosophila scavenger receptors, SR-CI and Eater, which together accounted for more than 90% of the dsRNA uptake into S2 cells. When expressed in mammalian cells, SR-CI was sufficient to mediate internalization of dsRNA fragments. Our data provide insight into the mechanism of dsRNA internalization by Drosophila cells. These results have implications for dsRNA delivery into mammalian cells.
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Affiliation(s)
- Johanna Ulvila
- Department of Pediatrics and Biocenter Oulu, University of Oulu, FIN-90014, Oulu, Finland
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