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Olie CS, O'Brien DP, Jones HBL, Liang Z, Damianou A, Sur-Erdem I, Pinto-Fernández A, Raz V, Kessler BM. Deubiquitinases in muscle physiology and disorders. Biochem Soc Trans 2024; 52:1085-1098. [PMID: 38716888 DOI: 10.1042/bst20230562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024]
Abstract
In vivo, muscle and neuronal cells are post-mitotic, and their function is predominantly regulated by proteostasis, a multilayer molecular process that maintains a delicate balance of protein homeostasis. The ubiquitin-proteasome system (UPS) is a key regulator of proteostasis. A dysfunctional UPS is a hallmark of muscle ageing and is often impacted in neuromuscular disorders (NMDs). Malfunction of the UPS often results in aberrant protein accumulation which can lead to protein aggregation and/or mis-localization affecting its function. Deubiquitinating enzymes (DUBs) are key players in the UPS, controlling protein turnover and maintaining the free ubiquitin pool. Several mutations in DUB encoding genes are linked to human NMDs, such as ATXN3, OTUD7A, UCHL1 and USP14, whilst other NMDs are associated with dysregulation of DUB expression. USP5, USP9X and USP14 are implicated in synaptic transmission and remodeling at the neuromuscular junction. Mice lacking USP19 show increased maintenance of lean muscle mass. In this review, we highlight the involvement of DUBs in muscle physiology and NMDs, particularly in processes affecting muscle regeneration, degeneration and inflammation following muscle injury. DUBs have recently garnered much respect as promising drug targets, and their roles in muscle maturation, regeneration and degeneration may provide the framework for novel therapeutics to treat muscular disorders including NMDs, sarcopenia and cachexia.
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Affiliation(s)
- Cyriel S Olie
- Department of Human Genetics, Leiden University Medical Centre, 2333ZC Leiden, The Netherlands
| | - Darragh P O'Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Hannah B L Jones
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Zhu Liang
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Andreas Damianou
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Ilknur Sur-Erdem
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, U.K
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical Centre, 2333ZC Leiden, The Netherlands
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, U.K
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Shan X, Zhang X, Huang G, Lv J, Ye Z, Jiang C, Jiang X, Cheng J, Lin H, Jiang H, Yue H, Wang Z, Xu W. A novel SNP in HUWE1 promoter confers increased risk of NOA by affecting the RA/RARα pathway in Chinese individuals. Andrology 2024; 12:338-348. [PMID: 37290064 DOI: 10.1111/andr.13474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND The ubiquitin ligase HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 is essential for the establishment and maintenance of spermatogonia. However, the role of HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 in regulating germ cell differentiation remains unclear, and clinical evidence linking HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 to male infertility pathogenesis is lacking. OBJECTIVE This study aims to investigate the role of HUWE1 in germ cell differentiation and the mechanism by which a HUWE1 single nucleotide polymorphism increases male infertility risk. MATERIALS AND METHODS We analyzed HUWE1 single nucleotide polymorphisms in 190 non-obstructive azoospermia patients of Han Chinese descent. We evaluated HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 regulation by retinoic acid receptor alpha using chromatin immunoprecipitation assays, electrophoretic mobility shift assays, and siRNA-mediated RARα knockdown. Using C18-4 spermatogonial cells, we determined whether HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 participated in retinoic acid-mediated retinoic acid receptor alpha signaling. We performed luciferase assays, cell counting kit-8 assays, immunofluorescence, quantitative real-time polymerase chain reaction, and western blotting. We quantified HUWE1 and retinoic acid receptor alpha in testicular biopsies from non-obstructive azoospermia and obstructive azoospermia patients using quantitative real-time polymerase chain reaction and immunofluorescence. RESULTS Three HUWE1 single nucleotide polymorphisms were significantly associated with spermatogenic failure in 190 non-obstructive azoospermia patients; one (rs34492591) was in the HUWE1 promoter. Retinoic acid receptor alpha regulates HUWE1 gene expression by binding to its promoter. HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 participates in retinoic acid/retinoic acid receptor alpha signaling pathway and regulates the expression of germ cell differentiation genes STRA8 and SCP3 to inhibit cell proliferation and reduce γH2AX accumulation. Notably, significantly lower levels of HUWE1 and RARα were detected in testicular biopsy samples from non-obstructive azoospermia patients. CONCLUSIONS An HUWE1 promoter single nucleotide polymorphism significantly downregulates its expression in non-obstructive azoospermia patients. Mechanistically, HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 regulates germ cell differentiation during meiotic prophase through its participation in retinoic acid/retinoic acid receptor alpha signaling and subsequent modulation of γH2AX. Taken together, these results strongly suggest that the genetic polymorphisms of HUWE1 are closely related to spermatogenesis and non-obstructive azoospermia pathogenesis.
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Affiliation(s)
- Xudong Shan
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
- Reproductive & Women-Children Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xueguang Zhang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Gelin Huang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jiao Lv
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Zixia Ye
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Chuan Jiang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xiaohui Jiang
- Human Sperm Bank, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Disease of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jianxing Cheng
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
| | - Haocheng Lin
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
| | - Hui Jiang
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
| | - Huanxun Yue
- Human Sperm Bank, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Disease of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Zhengrong Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Wenming Xu
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
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Olie CS, Pinto-Fernández A, Damianou A, Vendrell I, Mei H, den Hamer B, van der Wal E, de Greef JC, Raz V, Kessler BM. USP18 is an essential regulator of muscle cell differentiation and maturation. Cell Death Dis 2023; 14:231. [PMID: 37002195 PMCID: PMC10066380 DOI: 10.1038/s41419-023-05725-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/14/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023]
Abstract
The ubiquitin proteasomal system is a critical regulator of muscle physiology, and impaired UPS is key in many muscle pathologies. Yet, little is known about the function of deubiquitinating enzymes (DUBs) in the muscle cell context. We performed a genetic screen to identify DUBs as potential regulators of muscle cell differentiation. Surprisingly, we observed that the depletion of ubiquitin-specific protease 18 (USP18) affected the differentiation of muscle cells. USP18 depletion first stimulated differentiation initiation. Later, during differentiation, the absence of USP18 expression abrogated myotube maintenance. USP18 enzymatic function typically attenuates the immune response by removing interferon-stimulated gene 15 (ISG15) from protein substrates. However, in muscle cells, we found that USP18, predominantly nuclear, regulates differentiation independent of ISG15 and the ISG response. Exploring the pattern of RNA expression profiles and protein networks whose levels depend on USP18 expression, we found that differentiation initiation was concomitant with reduced expression of the cell-cycle gene network and altered expression of myogenic transcription (co) factors. We show that USP18 depletion altered the calcium channel gene network, resulting in reduced calcium flux in myotubes. Additionally, we show that reduced expression of sarcomeric proteins in the USP18 proteome was consistent with reduced contractile force in an engineered muscle model. Our results revealed nuclear USP18 as a critical regulator of differentiation initiation and maintenance, independent of ISG15 and its role in the ISG response.
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Affiliation(s)
- Cyriel Sebastiaan Olie
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Adán Pinto-Fernández
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Andreas Damianou
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Iolanda Vendrell
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Bianca den Hamer
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Erik van der Wal
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Jessica C de Greef
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Vered Raz
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands.
| | - Benedikt M Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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Yu Z, Li H, Zhu J, Wang H, Jin X. The roles of E3 ligases in Hepatocellular carcinoma. Am J Cancer Res 2022; 12:1179-1214. [PMID: 35411231 PMCID: PMC8984888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023] Open
Abstract
Hepatocarcinogenesis is a complex multistep biological process involving genetic and epigenetic alterations that are accompanied by activation of oncoproteins and inactivation of tumor suppressors, which in turn results in Hepatocellular carcinoma (HCC), one of the common tumors with high morbidity and mortality worldwide. The ubiquitin-proteasome system (UPS) is the key to protein degradation and regulation of physiological and pathological processes, and E3 ligases are key enzymes in the UPS that contain a variety of subfamily proteins involved in the regulation of some common signal pathways in HCC. There is growing evidence that many structural or functional dysfunctions of E3 are engaged in the development and progression of HCC. Herein, we review recent research advances in HCC-associated E3 ligases, describe their structure, classification, functional roles, and discuss some mechanisms of the abnormal activation or inactivation of the HCC-associated signal pathway due to the binding of E3 to known substrates. In addition, given the success of proteasome inhibitors in the treatment of malignant cancers, we characterize the current knowledge and future prospects for targeted therapies against aberrant E3 in HCC.
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Affiliation(s)
- Zongdong Yu
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of Lihuili Hospital, Ningbo UniversityNingbo 315040, Zhejiang, China
| | - Hong Li
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of Lihuili Hospital, Ningbo UniversityNingbo 315040, Zhejiang, China
| | - Jie Zhu
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of Lihuili Hospital, Ningbo UniversityNingbo 315040, Zhejiang, China
| | - Haibiao Wang
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of Lihuili Hospital, Ningbo UniversityNingbo 315040, Zhejiang, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of Lihuili Hospital, Ningbo UniversityNingbo 315040, Zhejiang, China
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5
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Zhang B, Hu X, Li Y, Ni Y, Xue L. Identification of methylation markers for diagnosis of autism spectrum disorder. Metab Brain Dis 2022; 37:219-228. [PMID: 34427843 DOI: 10.1007/s11011-021-00805-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
Autism spectrum disorder (ASD) is a hereditary heterogeneous neurodevelopmental disorder characterized by social and speech dysplasia. We collected the expression profiles of ASD in GSE26415, GSE42133 and GSE123302 from the gene expression omnibus (GEO) database, as well as methylation data of GSE109905. Differentially expressed genes (DEGs) between ASD and controls were obtained by differential expression analysis. Enrichment analysis identified the biological functions and signaling pathways involved by common genes in three groups of DEGs. Protein-protein interaction (PPI) networks were used to identify genes with the highest connectivity as key genes. In addition, we identified methylation markers by associating differentially methylated positions. Key methylation markers were identified using the least absolute shrink and selection operator (LASSO) model. Receiver operating characteristic curves and nomograms were used to identify the diagnostic role of key methylation markers for ASD. A total of 57 common genes were identified in the three groups of DEGs. These genes were mainly enriched in Sphingolipid metabolism and PPAR signaling pathway. In the PPI network, we identified seven key genes with higher connectivity, and used qRT-PCR experiments to verify the expressions. In addition, we identified 31 methylation markers and screened 3 key methylation markers (RUNX2, IMMP2L and MDM2) by LASSO model. Their methylation levels were closely related to the diagnostic effects of ASD. Our analysis identified RUNX2, IMMP2L and MDM2 as possible diagnostic markers for ASD. Identifying different biomarkers and risk genes will contribute to the diagnosis of ASD and the development of new clinical and drug treatments.
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Affiliation(s)
- Bei Zhang
- Department of quality management, The Fourth People's Hospital of Urumqi, Jianquan street, Urumqi, Xinjiang, 830002, China
| | - Xiaoyuan Hu
- Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Jianquan street, Tianshan District, Urumqi, Xinjiang, 830001, China
| | - Yuefei Li
- School of Public Health, Xinjiang Medical University, Liyushan Road, Xinshi District, Urumqi, Xinjiang, 830000, China
| | - Yongkang Ni
- School of Public Health, Xinjiang Medical University, Liyushan Road, Xinshi District, Urumqi, Xinjiang, 830000, China
| | - Lin Xue
- Department of quality management, The Fourth People's Hospital of Urumqi, Jianquan street, Urumqi, Xinjiang, 830002, China.
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6
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Na W, Wang Y, Gong P, Zhang X, Zhang K, Zhang H, Wang N, Li H. Screening of Reference Genes for RT-qPCR in Chicken Adipose Tissue and Adipocytes. Front Physiol 2021; 12:676864. [PMID: 34054585 PMCID: PMC8160385 DOI: 10.3389/fphys.2021.676864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
Reverse transcription quantitative real-time PCR is the most commonly used method to detect gene expression levels. In experiments, it is often necessary to correct and standardize the expression level of target genes with reference genes. Therefore, it is very important to select stable reference genes to obtain accurate quantitative results. Although application examples of reference genes in mammals have been reported, no studies have investigated the use of reference genes in studying the growth and development of adipose tissue and the proliferation and differentiation of preadipocytes in chickens. In this study, GeNorm, a reference gene stability statistical algorithm, was used to analyze the expression stability of 14 candidate reference genes in the abdominal adipose tissue of broilers at 1, 4, and 7 weeks of age, the proliferation and differentiation of primary preadipocytes, as well as directly isolated preadipocytes and mature adipocytes. The results showed that the expression of the TATA box binding protein (TBP) and hydroxymethylbilane synthase (HMBS) genes was most stable during the growth and development of abdominal adipose tissue of broilers, the expression of the peptidylprolyl isomerase A (PPIA) and HMBS genes was most stable during the proliferation of primary preadipocytes, the expression of the TBP and RPL13 genes was most stable during the differentiation of primary preadipocytes, and the expression of the TBP and HMBS genes was most stable in directly isolated preadipocytes and mature adipocytes. These results provide reference bases for accurately detecting the mRNA expression of functional genes in adipose tissue and adipocytes of chickens.
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Affiliation(s)
- Wei Na
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,College of Animal Science and Technology, Hainan University, Haikou, China
| | - Yuxiang Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Pengfei Gong
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xinyang Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ke Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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7
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Celebi G, Kesim H, Ozer E, Kutlu O. The Effect of Dysfunctional Ubiquitin Enzymes in the Pathogenesis of Most Common Diseases. Int J Mol Sci 2020; 21:ijms21176335. [PMID: 32882786 PMCID: PMC7503467 DOI: 10.3390/ijms21176335] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 12/14/2022] Open
Abstract
Ubiquitination is a multi-step enzymatic process that involves the marking of a substrate protein by bonding a ubiquitin and protein for proteolytic degradation mainly via the ubiquitin–proteasome system (UPS). The process is regulated by three main types of enzymes, namely ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3). Under physiological conditions, ubiquitination is highly reversible reaction, and deubiquitinases or deubiquitinating enzymes (DUBs) can reverse the effect of E3 ligases by the removal of ubiquitin from substrate proteins, thus maintaining the protein quality control and homeostasis in the cell. The dysfunction or dysregulation of these multi-step reactions is closely related to pathogenic conditions; therefore, understanding the role of ubiquitination in diseases is highly valuable for therapeutic approaches. In this review, we first provide an overview of the molecular mechanism of ubiquitination and UPS; then, we attempt to summarize the most common diseases affecting the dysfunction or dysregulation of these mechanisms.
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Affiliation(s)
- Gizem Celebi
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics, and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (G.C.); (H.K.); (E.O.)
| | - Hale Kesim
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics, and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (G.C.); (H.K.); (E.O.)
| | - Ebru Ozer
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics, and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (G.C.); (H.K.); (E.O.)
| | - Ozlem Kutlu
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Sabanci University, Istanbul 34956, Turkey
- Correspondence: ; Tel.: +90-216-483-9000 (ext. 2413)
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8
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Giles AC, Grill B. Roles of the HUWE1 ubiquitin ligase in nervous system development, function and disease. Neural Dev 2020; 15:6. [PMID: 32336296 PMCID: PMC7184716 DOI: 10.1186/s13064-020-00143-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
Huwe1 is a highly conserved member of the HECT E3 ubiquitin ligase family. Here, we explore the growing importance of Huwe1 in nervous system development, function and disease. We discuss extensive progress made in deciphering how Huwe1 regulates neural progenitor proliferation and differentiation, cell migration, and axon development. We highlight recent evidence indicating that Huwe1 regulates inhibitory neurotransmission. In covering these topics, we focus on findings made using both vertebrate and invertebrate in vivo model systems. Finally, we discuss extensive human genetic studies that strongly implicate HUWE1 in intellectual disability, and heighten the importance of continuing to unravel how Huwe1 affects the nervous system.
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Affiliation(s)
- Andrew C Giles
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, 33458, USA
| | - Brock Grill
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, 33458, USA.
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9
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The structure and regulation of the E3 ubiquitin ligase HUWE1 and its biological functions in cancer. Invest New Drugs 2020; 38:515-524. [PMID: 32008177 DOI: 10.1007/s10637-020-00894-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/10/2020] [Indexed: 12/21/2022]
Abstract
E3 ligases are a class of critical enzymes that can catalyse the transfer of ubiquitin (Ub) from an E2 enzyme to the substrate and are essential to cellular processes. The E3 ligase HUWE1 (also known as ARF-BP1, HECTH9, HSPC272, Ib772, LASU1, MULE, URE-B1, UREB1, and HECT, UBA and WWE domain-containing E3 ubiquitin protein ligase 1) is encoded by the huwe1 gene. HUWE1 is a key regulator of the DNA damage response, transcription, autophagy, apoptosis and metabolism in a variety of cancers. Due to its pivotal role in conferring substrate specificity, HUWE1 has attracted enormous attention as a promising anticancer drug target. In this review, we indicate the specific molecular structure of HUWE1 and its role in various cellular signalling pathways and highlight new insights into HUWE1 in cancer. Finally, we discuss outstanding questions regarding HUWE1 in oncology and highlight its limitations in drug development and clinical guidance to better define the role of HUWE1 in multiple cancers.
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10
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Suryadevara V, Willis MS. Walk the Line: The Role of Ubiquitin in Regulating Transcription in Myocytes. Physiology (Bethesda) 2019; 34:327-340. [PMID: 31389777 PMCID: PMC6863375 DOI: 10.1152/physiol.00055.2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 01/06/2023] Open
Abstract
The ubiquitin-proteasome offers novel targets for potential therapies with their specific activities and tissue localization. Recently, the expansion of our understanding of how ubiquitin ligases (E3s) specifically regulate transcription has demonstrated their roles in skeletal muscle, complementing their roles in protein quality control and protein degradation. This review focuses on skeletal muscle E3s that regulate transcription factors critical to myogenesis and the maintenance of skeletal muscle wasting diseases.
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Affiliation(s)
| | - Monte S Willis
- Department of Pathology & Laboratory Medicine, Indianapolis, Indiana
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Internal Medicine, Krannert Institute of Cardiology and Division of Cardiology, Indiana University School of Medicine, Indianapolis, Indiana
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11
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Shaping Striated Muscles with Ubiquitin Proteasome System in Health and Disease. Trends Mol Med 2019; 25:760-774. [PMID: 31235369 DOI: 10.1016/j.molmed.2019.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/03/2019] [Accepted: 05/23/2019] [Indexed: 02/06/2023]
Abstract
For long-lived contractile cells, such as striated muscle cells, maintaining proteome integrity is a challenging task. These cells require hundreds of components that must be properly synthesized, folded, and incorporated into the basic contractile unit, the sarcomere. Muscle protein quality control in cells is mainly guaranteed by the ubiquitin-proteasome system (UPS), the lysosome-autophagy system, and various molecular chaperones. Recent studies establish the concept of dedicated UPS in the regulation of sarcomere assembly during development and in adult life to maintain the intricate and interwoven organization of protein complexes in muscle. Failure of sarcomere protein quality control often represents the basis of severe myopathies and cardiomyopathies in human, further highlighting its importance in producing and maintaining the contractile machinery of muscle cells in shape.
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12
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Yanku Y, Bitman-Lotan E, Zohar Y, Kurant E, Zilke N, Eilers M, Orian A. Drosophila HUWE1 Ubiquitin Ligase Regulates Endoreplication and Antagonizes JNK Signaling During Salivary Gland Development. Cells 2018; 7:E151. [PMID: 30261639 PMCID: PMC6210797 DOI: 10.3390/cells7100151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 01/18/2023] Open
Abstract
The HECT-type ubiquitin ligase HECT, UBA and WWE Domain Containing 1, (HUWE1) regulates key cancer-related pathways, including the Myc oncogene. It affects cell proliferation, stress and immune signaling, mitochondria homeostasis, and cell death. HUWE1 is evolutionarily conserved from Caenorhabditis elegance to Drosophila melanogaster and Humans. Here, we report that the Drosophila ortholog, dHUWE1 (CG8184), is an essential gene whose loss results in embryonic lethality and whose tissue-specific disruption establishes its regulatory role in larval salivary gland development. dHUWE1 is essential for endoreplication of salivary gland cells and its knockdown results in the inability of these cells to replicate DNA. Remarkably, dHUWE1 is a survival factor that prevents premature activation of JNK signaling, thus preventing the disintegration of the salivary gland, which occurs physiologically during pupal stages. This function of dHUWE1 is general, as its inhibitory effect is observed also during eye development and at the organismal level. Epistatic studies revealed that the loss of dHUWE1 is compensated by dMyc proeitn expression or the loss of dmP53. dHUWE1 is therefore a conserved survival factor that regulates organ formation during Drosophila development.
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Affiliation(s)
- Yifat Yanku
- Rappaport Research Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
| | - Eliya Bitman-Lotan
- Rappaport Research Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
| | - Yaniv Zohar
- Rappaport Research Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
- Institute of Pathology, RAMBAM Medical Center, Haifa 30196, Israel.
| | - Estee Kurant
- Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel.
| | - Norman Zilke
- Genome-Scale Biology Research Program Institute of Biomedicine University of Helsinki, 00290 Helsinki, Finland.
| | - Martin Eilers
- Theodor Boveri Institute, Biocenter, University of Würzburg, D-97074 Würzburg, Germany.
| | - Amir Orian
- Rappaport Research Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
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13
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Zhang F, Li Y, Chen L, Cheng J, Wu P, Chu W, Zhang J. Characterization of the Ubiquitin Specific Protease (USP) family members in the fast and slow muscle fibers from Chinese perch (Siniperca chuatsi). Gene 2018; 677:1-9. [PMID: 30030202 DOI: 10.1016/j.gene.2018.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 11/16/2022]
Abstract
Skeletal muscle atrophy results from fasting, disuse and other systemic diseases. Muscle atrophy is associated with increased muscle protein degradation via the Ubiquitin proteasome system (UPS). The Ubiquitin Specific Proteases (USPs), also known as deubiquitinating enzymes, regulates a wide variety of cellular processes in skeletal muscle. In our study, among the 41 members of the USP family identified in the skeletal muscle transcriptome of Chinese perch, 24 USPs were differentially expressed between the fast and slow muscle fibers. The expressional profile of 4 muscle-related USPs (USP10, USP14, USP19, USP45) was investigated in the fast and slow muscle in response to fasting at 4 and 7 days. The results showed that the expression of USP10, USP14 and USP19 was significantly increased in the fast muscle after fasting for 4 days and 7 days. But only the USP10 and USP14 had significantly increased at 7 days of fasting in the slow muscle. The expression of MAFbx and MuRF1 up-regulated and major myofibrillar genes down-regulated, indicating that all of these four USPs are involved in the protein degradation of the fast and slow muscle.
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Affiliation(s)
- FangLiang Zhang
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China.
| | - YuLong Li
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Lin Chen
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Jia Cheng
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Ping Wu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - WuYing Chu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China; Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde 415000, China.
| | - JianShe Zhang
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China; Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde 415000, China.
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14
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Teves SS, An L, Bhargava-Shah A, Xie L, Darzacq X, Tjian R. A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes. eLife 2018; 7:35621. [PMID: 29939130 PMCID: PMC6037474 DOI: 10.7554/elife.35621] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/23/2018] [Indexed: 12/18/2022] Open
Abstract
Maintenance of transcription programs is challenged during mitosis when chromatin becomes condensed and transcription is silenced. How do the daughter cells re-establish the original transcription program? Here, we report that the TATA-binding protein (TBP), a key component of the core transcriptional machinery, remains bound globally to active promoters in mouse embryonic stem cells during mitosis. Using live-cell single-molecule imaging, we observed that TBP mitotic binding is highly stable, with an average residence time of minutes, in stark contrast to typical TFs with residence times of seconds. To test the functional effect of mitotic TBP binding, we used a drug-inducible degron system and found that TBP promotes the association of RNA Polymerase II with mitotic chromosomes, and facilitates transcriptional reactivation following mitosis. These results suggest that the core transcriptional machinery promotes efficient transcription maintenance globally.
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Affiliation(s)
- Sheila S Teves
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Luye An
- Department of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, United States
| | - Aarohi Bhargava-Shah
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Liangqi Xie
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Berkeley, United States
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15
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Transforming Growth Factor β-Induced Proliferative Arrest Mediated by TRIM26-Dependent TAF7 Degradation and Its Antagonism by MYC. Mol Cell Biol 2018; 38:MCB.00449-17. [PMID: 29203640 DOI: 10.1128/mcb.00449-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 11/27/2017] [Indexed: 01/07/2023] Open
Abstract
Recognition of gene promoters by RNA polymerase II is mediated by general transcription factor IID (TFIID), which has been thought to be a static complex and to play a passive role in the regulation of gene expression under the instruction of gene-specific transcription factors. Here we show that transforming growth factor β (TGF-β) induced degradation of the TFIID subunit TAF7 in cultured mouse mammary epithelial cells and that this effect was required for proliferative arrest in response to TGF-β stimulation. TGF-β stimulated transcription of the gene for the ubiquitin ligase TRIM26, which was shown to ubiquitylate TAF7 and thereby to target it for proteasomal degradation. Sustained exposure of cells to TGF-β resulted in recovery from proliferative arrest in association with amplification of the Myc proto-oncogene, with MYC inhibiting TRIM26 induction by TGF-β. Our data thus show that TFIID is not simply a general mediator of transcription but contributes to the regulation of transcription in response to cell stimulation, playing a key role in the cytostatic function of TGF-β.
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16
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Abstract
Human development requires intricate cell specification and communication pathways that allow an embryo to generate and appropriately connect more than 200 different cell types. Key to the successful completion of this differentiation programme is the quantitative and reversible regulation of core signalling networks, and post-translational modification with ubiquitin provides embryos with an essential tool to accomplish this task. Instigated by E3 ligases and reversed by deubiquitylases, ubiquitylation controls many processes that are fundamental for development, such as cell division, fate specification and migration. As aberrant function or regulation of ubiquitylation enzymes is at the roots of developmental disorders, cancer, and neurodegeneration, modulating the activity of ubiquitylation enzymes is likely to provide strategies for therapeutic intervention.
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17
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Abstract
This review by Vo ngoc et al. expands the view of the RNA polymerase II core promoter, which is comprised of classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. This model may eventually lead to a more unified conceptual understanding of the core promoter.
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Affiliation(s)
- Long Vo Ngoc
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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18
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Werner A, Manford AG, Rape M. Ubiquitin-Dependent Regulation of Stem Cell Biology. Trends Cell Biol 2017; 27:568-579. [PMID: 28528988 PMCID: PMC5643009 DOI: 10.1016/j.tcb.2017.04.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 04/04/2017] [Accepted: 04/10/2017] [Indexed: 12/21/2022]
Abstract
The growth of a metazoan body relies on a series of highly coordinated cell-fate decisions by stem cells which can undergo self-renewal, reversibly enter a quiescent state, or terminally commit to a cell specification program. To guide their decisions, stem cells make frequent use of ubiquitylation, a post-translational modification that can affect the activity, interaction landscape, or stability of stem cell proteins. In this review we discuss novel findings that have provided insight into ubiquitin-dependent mechanisms of stem cell control and revealed how an essential and highly conserved protein modification can shape metazoan development.
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Affiliation(s)
- Achim Werner
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Andrew G Manford
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA.
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19
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Johnson SA, Lin JJ, Walkey CJ, Leathers MP, Coarfa C, Johnson DL. Elevated TATA-binding protein expression drives vascular endothelial growth factor expression in colon cancer. Oncotarget 2017; 8:48832-48845. [PMID: 28415573 PMCID: PMC5564728 DOI: 10.18632/oncotarget.16384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/13/2017] [Indexed: 11/26/2022] Open
Abstract
The TATA-binding protein (TBP) plays a central role in eukaryotic gene transcription. Given its key function in transcription initiation, TBP was initially thought to be an invariant protein. However, studies showed that TBP expression is upregulated by oncogenic signaling pathways. Furthermore, depending on the cell type, small increases in cellular TBP amounts can induce changes in cellular growth properties towards a transformed phenotype. Here we sought to identify the specific TBP-regulated gene targets that drive its ability to induce tumorigenesis. Using microarray analysis, our results reveal that increases in cellular TBP concentrations produce selective alterations in gene expression that include an enrichment for genes involved in angiogenesis. Accordingly, we find that TBP levels modulate VEGFA expression, the master regulator of angiogenesis. Increases in cellular TBP amounts induce VEGFA expression and secretion to enhance cell migration and tumor vascularization. TBP mediates changes in VEGFA transcription requiring its recruitment at a hypoxia-insensitive proximal TSS, revealing a mechanism for VEGF regulation under non-stress conditions. The results are clinically relevant as TBP expression is significantly increased in both colon adenocarcinomas as well as adenomas relative to normal tissue. Furthermore, TBP expression is positively correlated with VEGFA expression. Collectively, these studies support the idea that increases in TBP expression contribute to enhanced VEGFA transcription early in colorectal cancer development to drive tumorigenesis.
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Affiliation(s)
- Sandra A.S. Johnson
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Justin J. Lin
- Zymo Research, Irvine, California, United States of America
| | - Christopher J. Walkey
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael P. Leathers
- Department of Orthopedic Surgery, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, California, United States of America
| | - Cristian Coarfa
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Deborah L. Johnson
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
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20
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Sander B, Xu W, Eilers M, Popov N, Lorenz S. A conformational switch regulates the ubiquitin ligase HUWE1. eLife 2017; 6:e21036. [PMID: 28193319 PMCID: PMC5308896 DOI: 10.7554/elife.21036] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/27/2017] [Indexed: 12/27/2022] Open
Abstract
The human ubiquitin ligase HUWE1 has key roles in tumorigenesis, yet it is unkown how its activity is regulated. We present the crystal structure of a C-terminal part of HUWE1, including the catalytic domain, and reveal an asymmetric auto-inhibited dimer. We show that HUWE1 dimerizes in solution and self-associates in cells, and that both occurs through the crystallographic dimer interface. We demonstrate that HUWE1 is inhibited in cells and that it can be activated by disruption of the dimer interface. We identify a conserved segment in HUWE1 that counteracts dimer formation by associating with the dimerization region intramolecularly. Our studies reveal, intriguingly, that the tumor suppressor p14ARF binds to this segment and may thus shift the conformational equilibrium of HUWE1 toward the inactive state. We propose a model, in which the activity of HUWE1 underlies conformational control in response to physiological cues-a mechanism that may be exploited for cancer therapy.
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Affiliation(s)
- Bodo Sander
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Wenshan Xu
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
- Department of Radiation Oncology, University Hospital Würzburg, Würzburg, Germany
| | - Martin Eilers
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
- Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Nikita Popov
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
- Department of Radiation Oncology, University Hospital Würzburg, Würzburg, Germany
| | - Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
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21
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Consalvi S, Brancaccio A, Dall'Agnese A, Puri PL, Palacios D. Praja1 E3 ubiquitin ligase promotes skeletal myogenesis through degradation of EZH2 upon p38α activation. Nat Commun 2017; 8:13956. [PMID: 28067271 PMCID: PMC5423270 DOI: 10.1038/ncomms13956] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/16/2016] [Indexed: 12/18/2022] Open
Abstract
Polycomb proteins are critical chromatin modifiers that regulate stem cell differentiation via transcriptional repression. In skeletal muscle progenitors Enhancer of zeste homologue 2 (EZH2), the catalytic subunit of Polycomb Repressive Complex 2 (PRC2), contributes to maintain the chromatin of muscle genes in a repressive conformation, whereas its down-regulation allows the progression through the myogenic programme. Here, we show that p38α kinase promotes EZH2 degradation in differentiating muscle cells through phosphorylation of threonine 372. Biochemical and genetic evidence demonstrates that the MYOD-induced E3 ubiquitin ligase Praja1 (PJA1) is involved in regulating EZH2 levels upon p38α activation. EZH2 premature degradation in proliferating myoblasts is prevented by low levels of PJA1, its cytoplasmic localization and the lower activity towards unphosphorylated EZH2. Our results indicate that signal-dependent degradation of EZH2 is a prerequisite for satellite cells differentiation and identify PJA1 as a new player in the epigenetic control of muscle gene expression. In skeletal muscle progenitors, EZH2 maintains myogenic genes in a repressed state, but during differentiation its levels are reduced via unknown mechanisms. Here the authors show that during myogenesis, p38α kinase phosphorylates EZH2 and targets it for degradation by the ubiquitin ligase PRAJA1.
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Affiliation(s)
- Silvia Consalvi
- Laboratory of Epigenetics and Regenerative Pharmacology, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Arianna Brancaccio
- Laboratory of Epigenetics and Signal Transduction, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy.,Department of Anatomy, Histology, Forensic Medicine and Orthopedics, Via Scarpa 14, Sapienza University, 00161 Rome, Italy
| | - Alessandra Dall'Agnese
- Sanford-Burnham-Prebys Medical Discovery Institute, Development Aging and Regeneration Program, La Jolla 92037, California, USA
| | - Pier Lorenzo Puri
- Laboratory of Epigenetics and Regenerative Pharmacology, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy.,Sanford-Burnham-Prebys Medical Discovery Institute, Development Aging and Regeneration Program, La Jolla 92037, California, USA
| | - Daniela Palacios
- Laboratory of Epigenetics and Signal Transduction, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
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22
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He M, Zhou Z, Shah AA, Zou H, Tao J, Chen Q, Wan Y. The emerging role of deubiquitinating enzymes in genomic integrity, diseases, and therapeutics. Cell Biosci 2016; 6:62. [PMID: 28031783 PMCID: PMC5168870 DOI: 10.1186/s13578-016-0127-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/05/2016] [Indexed: 02/05/2023] Open
Abstract
The addition of mono-ubiquitin or poly-ubiquitin chain to signaling proteins in response to DNA damage signal is thought to be a critical event that facilitates the recognition of DNA damage lesion site, the activation of checkpoint function, termination and checkpoint response and the recruitment of DNA repair proteins. Despite the ubiquitin modifiers, removal of ubiquitin from the functional proteins by the deubiquitinating enzymes (DUBs) plays an important role in orchestrating DNA damage response as well as DNA repair processes. Deregulated ubiquitination and deubiquitination could lead to genome instability that in turn causes tumorigenesis. Recent TCGA study has further revealed the connection between mutations in alteration of DUBs and various types of tumors. In addition, emerging drug design based on DUBs provides a new avenue for anti-cancer therapy. In this review, we will summarize the role of deubiquitination and specificity of DUBs, and highlight the recent discoveries of DUBs in the modulation of ubiquitin-mediated DNA damage response and DNA damage repair. We will furthermore discuss the DUBs involved in the tumorigenesis as well as interception of deubiquitination as a novel strategy for anti-cancer therapy.
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Affiliation(s)
- Mingjing He
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA ; State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041 Sichuan People's Republic of China
| | - Zhuan Zhou
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Anil A Shah
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Haojing Zou
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Jin Tao
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041 Sichuan People's Republic of China
| | - Yong Wan
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
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23
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Yatsenko SA, Mittal P, Wood-Trageser MA, Jones MW, Surti U, Edwards RP, Sood AK, Rajkovic A. Highly heterogeneous genomic landscape of uterine leiomyomas by whole exome sequencing and genome-wide arrays. Fertil Steril 2016; 107:457-466.e9. [PMID: 27889101 DOI: 10.1016/j.fertnstert.2016.10.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To determine the genomic signatures of human uterine leiomyomas and prevalence of MED12 mutations in human uterine leiomyosarcomas. DESIGN Retrospective cohort study. SETTING Not applicable. PATIENT(S) This study included a set of 16 fresh frozen leiomyoma and corresponding unaffected myometrium specimens as well as 153 leiomyosarcomas collected from women diagnosed with uterine leiomyomas or leiomyosarcomas who underwent clinically indicated abdominal hysterectomy. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Whole exome sequencing and high-resolution X-chromosome and whole genome single nucleotide polymorphism microarray analyses were performed on leiomyoma samples negative for the known MED12 mutations and compared with their corresponding myometrium. Leiomyosarcoma specimens were examined for exon 2 MED12 mutations to evaluate the frequency of MED12 mutated leiomyosarcomas. RESULT(S) Our results indicate remarkable genomic heterogeneity of leiomyoma lesions. MED12-negative leiomyomas contain copy number alterations involving the Mediator complex subunits such as MED8, MED18, CDK8, and long intergenic nonprotein coding RNA340 (CASC15), which may affect the Mediator architecture and/or its transcriptional activity. We also identified mutations in a number of genes that were implicated in leiomyomagenesis such as COL4A6, DCN, and AHR, as well as novel genes: NRG1, ADAM18, HUWE1, FBXW4, FBXL13, and CAPRIN1. CONCLUSION(S) Mutations in genes implicated in cell-to-cell interactions and remodeling of the extracellular matrix and genomic aberrations involving genes coding for the Mediator complex subunits were identified in uterine leiomyomas. Additionally, we discovered that ∼4.6% of leiomyosarcomas harbored MED12 exon 2 mutations, but the relevance of this association with molecular pathogenesis of leiomyosarcoma remains unknown.
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Affiliation(s)
- Svetlana A Yatsenko
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, Magee-Women's Hospital of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Priya Mittal
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania; Magee-Women's Research Institute, Pittsburgh, Pennsylvania; Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michelle A Wood-Trageser
- Department of Pathology, Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mirka W Jones
- Department of Pathology, Magee-Women's Hospital of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Urvashi Surti
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, Magee-Women's Hospital of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania; Magee-Women's Research Institute, Pittsburgh, Pennsylvania
| | - Robert P Edwards
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Magee-Women's Research Institute, Pittsburgh, Pennsylvania
| | - Anil K Sood
- Department of Gynecologic Oncology and Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aleksandar Rajkovic
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pathology, Magee-Women's Hospital of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania; Magee-Women's Research Institute, Pittsburgh, Pennsylvania.
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Nakazato A, Maeda R, Ishikawa K, Suzuki H, Tamura TA. TBP-like protein (TLP) represses myogenesis via inhibition of the myogenin promoter. Biochem Biophys Res Commun 2016; 479:814-819. [PMID: 27680312 DOI: 10.1016/j.bbrc.2016.09.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 09/24/2016] [Indexed: 11/30/2022]
Abstract
TBP-like protein (TLP) is one of the metazoan-restricted transcription factors participating in development and differentiation, though the molecular mechanism by which TLP regulates these processes remains unclear. In this study, we investigated the relationship between TLP and myogenesis of mouse C2C12 myoblasts. We found that TLP gene expression decreases during myogenic differentiation. Overexpression and knockdown of TLP revealed that the levels of muscle-specific myosin heavy chain and the myogenic transcription factor myogenin are downregulated by TLP. TLP inhibits the progression of morphological change from myoblasts to myotubes, thereby suppressing myogenesis. We further show that TLP represses the promoter activity of myogenin. The proximal AT-rich sequence of the myogenin promoter is responsible for TLP-mediated transcriptional repression. The results of this study suggest that TLP inhibits myogenesis through downregulation of the myogenin gene.
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Affiliation(s)
- Aki Nakazato
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Ryo Maeda
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Kohei Ishikawa
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Hidefumi Suzuki
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Taka-Aki Tamura
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba, 263-8522, Japan.
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Malecova B, Dall'Agnese A, Madaro L, Gatto S, Coutinho Toto P, Albini S, Ryan T, Tora L, Puri PL. TBP/TFIID-dependent activation of MyoD target genes in skeletal muscle cells. eLife 2016; 5. [PMID: 26880551 PMCID: PMC4775216 DOI: 10.7554/elife.12534] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/21/2016] [Indexed: 02/07/2023] Open
Abstract
Change in the identity of the components of the transcription pre-initiation complex is proposed to control cell type-specific gene expression. Replacement of the canonical TFIID-TBP complex with TRF3/TBP2 was reported to be required for activation of muscle-gene expression. The lack of a developmental phenotype in TBP2 null mice prompted further analysis to determine whether TBP2 deficiency can compromise adult myogenesis. We show here that TBP2 null mice have an intact regeneration potential upon injury and that TBP2 is not expressed in established C2C12 muscle cell or in primary mouse MuSCs. While TFIID subunits and TBP are downregulated during myoblast differentiation, reduced amounts of these proteins form a complex that is detectable on promoters of muscle genes and is essential for their expression. This evidence demonstrates that TBP2 does not replace TBP during muscle differentiation, as previously proposed, with limiting amounts of TFIID-TBP being required to promote muscle-specific gene expression. DOI:http://dx.doi.org/10.7554/eLife.12534.001 The muscles that allow animal’s to move are built predominantly of cells called myofibers. Like other specialized cell types, these myofibers develop via a regulated set of events called differentiation. In adults, this phenomenon occurs when muscles regenerate after an injury, and new myofibers differentiate from so-called satellite cells that already reside within the muscles. Differentiation is regulated at the genetic level, and the development of myofibers relies on the activation of muscle-specific genes. A gene’s expression is typically controlled via a nearby regulatory region of DNA called a promoter that can be recognized by various molecular machines made from protein complexes. In most adult tissues, such regulatory machineries contain a complex called TFIID. Previously it was reported that the TFIID complex was eliminated from cells during muscle differentiation, and that an alternative protein complex called TBP2/TAF3 recognizes and regulates the promoters of muscle-specific genes. However, Malecova et al. have now discovered that TFIID is actually present, albeit at reduced amounts, in differentiated muscles and that it drives the activation of muscle-specific genes during differentiation. Further experiments also showed that the TBP2 protein is not required for differentiation of muscle cells or for the regeneration of injured muscles, and is actually absent in muscle cells. Further studies are now needed to explore how the TFIID-containing complex works with other regulatory protein complexes that are known to help make muscle-specific genes accessible to TFIID. It will also be important to study the relationship between the down-regulation of TFIID components and the activation of muscle-specific genes that typically occurs in mature myofbers. Together these efforts will allow the various aspects of gene regulation to be integrated, which will help provide a more complete understanding of the process of muscle differentiation. DOI:http://dx.doi.org/10.7554/eLife.12534.002
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Affiliation(s)
- Barbora Malecova
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Alessandra Dall'Agnese
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Luca Madaro
- Fondazione Santa Lucia - Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Sole Gatto
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Paula Coutinho Toto
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Sonia Albini
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Tammy Ryan
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Làszlò Tora
- Cellular Signaling and Nuclear Dynamics Program, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CU de Strasbourg, France
| | - Pier Lorenzo Puri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States.,Fondazione Santa Lucia - Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
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