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Sun X, Cui Y, Feng H, Liu H, Liu X. TGF-β signaling controls Foxp3 methylation and T reg cell differentiation by modulating Uhrf1 activity. J Exp Med 2019; 216:2819-2837. [PMID: 31515281 PMCID: PMC6888975 DOI: 10.1084/jem.20190550] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/28/2019] [Accepted: 08/28/2019] [Indexed: 01/02/2023] Open
Abstract
Regulatory T (T reg) cells are required for the maintenance of immune homeostasis. Both TGF-β signaling and epigenetic modifications are important for Foxp3 induction, but how TGF-β signaling participates in the epigenetic regulation of Foxp3 remains largely unknown. Here we showed that T cell-specific ablation of Uhrf1 resulted in T reg-biased differentiation in TCR-stimulated naive T cells in the absence of TGF-β signaling, and these Foxp3+ T cells had a suppressive function. Adoptive transfer of Uhrf1 -/- naive T cells could significantly suppress colitis due to increased iT reg cell generation. Mechanistically, Uhrf1 was induced upon TCR stimulation and participated in the maintenance of DNA methylation patterns of T reg cell-specific genes during cell division, while it was phosphorylated upon TGF-β stimulation and sequestered outside the nucleus, and ultimately underwent proteasome-dependent degradation. Collectively, our study reveals a novel epigenetic mechanism of TGF-β-mediated iT reg cell differentiation by modulating Uhrf1 activity and suggests that Uhrf1 may be a potential therapeutic target in inflammatory diseases for generating stable iT reg cells.
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Affiliation(s)
- Xiang Sun
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu Cui
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Haiyun Feng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Haifeng Liu
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaolong Liu
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China .,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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52
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Ye F, Huang J, Wang H, Luo C, Zhao K. Targeting epigenetic machinery: Emerging novel allosteric inhibitors. Pharmacol Ther 2019; 204:107406. [PMID: 31521697 DOI: 10.1016/j.pharmthera.2019.107406] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2019] [Indexed: 12/13/2022]
Abstract
Epigenetics has emerged as an extremely exciting fast-growing area of biomedical research in post genome era. Epigenetic dysfunction is tightly related with various diseases such as cancer and aging related degeneration, potentiating epigenetics modulators as important therapeutics targets. Indeed, inhibitors of histone deacetylase and DNA methyltransferase have been approved for treating blood tumor malignancies, whereas inhibitors of histone methyltransferase and histone acetyl-lysine recognizer bromodomain are in clinical stage. However, it remains a great challenge to discover potent and selective inhibitors by targeting catalytic site, as the same subfamily of epigenetic enzymes often share high sequence identity and very conserved catalytic core pocket. It is well known that epigenetic modifications are usually carried out by multi-protein complexes, and activation of catalytic subunit is often tightly regulated by other interactive protein component, especially in disease conditions. Therefore, it is not unusual that epigenetic complex machinery may exhibit allosteric regulation site induced by protein-protein interactions. Targeting allosteric site emerges as a compelling alternative strategy to develop epigenetic drugs with enhanced druggability and pharmacological profiles. In this review, we highlight recent progress in the development of allosteric inhibitors for epigenetic complexes through targeting protein-protein interactions. We also summarized the status of clinical applications of those inhibitors. Finally, we provide perspectives of future novel allosteric epigenetic machinery modulators emerging from otherwise undruggable single protein target.
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Affiliation(s)
- Fei Ye
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Jing Huang
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongbo Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
| | - Cheng Luo
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, South Dong Qing Road, Guizhou 550025, China.
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
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53
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Hahm JY, Kim JY, Park JW, Kang JY, Kim KB, Kim SR, Cho H, Seo SB. Methylation of UHRF1 by SET7 is essential for DNA double-strand break repair. Nucleic Acids Res 2019; 47:184-196. [PMID: 30357346 PMCID: PMC6326791 DOI: 10.1093/nar/gky975] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/06/2018] [Indexed: 12/13/2022] Open
Abstract
Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is a key epigenetic regulator of DNA methylation maintenance and heterochromatin formation. The roles of UHRF1 in DNA damage repair also have been emphasized in recent years. However, the regulatory mechanism of UHRF1 remains elusive. In this study, we showed that UHRF1 is methylated by SET7 and demethylation is catalyzed by LSD1. In addition, methylation of UHRF1 is induced in response to DNA damage and its phosphorylation in S phase is a prerequisite for interaction with SET7. Furthermore, UHRF1 methylation catalyzes the conjugation of polyubiquitin chains to PCNA and promotes homologous recombination for DNA repair. SET7-mediated UHRF1 methylation is also shown to be essential for cell viability against DNA damage. Our data revealed the regulatory mechanism underlying the UHRF1 methylation status by SET7 and LSD1 in double-strand break repair pathway.
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Affiliation(s)
- Ja Young Hahm
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ji-Young Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jin Woo Park
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Joo-Young Kang
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kee-Beom Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Se-Ryeon Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hana Cho
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sang-Beom Seo
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
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54
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Qi X, Yu XJ, Wang XM, Song TN, Zhang J, Guo XZ, Li GJ, Shao M. Knockdown of KCNQ1OT1 Suppresses Cell Invasion and Sensitizes Osteosarcoma Cells to CDDP by Upregulating DNMT1-Mediated Kcnq1 Expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 17:804-818. [PMID: 31454677 PMCID: PMC6716066 DOI: 10.1016/j.omtn.2019.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/17/2022]
Abstract
Osteosarcoma is a malignant bone tumor, with a high incidence worldwide. The involvement of long non-coding RNAs (lncRNAs) in cancers and their molecular association with the progression of osteosarcoma have been previously discussed. We conducted the present study to examine the effect of lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) on osteosarcoma cell invasion and chemosensitivity to cisplatin (CDDP). After determination of the expression of Kcnq1 in osteosarcoma tissues and cells, the plasmids with overexpression or knockdown KCNQ1OT1 were introduced into the cells to aid the identification of cell proliferation, migration, invasion, chemosensitivity to CDDP, and apoptosis. Then, the interaction between KCNQ1OT1 and the Kcnq1/DNA methyltransferase 1 (DNMT1) axis was evaluated by measuring the level of Kcnq1 promoter region methylation and DNMT1 enrichment of the Kcnq1 promoter region. Low Kcnq1 expression and high KCNQ1OT1 expression were shown in osteosarcoma tissues and cells. Kcnq1 was negatively mediated by KCNQ1OT1 via DNMT1. The overexpression of Kcnq1 or knockdown of KCNQ1OT1 inhibited the proliferation, migration, and invasion, and it promoted the chemosensitivity to CDDP and apoptosis of MG-63 cells and its CDDP-resistant cell lines. Moreover, the same trend was observed in the cells following methylation inhibitor treatment. Collectively, knockdown of KCNQ1OT1 can inhibit the osteosarcoma progression through the Kcnq1/DNMT1 axis.
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Affiliation(s)
- Xu Qi
- Department of Neurology, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
| | - Xiao-Jun Yu
- The 1st Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
| | - Xu-Ming Wang
- The 1st Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
| | - Tie-Nan Song
- The 1st Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
| | - Jie Zhang
- The 1st Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
| | - Xin-Zhen Guo
- The 1st Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
| | - Guo-Jun Li
- The 1st Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
| | - Ming Shao
- The 1st Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China.
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55
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Georges A, Coyaud E, Marcon E, Greenblatt J, Raught B, Frappier L. USP7 Regulates Cytokinesis through FBXO38 and KIF20B. Sci Rep 2019; 9:2724. [PMID: 30804394 PMCID: PMC6389929 DOI: 10.1038/s41598-019-39368-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/18/2019] [Indexed: 01/13/2023] Open
Abstract
The ubiquitin specific protease 7 (USP7 or HAUSP) is known to regulate a variety of cellular processes by binding and deubiquitylating specific target proteins. To gain a more comprehensive understanding of its interactions and functions, we used affinity purification coupled to mass spectrometry to profile USP7 interactions. This revealed a novel interaction with FBXO38, a poorly characterized F-box protein. We showed that USP7 stabilizes FBXO38 dependent on its catalytic activity by protecting FBXO38 from proteasomal degradation. We used a BioID approach to profile the protein interactions (and putative functions) of FBXO38, revealing an interaction with KIF20B, a Kinesin-6 protein required for efficient cytokinesis. FBXO38 was shown to function independently from an SCF complex to stabilize KIF20B. Consequently, depletion of either FBXO38 or USP7 led to dramatic decreases in KIF20B levels and KIF20B at the midbody, which were manifested in cytokinetic defects. Furthermore, cytokinetic defects associated with USP7 silencing were rescued by restoring FBXO38 or KIF20B. The results indicate a novel mechanism of regulating cytokinesis through USP7 and FBXO38.
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Affiliation(s)
- Anna Georges
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Etienne Coyaud
- The Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre, University of Toronto, Toronto, Canada
| | - Brian Raught
- The Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lori Frappier
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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56
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USP7: Structure, substrate specificity, and inhibition. DNA Repair (Amst) 2019; 76:30-39. [PMID: 30807924 DOI: 10.1016/j.dnarep.2019.02.005] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/07/2019] [Indexed: 12/24/2022]
Abstract
Turnover of cellular proteins is regulated by Ubiquitin Proteasome System (UPS). Components of this pathway, including the proteasome, ubiquitinating enzymes and deubiquitinating enzymes, are highly specialized and tightly regulated. In this mini-review we focus on the de-ubiquitinating enzyme USP7, and summarize latest advances in understanding its structure, substrate specificity and relevance to human cancers. There is increasing interest in UPS components as targets for cancer therapy and here we also overview the recent progress in the development of small molecule inhibitors that target USP7.
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57
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Bowler EH, Bell J, Divecha N, Skipp P, Ewing RM. Proteomic Analysis of Azacitidine-Induced Degradation Profiles Identifies Multiple Chromatin and Epigenetic Regulators Including Uhrf1 and Dnmt1 as Sensitive to Azacitidine. J Proteome Res 2019; 18:1032-1042. [PMID: 30672294 DOI: 10.1021/acs.jproteome.8b00745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is a critical epigenetic modification that is established and maintained across the genome by DNA methyltransferase enzymes (Dnmts). Altered patterns of DNA methylation are a frequent occurrence in many tumor genomes, and inhibitors of Dnmts have become important epigenetic drugs. Azacitidine is a cytidine analog that is incorporated into DNA and induces the specific inhibition and proteasomal-mediated degradation of Dnmts. The downstream effects of azacitidine on CpG methylation and on gene transcription have been widely studied in many systems, but how azacitidine impacts the proteome is not well-understood. In addition, with its specific ability to induce the rapid degradation of Dnmts (in particular, the primary maintenance DNA methyltransferase, Dnmt1), it may be employed as a specific chemical knockdown for investigating the Dnmt1-associated functional or physical interactome. In this study, we use quantitative proteomics to analyze the degradation profile of proteins in the nuclear proteome of cells treated with azacitidine. We identify specific proteins as well as multiple pathways and processes that are impacted by azacitidine. The Dnmt1 interaction partner, Uhrf1, exhibits significant azacitidine-induced degradation, and this azacitidine-induced degradation is independent of the levels of Dnmt1 protein. We identify multiple other chromatin- and epigenetic-associated factors, including the bromodomain-containing transcriptional regulator, Brd2. We show that azacitidine induces highly specific perturbations of the Dnmt1-associated proteome, and while interaction partners such as Uhrf1 are sensitive to azacitidine, others such as the Dnmt1 interaction partner and stability regulator, Usp7, are not. In summary, we have conducted the first comprehensive proteomic analysis of the azacitidine-sensitive nuclear proteome, and we show how 5-azacitidine can be used as a specific probe to explore Dnmt- and chromatin-related protein networks.
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Affiliation(s)
- Emily H Bowler
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Joseph Bell
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Nullin Divecha
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Paul Skipp
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Rob M Ewing
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
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58
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Ren W, Gao L, Song J. Structural Basis of DNMT1 and DNMT3A-Mediated DNA Methylation. Genes (Basel) 2018; 9:genes9120620. [PMID: 30544982 PMCID: PMC6316889 DOI: 10.3390/genes9120620] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/30/2018] [Accepted: 12/04/2018] [Indexed: 01/01/2023] Open
Abstract
DNA methylation, one of the major epigenetic mechanisms, plays critical roles in regulating gene expression, genomic stability and cell lineage commitment. The establishment and maintenance of DNA methylation in mammals is achieved by two groups of DNA methyltransferases (DNMTs): DNMT3A and DNMT3B, which are responsible for installing DNA methylation patterns during gametogenesis and early embryogenesis, and DNMT1, which is essential for propagating DNA methylation patterns during replication. Both groups of DNMTs are multi-domain proteins, containing a large N-terminal regulatory region in addition to the C-terminal methyltransferase domain. Recent structure-function investigations of the individual domains or large fragments of DNMT1 and DNMT3A have revealed the molecular basis for their substrate recognition and specificity, intramolecular domain-domain interactions, as well as their crosstalk with other epigenetic mechanisms. These studies highlight a multifaceted regulation for both DNMT1 and DNMT3A/3B, which is essential for the precise establishment and maintenance of lineage-specific DNA methylation patterns in cells. This review summarizes current understanding of the structure and mechanism of DNMT1 and DNMT3A-mediated DNA methylation, with emphasis on the functional cooperation between the methyltransferase and regulatory domains.
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Affiliation(s)
- Wendan Ren
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
| | - Linfeng Gao
- Environmental Toxicology Program, University of California, Riverside, CA 92521, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
- Environmental Toxicology Program, University of California, Riverside, CA 92521, USA.
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59
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Shan H, Li X, Xiao X, Dai Y, Huang J, Song J, Liu M, Yang L, Lei H, Tong Y, Zhou L, Xu H, Wu Y. USP7 deubiquitinates and stabilizes NOTCH1 in T-cell acute lymphoblastic leukemia. Signal Transduct Target Ther 2018; 3:29. [PMID: 30370059 PMCID: PMC6202415 DOI: 10.1038/s41392-018-0028-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/29/2018] [Accepted: 09/12/2018] [Indexed: 02/05/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a highly aggressive leukemia that is primarily caused by aberrant activation of the NOTCH1 signaling pathway. Recent studies have revealed that posttranslational modifications, such as ubiquitination, regulate NOTCH1 stability, activity, and localization. However, the specific deubiquitinase that affects NOTCH1 protein stability remains unestablished. Here, we report that ubiquitin-specific protease 7 (USP7) can stabilize NOTCH1. USP7 deubiquitinated NOTCH1 in vivo and in vitro, whereas knockdown of USP7 increased the ubiquitination of NOTCH1. USP7 interacted with NOTCH1 protein in T-ALL cells, and the MATH and UBL domains of USP7 were responsible for this interaction. Depletion of USP7 significantly suppressed the proliferation of T-ALL cells in vitro and in vivo, accompanied by downregulation of the NOTCH1 protein level. Similarly, pharmacologic inhibition of USP7 led to apoptosis of T-ALL cells. More importantly, we found that USP7 was significantly upregulated in human T-ALL cell lines and patient samples, and a USP7 inhibitor exhibited cell cytotoxicity toward primary T-ALL cells, indicating the clinical relevance of these findings. Overall, our results demonstrate that USP7 is a novel deubiquitinase that stabilizes NOTCH1. Therefore, USP7 may be a promising therapeutic target in the currently incurable T-ALL. Inhibiting the protein ubiquitin-specific protease 7 (USP-7) may offer a treatment option for patients with T-cell acute lymphoblastic leukemia (T-ALL), an incurable and aggressive cancer. T-ALL is primarily caused by aberrant activation of the protein NOTCH1, which regulates gene expression relating to cell survival, proliferation, and metastasis. Ying-Li Wu, from China’s Shanghai Jiao Tong University School of Medicine, and a team of researchers report that, in their experiments, USP-7 prevented the breakdown of NOTCH1 by removing the protein tag that would normally signal it for degradation. In addition, USP-7 expression was upregulated in all human T-ALL cells and samples tested. Inhibition of USP-7 suppressed the proliferation of T-ALL cells in vitro and in vivo. These results reveal the role of USP-7 in the pathophysiology of T-ALL and offer USP-7 as a promising potential therapeutic target.
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Affiliation(s)
- Huizhuang Shan
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Xiangyun Li
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Xinhua Xiao
- 2Department of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, No.197, Ruijin Er Road, Shanghai, China
| | - Yuting Dai
- 2Department of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, No.197, Ruijin Er Road, Shanghai, China
| | - Jinyan Huang
- 2Department of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, No.197, Ruijin Er Road, Shanghai, China
| | - Junjun Song
- 3Shanghai University of Medicine & Health Sciences, No.279, Zhouzhu Road, Shanghai, China
| | - Meng Liu
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Li Yang
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Hu Lei
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Yin Tong
- 4Department of Hematology, Shanghai First People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 China
| | - Li Zhou
- 2Department of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, No.197, Ruijin Er Road, Shanghai, China
| | - Hanzhang Xu
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Yingli Wu
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
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60
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Georges A, Marcon E, Greenblatt J, Frappier L. Identification and Characterization of USP7 Targets in Cancer Cells. Sci Rep 2018; 8:15833. [PMID: 30367141 PMCID: PMC6203733 DOI: 10.1038/s41598-018-34197-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin specific protease, USP7, regulates multiple cellular pathways relevant for cancer through its ability to bind and sometimes stabilize specific target proteins through deubiquitylation. To gain a more complete profile of USP7 interactions in cancer cells, we performed affinity purification coupled to mass spectrometry to identify USP7 binding targets in gastric carcinoma cells. This confirmed reported associations of USP7 with USP11, PPM1G phosphatase and TRIP12 E3 ubiquitin ligase as well as identifying novel interactions with two DEAD/DEAH-box RNA helicases, DDX24 and DHX40. Using USP7 binding pocket mutants, we show that USP11, PPM1G, TRIP12 and DDX24 bind USP7 through its TRAF domain binding pocket, while DHX40 interacts with USP7 through a distinct binding pocket in the Ubl2 domain. P/A/ExxS motifs in USP11 and DDX24 that are critical for USP7 binding were also identified. Modulation of USP7 expression levels and inhibition of USP7 catalytic activity in multiple cells lines showed that USP7 consistently stabilizes DDX24, DHX40 and TRIP12 dependent on its catalytic activity, while USP11 and PPM1G levels were not consistently affected. Our study better defines the mechanisms of USP7 interaction with known targets and identifies DDX24 and DHX40 as new targets that are specifically bound and regulated by USP7.
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Affiliation(s)
- Anna Georges
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre, University of Toronto, Toronto, Canada
| | - Lori Frappier
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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61
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Gowher H, Jeltsch A. Mammalian DNA methyltransferases: new discoveries and open questions. Biochem Soc Trans 2018; 46:1191-1202. [PMID: 30154093 PMCID: PMC6581191 DOI: 10.1042/bst20170574] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 11/17/2022]
Abstract
As part of the epigenetic network, DNA methylation is a major regulator of chromatin structure and function. In mammals, it mainly occurs at palindromic CpG sites, but asymmetric methylation at non-CpG sites is also observed. Three enzymes are involved in the generation and maintenance of DNA methylation patterns. DNMT1 has high preference for hemimethylated CpG sites, and DNMT3A and DNMT3B equally methylate unmethylated and hemimethylated DNA, and also introduce non-CpG methylation. Here, we review recent observations and novel insights into the structure and function of mammalian DNMTs (DNA methyltransferases), including new structures of DNMT1 and DNMT3A, data on their mechanism, regulation by post-translational modifications and on the function of DNMTs in cells. In addition, we present news findings regarding the allosteric regulation and targeting of DNMTs by chromatin modifications and chromatin proteins. In combination, the recent publications summarized here impressively illustrate the intensity of ongoing research in this field. They provide a deeper understanding of key mechanistic properties of DNMTs, but they also document still unsolved issues, which need to be addressed in future research.
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Affiliation(s)
- Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
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Pajares MA, Pérez-Sala D. Mammalian Sulfur Amino Acid Metabolism: A Nexus Between Redox Regulation, Nutrition, Epigenetics, and Detoxification. Antioxid Redox Signal 2018; 29:408-452. [PMID: 29186975 DOI: 10.1089/ars.2017.7237] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE Transsulfuration allows conversion of methionine into cysteine using homocysteine (Hcy) as an intermediate. This pathway produces S-adenosylmethionine (AdoMet), a key metabolite for cell function, and provides 50% of the cysteine needed for hepatic glutathione synthesis. The route requires the intake of essential nutrients (e.g., methionine and vitamins) and is regulated by their availability. Transsulfuration presents multiple interconnections with epigenetics, adenosine triphosphate (ATP), and glutathione synthesis, polyol and pentose phosphate pathways, and detoxification that rely mostly in the exchange of substrates or products. Major hepatic diseases, rare diseases, and sensorineural disorders, among others that concur with oxidative stress, present impaired transsulfuration. Recent Advances: In contrast to the classical view, a nuclear branch of the pathway, potentiated under oxidative stress, is emerging. Several transsulfuration proteins regulate gene expression, suggesting moonlighting activities. In addition, abnormalities in Hcy metabolism link nutrition and hearing loss. CRITICAL ISSUES Knowledge about the crossregulation between pathways is mostly limited to the hepatic availability/removal of substrates and inhibitors. However, advances regarding protein-protein interactions involving oncogenes, identification of several post-translational modifications (PTMs), and putative moonlighting activities expand the potential impact of transsulfuration beyond methylations and Hcy. FUTURE DIRECTIONS Increasing the knowledge on transsulfuration outside the liver, understanding the protein-protein interaction networks involving these enzymes, the functional role of their PTMs, or the mechanisms controlling their nucleocytoplasmic shuttling may provide further insights into the pathophysiological implications of this pathway, allowing design of new therapeutic interventions. Antioxid. Redox Signal. 29, 408-452.
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Affiliation(s)
- María A Pajares
- 1 Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas (CSIC) , Madrid, Spain .,2 Molecular Hepatology Group, Instituto de Investigación Sanitaria La Paz (IdiPAZ) , Madrid, Spain
| | - Dolores Pérez-Sala
- 1 Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas (CSIC) , Madrid, Spain
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The Arginine Methyltransferase PRMT6 Regulates DNA Methylation and Contributes to Global DNA Hypomethylation in Cancer. Cell Rep 2018; 21:3390-3397. [PMID: 29262320 DOI: 10.1016/j.celrep.2017.11.082] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 09/27/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022] Open
Abstract
DNA methylation plays crucial roles in chromatin structure and gene expression. Aberrant DNA methylation patterns, including global hypomethylation and regional hypermethylation, are associated with cancer and implicated in oncogenic events. How DNA methylation is regulated in developmental and cellular processes and dysregulated in cancer is poorly understood. Here, we show that PRMT6, a protein arginine methyltransferase responsible for asymmetric dimethylation of histone H3 arginine 2 (H3R2me2a), negatively regulates DNA methylation and that PRMT6 upregulation contributes to global DNA hypomethylation in cancer. Mechanistically, PRMT6 overexpression impairs chromatin association of UHRF1, an accessory factor of DNMT1, resulting in passive DNA demethylation. The effect is likely due to elevated H3R2me2a, which inhibits the interaction between UHRF1 and histone H3. Our work identifies a mechanistic link between protein arginine methylation and DNA methylation, which is disrupted in cancer.
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64
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Yeasmin Khusbu F, Chen FZ, Chen HC. Targeting ubiquitin specific protease 7 in cancer: A deubiquitinase with great prospects. Cell Biochem Funct 2018; 36:244-254. [PMID: 29781103 DOI: 10.1002/cbf.3336] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/21/2018] [Accepted: 04/23/2018] [Indexed: 12/20/2022]
Abstract
Deubiquitinase (DUB)-mediated cleavage of ubiquitin chain balances ubiquitination and deubiquitination for determining protein fate. USP7 is one of the best characterized DUBs and functionally important. Numerous proteins have been identified as potential substrates and binding partners of USP7; those play crucial roles in diverse array of cellular and biological processes including tumour suppression, cell cycle, DNA repair, chromatin remodelling, and epigenetic regulation. This review aims at summarizing the current knowledge of this wide association of USP7 with many cellular processes that enlightens the possibility of abnormal USP7 activity in promoting oncogenesis and the importance of identification of specific inhibitors.
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Affiliation(s)
- Farjana Yeasmin Khusbu
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Fang-Zhi Chen
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Han-Chun Chen
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
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65
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Dan J, Rousseau P, Hardikar S, Veland N, Wong J, Autexier C, Chen T. Zscan4 Inhibits Maintenance DNA Methylation to Facilitate Telomere Elongation in Mouse Embryonic Stem Cells. Cell Rep 2018; 20:1936-1949. [PMID: 28834755 DOI: 10.1016/j.celrep.2017.07.070] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/20/2017] [Accepted: 07/25/2017] [Indexed: 11/30/2022] Open
Abstract
Proper telomere length is essential for embryonic stem cell (ESC) self-renewal and pluripotency. Mouse ESCs (mESCs) sporadically convert to a transient totipotent state similar to that of two-cell (2C) embryos to recover shortened telomeres. Zscan4, which exhibits a burst of expression in 2C-like mESCs, is required for telomere extension in these cells. However, the mechanism by which Zscan4 extends telomeres remains elusive. Here, we show that Zscan4 facilitates telomere elongation by inducing global DNA demethylation through downregulation of Uhrf1 and Dnmt1, major components of the maintenance DNA methylation machinery. Mechanistically, Zscan4 recruits Uhrf1 and Dnmt1 and promotes their degradation, which depends on the E3 ubiquitin ligase activity of Uhrf1. Blocking DNA demethylation prevents telomere elongation associated with Zscan4 expression, suggesting that DNA demethylation mediates the effect of Zscan4. Our results define a molecular pathway that contributes to the maintenance of telomere length homeostasis in mESCs.
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Affiliation(s)
- Jiameng Dan
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Philippe Rousseau
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Nicolas Veland
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Chantal Autexier
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada; Division of Experimental Medicine, Department of Anatomy and Cell Biology, McGill University, Montréal, Québec H3A 0C7, Canada
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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66
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Tsai TS, St John JC. The effects of mitochondrial DNA supplementation at the time of fertilization on the gene expression profiles of porcine preimplantation embryos. Mol Reprod Dev 2018; 85:490-504. [PMID: 29663563 DOI: 10.1002/mrd.22985] [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: 11/19/2017] [Accepted: 04/10/2018] [Indexed: 01/20/2023]
Abstract
Mitochondrial DNA (mtDNA) deficient metaphase II porcine oocytes are less likely to fertilize and more likely to arrest during preimplantation development. However, they can be supplemented with autologous populations of mitochondria at the time of fertilization, which significantly increases mtDNA copy number by the 2-cell stage due to the modulation of DNA methylation at a CpG island of the gene encoding the mtDNA-specific polymerase, POLG, and promotes preimplantation development. Although mitochondrial supplementation does not increase development rates or mtDNA copy number in oocytes with normal levels of mtDNA copy number, we tested whether this approach would also impact on chromosomal gene expression patterns in these oocytes at each stage of preimplantation development. Here, we have compared the gene expression profiles of embryos produced by mitochondrial supplementation at the time of fertilization with embryos produced by in vitro fertilization (IVF) using a panel of genes associated with different stages of preimplantation development. When compared to IVF-derived embryos, 27 (34%) genes were differentially expressed in supplemented embryos but this was restricted to one or two developmental stages. However, 53 (66%) genes were comparably expressed across all six stages and by the blastocyst stage 4 (5%) genes were differentially expressed. We conclude that additional copies of mtDNA can induce changes in gene expression at various stages of preimplantation development with the first changes occurring prior to maternal-to-zygotic transition (MZT). However, these changes appear to be transitory suggesting that some genomic resetting is taking place.
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Affiliation(s)
- Te-Sha Tsai
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, Australia.,Centre for Genetic Diseases, Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Justin C St John
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, Australia.,Centre for Genetic Diseases, Department of Molecular and Translational Science, Monash University, Clayton, Australia
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67
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Jing B, Liu M, Yang L, Cai HY, Chen JB, Li ZX, Kou X, Wu YZ, Qin DJ, Zhou L, Jin J, Lei H, Xu HZ, Wang WW, Wu YL. Characterization of naturally occurring pentacyclic triterpenes as novel inhibitors of deubiquitinating protease USP7 with anticancer activity in vitro. Acta Pharmacol Sin 2018; 39:492-498. [PMID: 29168472 PMCID: PMC5843828 DOI: 10.1038/aps.2017.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/21/2017] [Indexed: 12/23/2022] Open
Abstract
Deubiquitinating protease USP7 is a promising therapeutic target for cancer treatment, and interest in developing USP7 inhibitors has greatly increased. In the present study, we reported a series of natural pentacyclic triterpenes with USP7 inhibitory activity in vitro. Among them, both the ursane triterpenes and oleanane triterpenes were more active than the lupine triterpenes, whereas ursolic acid was the most potent with IC50 of 7.0±1.5 μmol/L. Molecular docking studies showed that ursolic acid might occupy the ubiquitin binding pocket of USP7, with the 17-carboxyl group and 3-hydroxyl group playing a vital role in the USP7-ursolic acid interaction. Using the cellular thermal shift assay, we demonstrated that ursolic acid interacted with USP7 in RPMI8226 human myeloma cells. Ursolic acid dose-dependently inhibited the proliferation of the myeloma cells with IC50 of 6.56 μmol/L, accompanied by reductions in USP7 substrates such as MDM2, UHRF1 and DNMT1. Overexpression of USP7 partially, but significantly attenuated ursolic acid-induced cell death as well as downregulation of MDM2, UHRF1 and DNMT1. In conclusion, we demonstrate for the first time that pentacyclic triterpenes represent a novel scaffold for developing USP7 inhibitors and that USP7 inhibition contributes to the anti-cancer effect of ursolic acid.
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Affiliation(s)
- Bo Jing
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Meng Liu
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Li Yang
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Hai-yan Cai
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Jie-bo Chen
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Ze-xi Li
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Xi Kou
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Yun-zhao Wu
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Dong-jun Qin
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Li Zhou
- Department of Hematology, Rui-Jin
Hospital, Shanghai Jiao-Tong University School of Medicine,
Shanghai
200025, China
| | - Jin Jin
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Hu Lei
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Han-zhang Xu
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Wei-wei Wang
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
| | - Ying-li Wu
- Hongqiao International Institute of
Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology
Division of Shanghai Universities E-Institutes, Key Laboratory of Cell
Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao
Tong University School of Medicine, Shanghai
200025, China
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68
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LINE-1 hypomethylation is inversely correlated with UHRF1 overexpression in gastric cancer. Oncol Lett 2018; 15:6666-6670. [PMID: 29616129 DOI: 10.3892/ol.2018.8121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/13/2018] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is an important epigenetic modification that alters gene expression; DNA hypomethylation contributes to tumorigenesis through multiple processes. In the present study, the methylation of long interspersed element-1 (LINE-1) in 95 gastric cancer (GC) tissues and matched adjacent normal tissues was investigated by pyrosequencing. LINE-1 methylation was compared with the expression of ubiquitin-like with PHD and ring-finger protein 1 (UHRF1), an essential regulator of DNA methylation, using reverse transcription-quantitative polymerase chain reaction. Significant hypomethylation of LINE-1 and overexpression of UHRF1 were observed in GC tissues compared with the matched controls (P<0.001 and P=0.001, respectively). LINE-1 hypomethylation was inversely correlated with UHRF1 overexpression in GC tissues (r=-0.026, P=0.028). In addition, LINE-1 hypomethylation in GC was significantly associated with Lauren's histological classification, tumor differentiation and background intestinal metaplasia (P=0.014, P=0.042 and P=0.034, respectively). These results suggest that LINE-1 hypomethylation may be a potential biomarker for GC and it is indirectly regulated by UHRF1 overexpression.
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69
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Yarychkivska O, Tavana O, Gu W, Bestor TH. Independent functions of DNMT1 and USP7 at replication foci. Epigenetics Chromatin 2018; 11:9. [PMID: 29482658 PMCID: PMC5828336 DOI: 10.1186/s13072-018-0179-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/16/2018] [Indexed: 01/06/2023] Open
Abstract
Background It has been reported that USP7 (ubiquitin-specific protease 7) prevents ubiquitylation and degradation of DNA methyltransferase 1 (DNMT1) by direct binding of USP7 to the glycine-lysine (GK) repeats that join the N-terminal regulatory domain of DNMT1 to the C-terminal methyltransferase domain. The USP7-DNMT1 interaction was reported to be mediated by acetylation of lysine residues within the (GK) repeats. Results We found that DNMT1 is present at normal levels in mouse and human cells that contain undetectable levels of USP7. Substitution of the (GK) repeats by (GQ) repeats prevents lysine acetylation but does not affect the stability of DNMT1 or the ability of the mutant protein to restore genomic methylation levels when expressed in Dnmt1-null ES cells. Furthermore, both USP7 and PCNA are recruited to sites of DNA replication independently of the presence of DNMT1, and there is no evidence that DNMT1 is degraded in cycling cells after S phase. Conclusions Multiple lines of evidence indicate that homeostasis of DNMT1 in somatic cells is controlled primarily at the level of transcription and that interaction of USP7 with the (GK) repeats of DNMT1 is unlikely to play a major role in the stabilization of DNMT1 protein.
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Affiliation(s)
- Olya Yarychkivska
- Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, 701 W. 168th St, New York, NY, 10032, USA
| | - Omid Tavana
- Department of Pathology and Cell Biology, Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Wei Gu
- Department of Pathology and Cell Biology, Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Timothy H Bestor
- Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, 701 W. 168th St, New York, NY, 10032, USA.
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70
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Nakamura K, Baba Y, Kosumi K, Harada K, Shigaki H, Miyake K, Kiyozumi Y, Ohuchi M, Kurashige J, Ishimoto T, Iwatsuki M, Sakamoto Y, Yoshida N, Watanabe M, Nakao M, Baba H. UHRF1 regulates global DNA hypomethylation and is associated with poor prognosis in esophageal squamous cell carcinoma. Oncotarget 2018; 7:57821-57831. [PMID: 27507047 PMCID: PMC5295392 DOI: 10.18632/oncotarget.11067] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/19/2016] [Indexed: 01/27/2023] Open
Abstract
Background Global DNA hypomethylation contributes to oncogenesis through various mechanisms. The level of long interspersed nucleotide element-1 (LINE- 1) methylation is considered a surrogate marker of global DNA methylation, and is attracting interest as a good predictor of cancer prognosis. However, the mechanism how LINE-1 (global DNA) methylation is controlled in cancer cells remains to be fully elucidated. Ubiquitin-like with PHD and RING finger domain 1 (UHRF1) plays a crucial role in DNA methylation. UHRF1 is overexpressed in many cancers, and UHRF1 overexpression may be a mechanism underlying DNA hypomethylation in cancer cells. Nonetheless, the relationship between UHRF1, LINE-1 methylation level, and clinical outcome in esophageal squamous cell carcinoma (ESCC) remains unclear. Results In ESCC cell lines, vector-mediated UHRF1 overexpression caused global DNA (LINE-1) hypomethylation and, conversely, UHRF1 knockdown using siRNA increased the global DNA methylation level. In ESCC tissues, UHRF1 expression was significantly associated with LINE-1 methylation levels. Furthermore, UHRF1 overexpression correlated with poor prognosis in our cohort of 160 ESCC patients. Materials and Methods The relationships between UHRF1 expression and LINE-1 methylation level (i.e., global DNA methylation level) were investigated using ESCC tissues and cell lines. In addition, we examined the correlation between UHRF1 expression, LINE-1 methylation, and clinical outcome in patients with ESCC. Conclusions Our results suggest that UHRF1 is a key epigenetic regulator of DNA methylation and might be a potential target for cancer treatment.
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Affiliation(s)
- Kenichi Nakamura
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Keisuke Kosumi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Kazuto Harada
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Hironobu Shigaki
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Keisuke Miyake
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Yuki Kiyozumi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Mayuko Ohuchi
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Junji Kurashige
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Takatsugu Ishimoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Masaaki Iwatsuki
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Yasuo Sakamoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
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Ashraf W, Bronner C, Zaayter L, Ahmad T, Richert L, Alhosin M, Ibrahim A, Hamiche A, Mely Y, Mousli M. Interaction of the epigenetic integrator UHRF1 with the MYST domain of TIP60 inside the cell. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:188. [PMID: 29268763 PMCID: PMC5740878 DOI: 10.1186/s13046-017-0659-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/04/2017] [Indexed: 12/17/2022]
Abstract
Background The nuclear epigenetic integrator UHRF1 is known to play a key role with DNMT1 in maintaining the DNA methylation patterns during cell division. Among UHRF1 partners, TIP60 takes part in epigenetic regulations through its acetyltransferase activity. Both proteins are involved in multiple cellular functions such as chromatin remodeling, DNA damage repair and regulation of stability and activity of other proteins. The aim of this work was to investigate the interaction between UHRF1 and TIP60 in order to elucidate the dialogue between these two proteins. Methods Biochemical (immunoprecipitation and pull-down assays) and microscopic (confocal and fluorescence lifetime imaging microscopy; FLIM) techniques were used to analyze the interaction between TIP60 and UHRF1 in vitro and in vivo. Global methylation levels were assessed by using a specific kit. The results were statistically analyzed using Graphpad prism and Origin. Results Our study shows that UHRF1, TIP60 and DNMT1 were found in the same epigenetic macro-molecular complex. In vitro pull-down assay showed that deletion of either the zinc finger in MYST domain or deletion of whole MYST domain from TIP60 significantly reduced its interaction with UHRF1. Confocal and FLIM microscopy showed that UHRF1 co-localized with TIP60 in the nucleus and confirmed that both proteins interacted together through the MYST domain of TIP60. Moreover, overexpression of TIP60 reduced the DNA methylation levels in HeLa cells along with downregulation of UHRF1 and DNMT1. Conclusion Our data demonstrate for the first time that TIP60 through its MYST domain directly interacts with UHRF1 which might be of high interest for the development of novel oncogenic inhibitors targeting this interaction.
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Affiliation(s)
- Waseem Ashraf
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Christian Bronner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - Liliyana Zaayter
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Tanveer Ahmad
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Ludovic Richert
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Mahmoud Alhosin
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulkhaleg Ibrahim
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch, France.,BioTechnology Research Center (BTRC), Tripoli, Libya
| | - Ali Hamiche
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - Yves Mely
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France
| | - Marc Mousli
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401, Illkirch Cedex, France.
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72
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Yoon JH, You BH, Park CH, Kim YJ, Nam JW, Lee SK. The long noncoding RNA LUCAT1 promotes tumorigenesis by controlling ubiquitination and stability of DNA methyltransferase 1 in esophageal squamous cell carcinoma. Cancer Lett 2017; 417:47-57. [PMID: 29247823 DOI: 10.1016/j.canlet.2017.12.016] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022]
Abstract
Available targeted therapies for esophageal squamous cell carcinoma (ESCC) are limited; thus, further genetic and epigenetic studies are needed. Recently, many long noncoding RNAs (lncRNAs) have been reported to be involved in various cancers. Here, we investigated whether the lncRNA LUCAT1 was related to the carcinogenesis of ESCC based on previous studies in lung cancer. LUCAT1 was significantly upregulated in ESCC cell lines and cancer tissue compared with normal cells and adjacent normal tissues. LUCAT1 knockdown reduced cell proliferation, induced apoptosis, and upregulated tumor-suppressor genes by reducing DNA methylation in KYSE-30 cells. Moreover, LUCAT1 siRNA reduced DNA methyltransferase 1 (DNMT1) protein levels without affecting transcription. Patients with high LUCAT1 expression had significantly lower survival rates than patients with low LUCAT1 expression. Our results thus suggest that LUCAT1 regulates the stability of DNMT1 and inhibits the expression of tumor suppressors through DNA methylation, leading to the formation and metastasis of ESCC. We identified LUCAT1 as a potential target for drug development and as a biomarker for ESCC.
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Affiliation(s)
- Jung-Ho Yoon
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Republic of Korea
| | - Bo-Hyun You
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Republic of Korea
| | - Chan Hyuk Park
- Division of Gastroenterology, Institute of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Yeong Jin Kim
- Division of Gastroenterology, Institute of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Republic of Korea; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133791, Republic of Korea
| | - Sang Kil Lee
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Republic of Korea; Division of Gastroenterology, Institute of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea.
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73
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Ubiquitome Analysis Reveals PCNA-Associated Factor 15 (PAF15) as a Specific Ubiquitination Target of UHRF1 in Embryonic Stem Cells. J Mol Biol 2017; 429:3814-3824. [DOI: 10.1016/j.jmb.2017.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/26/2017] [Accepted: 10/12/2017] [Indexed: 12/30/2022]
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74
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Kim RQ, Sixma TK. Regulation of USP7: A High Incidence of E3 Complexes. J Mol Biol 2017; 429:3395-3408. [DOI: 10.1016/j.jmb.2017.05.028] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/26/2017] [Accepted: 05/30/2017] [Indexed: 01/03/2023]
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75
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Choudhry H, Zamzami MA, Omran Z, Wu W, Mousli M, Bronner C, Alhosin M. Targeting microRNA/UHRF1 pathways as a novel strategy for cancer therapy. Oncol Lett 2017; 15:3-10. [PMID: 29285183 PMCID: PMC5738699 DOI: 10.3892/ol.2017.7290] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022] Open
Abstract
Ubiquitin-like containing plant homeodomain and RING finger domains 1 (UHRF1) is an anti-apoptotic protein involved in the silencing of several tumor suppressor genes (TSGs) through epigenetic modifications including DNA methylation and histone post-translational alterations, and also epigenetic-independent mechanisms. UHRF1 overexpression is observed in a number of solid tumors and hematological malignancies, and is considered a primary mechanism in inhibiting apoptosis. UHRF1 exerts its inhibitory activity on TSGs by binding to functional domains and therefore influences several epigenetic actors including DNA methyltransferase, histone deacetylase 1, histone acetyltransferase Tat-interacting protein 60 and histone methyltransferases G9a and Suv39H1. UHRF1 is considered to control a large macromolecular protein complex termed epigenetic code replication machinery, in order to maintain epigenetic silencing of TSGs during cell division, thus enabling cancer cells to escape apoptosis. MicroRNAs (miRNAs) are able to regulate the expression of its target gene by functioning as either an oncogene or a tumor suppressor. In the present review, the role of tumor suppressive miRNAs in the regulation of UHRF1, and the importance of targeting the microRNA/UHRF1 pathways in order to induce the reactivation of silenced TSGs and subsequent apoptosis are discussed.
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Affiliation(s)
- Hani Choudhry
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ziad Omran
- College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Marc Mousli
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, 67401 Illkirch Cedex, France
| | - Christian Bronner
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), National Institute of Health and Medical Research U964, National Center for Scientific Research UMR7104, University of Strasbourg, 67404 Illkirch Cedex, France
| | - Mahmoud Alhosin
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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76
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Ye J, Zhang Y, Liang W, Huang J, Wang L, Zhong X. UHRF1 is an Independent Prognostic Factor and a Potential Therapeutic Target of Esophageal Squamous Cell Carcinoma. J Cancer 2017; 8:4027-4039. [PMID: 29187878 PMCID: PMC5706005 DOI: 10.7150/jca.21256] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/10/2017] [Indexed: 12/15/2022] Open
Abstract
Purpose: Ubiquitin-like with plant homeodomain and ring-finger domains 1 (UHRF1) plays an essential role in DNA methylation, and the overexpression of UHRF1 is associated with poor prognosis in various cancers. Esophageal squamous cell carcinoma (ESCC) accounts for approximately 90% of esophageal cancer cases in China, but the five-year survival rate for patients is less than 10% due to limited clinical approaches for early diagnosis and treatment. The present research aimed to investigate the expression of UHRF1 in ESCC and its biological role in ESCC development. Methods: UHRF1 expression in ESCC and normal esophageal tissues was examined using immunohistochemical staining, followed by analysis of the correlation between UHRF1 expression and clinical features. In addition, the effects of lentivirus-mediated RNA interference of UHRF1 on global DNA methylation, cell proliferation, cell cycle progression and apoptosis and were investigated in ESCC cells. Results: UHRF1 was overexpressed in ESCC tissues and was an independent prognostic factor for ESCC patients. In ESCC cells, knockdown of UHRF1 caused global DNA hypomethylation, inhibited cell proliferation and induced apoptosis. Furthermore, UHRF1 depletion induced cell cycle arrest at the G2/M phase, accompanied by activation of Wee1 and DNA damage response pathway. Conclusions: Our findings identify UHRF1 as a promising prognostic marker for ESCC and suggest that UHRF1 may be a potential therapy target for ESCC patients with elevated UHRF1 expression.
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Affiliation(s)
- Jiecheng Ye
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Yong Zhang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weiye Liang
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Jianxian Huang
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Lihui Wang
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Xueyun Zhong
- Department of Pathology, Medical College, Jinan University, Guangzhou 510632, China.,Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
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77
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Lamberto I, Liu X, Seo HS, Schauer NJ, Iacob RE, Hu W, Das D, Mikhailova T, Weisberg EL, Engen JR, Anderson KC, Chauhan D, Dhe-Paganon S, Buhrlage SJ. Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7. Cell Chem Biol 2017; 24:1490-1500.e11. [PMID: 29056421 DOI: 10.1016/j.chembiol.2017.09.003] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/09/2017] [Accepted: 09/05/2017] [Indexed: 01/30/2023]
Abstract
Deubiquitinating enzymes (DUBs) have garnered significant attention as drug targets in the last 5-10 years. The excitement stems in large part from the powerful ability of DUB inhibitors to promote degradation of oncogenic proteins, especially proteins that are challenging to directly target but which are stabilized by DUB family members. Highly optimized and well-characterized DUB inhibitors have thus become highly sought after tools. Most reported DUB inhibitors, however, are polypharmacological agents possessing weak (micromolar) potency toward their primary target, limiting their utility in target validation and mechanism studies. Due to a lack of high-resolution DUB⋅small-molecule ligand complex structures, no structure-guided optimization efforts have been reported for a mammalian DUB. Here, we report a small-molecule⋅ubiquitin-specific protease (USP) family DUB co-structure and rapid design of potent and selective inhibitors of USP7 guided by the structure. Interestingly, the compounds are non-covalent active-site inhibitors.
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Affiliation(s)
- Ilaria Lamberto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xiaoxi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathan J Schauer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Wanyi Hu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deepika Das
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tatiana Mikhailova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dharminder Chauhan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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78
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Ludwig AK, Zhang P, Hastert FD, Meyer S, Rausch C, Herce HD, Müller U, Lehmkuhl A, Hellmann I, Trummer C, Storm C, Leonhardt H, Cardoso MC. Binding of MBD proteins to DNA blocks Tet1 function thereby modulating transcriptional noise. Nucleic Acids Res 2017; 45:2438-2457. [PMID: 27923996 PMCID: PMC5389475 DOI: 10.1093/nar/gkw1197] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/20/2016] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a hallmark of various human disorders, indicating that the spatial and temporal regulation of methylation readers and modifiers is imperative for development and differentiation. In particular, the cross-regulation between 5-methylcytosine binders (MBD) and modifiers (Tet) has not been investigated. Here, we show that binding of Mecp2 and Mbd2 to DNA protects 5-methylcytosine from Tet1-mediated oxidation. The mechanism is not based on competition for 5-methylcytosine binding but on Mecp2 and Mbd2 directly restricting Tet1 access to DNA. We demonstrate that the efficiency of this process depends on the number of bound MBDs per DNA molecule. Accordingly, we find 5-hydroxymethylcytosine enriched at heterochromatin of Mecp2-deficient neurons of a mouse model for Rett syndrome and Tet1-induced reexpression of silenced major satellite repeats. These data unveil fundamental regulatory mechanisms of Tet enzymes and their potential pathophysiological role in Rett syndrome. Importantly, it suggests that Mecp2 and Mbd2 have an essential physiological role as guardians of the epigenome.
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Affiliation(s)
- Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Stephanie Meyer
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Henry D Herce
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Udo Müller
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Carina Trummer
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Christian Storm
- Chemical Plant Ecology, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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79
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Zhang P, Rausch C, Hastert FD, Boneva B, Filatova A, Patil SJ, Nuber UA, Gao Y, Zhao X, Cardoso MC. Methyl-CpG binding domain protein 1 regulates localization and activity of Tet1 in a CXXC3 domain-dependent manner. Nucleic Acids Res 2017; 45:7118-7136. [PMID: 28449087 PMCID: PMC5499542 DOI: 10.1093/nar/gkx281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 03/30/2017] [Accepted: 04/06/2017] [Indexed: 12/20/2022] Open
Abstract
Cytosine modifications diversify and structure the genome thereby controlling proper development and differentiation. Here, we focus on the interplay of the 5-methylcytosine reader Mbd1 and modifier Tet1 by analyzing their dynamic subcellular localization and the formation of the Tet oxidation product 5-hydroxymethylcytosine in mammalian cells. Our results demonstrate that Mbd1 enhances Tet1-mediated 5-methylcytosine oxidation. We show that this is due to enhancing the localization of Tet1, but not of Tet2 and Tet3 at heterochromatic DNA. We find that the recruitment of Tet1 and concomitantly its catalytic activity eventually leads to the displacement of Mbd1 from methylated DNA. Finally, we demonstrate that increased Tet1 heterochromatin localization and 5-methylcytosine oxidation are dependent on the CXXC3 domain of Mbd1, which recognizes unmethylated CpG dinucleotides. The Mbd1 CXXC3 domain deletion isoform, which retains only binding to methylated CpGs, on the other hand, blocks Tet1-mediated 5-methylcytosine to 5-hydroxymethylcytosine conversion, indicating opposite biological effects of Mbd1 isoforms. Our study provides new insights on how cytosine modifications, their modifiers and readers cross-regulate themselves.
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Affiliation(s)
- Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian D. Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Boyana Boneva
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Alina Filatova
- Stem Cell and Developmental Biology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sujit J. Patil
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Ulrike A. Nuber
- Stem Cell and Developmental Biology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Yu Gao
- Waisman Center & Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Xinyu Zhao
- Waisman Center & Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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80
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Jiang L, Xiong J, Zhan J, Yuan F, Tang M, Zhang C, Cao Z, Chen Y, Lu X, Li Y, Wang H, Wang L, Wang J, Zhu WG, Wang H. Ubiquitin-specific peptidase 7 (USP7)-mediated deubiquitination of the histone deacetylase SIRT7 regulates gluconeogenesis. J Biol Chem 2017; 292:13296-13311. [PMID: 28655758 DOI: 10.1074/jbc.m117.780130] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Sirtuin 7 (SIRT7), a member of the NAD+-dependent class III histone deacetylases, is involved in the regulation of various cellular processes and in resisting various stresses, such as hypoxia, low glucose levels, and DNA damage. Interestingly, SIRT7 is linked to the control of glycolysis, suggesting a role in glucose metabolism. Given the important roles of SIRT7, it is critical to clarify how SIRT7 activity is potentially regulated. It has been reported that some transcriptional and post-transcriptional regulatory mechanisms are involved. However, little is known how SIRT7 is regulated by the post-translational modifications. Here, we identified ubiquitin-specific peptidase 7 (USP7), a deubiquitinase, as a negative regulator of SIRT7. We showed that USP7 interacts with SIRT7 both in vitro and in vivo, and we further demonstrated that SIRT7 undergoes endogenous Lys-63-linked polyubiquitination, which is removed by USP7. Although the USP7-mediated deubiquitination of SIRT7 had no effect on its stability, the deubiquitination repressed its enzymatic activity. We also showed that USP7 coordinates with SIRT7 to regulate the expression of glucose-6-phosphatase catalytic subunit (G6PC), a gluconeogenic gene. USP7 depletion by RNA interference increased both G6PC expression and SIRT7 enzymatic activity. Moreover, SIRT7 targeted the G6PC promoter through the transcription factor ELK4 but not through forkhead box O1 (FoxO1). In summary, SIRT7 is a USP7 substrate and has a novel role as a regulator of gluconeogenesis. Our study may provide the basis for new clinical approaches to treat metabolic disorders related to glucose metabolism.
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Affiliation(s)
- Lu Jiang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Jiannan Xiong
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Junsi Zhan
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Fengjie Yuan
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Ming Tang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Chaohua Zhang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Ziyang Cao
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Yongcan Chen
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Xiaopeng Lu
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Yinglu Li
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Hui Wang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Lina Wang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center
| | - Jiadong Wang
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191 and
| | - Wei-Guo Zhu
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, .,Peking-Tsinghua University Center for Life Science, and.,the Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Haiying Wang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Post-translational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center,
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81
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Smets M, Link S, Wolf P, Schneider K, Solis V, Ryan J, Meilinger D, Qin W, Leonhardt H. DNMT1 mutations found in HSANIE patients affect interaction with UHRF1 and neuronal differentiation. Hum Mol Genet 2017; 26:1522-1534. [PMID: 28334952 PMCID: PMC5393148 DOI: 10.1093/hmg/ddx057] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/09/2017] [Indexed: 12/26/2022] Open
Abstract
DNMT1 is recruited to substrate sites by PCNA and UHRF1 to maintain DNA methylation after replication. The cell cycle dependent recruitment of DNMT1 is mediated by the PCNA-binding domain (PBD) and the targeting sequence (TS) within the N-terminal regulatory domain. The TS domain was found to be mutated in patients suffering from hereditary sensory and autonomic neuropathies with dementia and hearing loss (HSANIE) and autosomal dominant cerebellar ataxia deafness and narcolepsy (ADCA-DN) and is associated with global hypomethylation and site specific hypermethylation. With functional complementation assays in mouse embryonic stem cells, we showed that DNMT1 mutations P496Y and Y500C identified in HSANIE patients not only impair DNMT1 heterochromatin association, but also UHRF1 interaction resulting in hypomethylation. Similar DNA methylation defects were observed when DNMT1 interacting domains in UHRF1, the UBL and the SRA domain, were deleted. With cell-based assays, we could show that HSANIE associated mutations perturb DNMT1 heterochromatin association and catalytic complex formation at methylation sites and decrease protein stability in late S and G2 phase. To investigate the neuronal phenotype of HSANIE mutations, we performed DNMT1 rescue assays and could show that cells expressing mutated DNMT1 were prone to apoptosis and failed to differentiate into neuronal lineage. Our results provide insights into the molecular basis of DNMT1 dysfunction in HSANIE patients and emphasize the importance of the TS domain in the regulation of DNA methylation in pluripotent and differentiating cells.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Heinrich Leonhardt
- To whom correspondence should be addressed. Tel: +49 89 218074232; Fax: +49 89 218074236;
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PIM1 induces cellular senescence through phosphorylation of UHRF1 at Ser311. Oncogene 2017; 36:4828-4842. [PMID: 28394343 DOI: 10.1038/onc.2017.96] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 01/23/2017] [Accepted: 02/26/2017] [Indexed: 12/13/2022]
Abstract
PIM1 is a proto-oncogene, encoding a serine/threonine protein kinase that regulates cell proliferation, survival, differentiation and apoptosis. Previous reports suggest that overexpression of PIM1 can induce cellular senescence. However, the molecular mechanism underlying this process is not fully understood. Here we report that UHRF1 is a novel substrate of PIM1 kinase, which could be phosphorylated at Ser311 and therefore promoted to degradation. Our data demonstrates that PIM1 destabilizes UHRF1, leading to DNA hypomethylation, which consequently results in genomic instability, increased p16 expression and subsequent induction of cellular senescence. Taken together, our results suggest that down-regulation of UHRF1 is an important mechanism of PIM1-mediated cellular senescence.
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83
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Misregulation of DNA Methylation Regulators in Cancer. DNA AND HISTONE METHYLATION AS CANCER TARGETS 2017. [DOI: 10.1007/978-3-319-59786-7_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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84
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Deoxycholic Acid Could Induce Apoptosis and Trigger Gastric Carcinogenesis on Gastric Epithelial Cells by Quantitative Proteomic Analysis. Gastroenterol Res Pract 2016; 2016:9638963. [PMID: 28070185 PMCID: PMC5192292 DOI: 10.1155/2016/9638963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/10/2016] [Accepted: 10/23/2016] [Indexed: 01/26/2023] Open
Abstract
Background. Pathologic duodenogastric reflux can induce or aggravate gastritis because of the presence of bile acids. Bile reflux has been generally considered to be associated with intestinal metaplasia and gastric cancer. However, the pathogenic mechanisms of the effects of bile acids on gastric mucosa are still unknown. Methods. To explore the mechanisms by which bile acids induce gastric mucosal lesions, we examined cell apoptosis in the gastric epithelial cell line GES-1 and investigated the changes in protein profiles of GES-1 cells in response to a bile acid deoxycholic acid using a proteomics approach. Changes in the profiles of the differently expressed proteins were analyzed using the DAVID and STRING programs. Results. We found apoptosis was significantly induced in GES-1 cells by deoxycholic acid. Using liquid chromatographic/tandem mass spectrometric (LC-MS/MS) methods, 134 upregulated proteins and 214 downregulated proteins were identified in the bile acid treated GES-1 cells. Bioinformatics analysis revealed the interactions and signaling networks of these differentially expressed proteins. Conclusion. These findings may improve the understanding of the molecular mechanisms underlying the pathogenicity of bile acids on gastric mucosa.
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85
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Alhosin M, Omran Z, Zamzami MA, Al-Malki AL, Choudhry H, Mousli M, Bronner C. Signalling pathways in UHRF1-dependent regulation of tumor suppressor genes in cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:174. [PMID: 27839516 PMCID: PMC5108085 DOI: 10.1186/s13046-016-0453-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/02/2016] [Indexed: 12/13/2022]
Abstract
Epigenetic silencing of tumor suppressor genes (TSGs) through DNA methylation and histone changes is a main hallmark of cancer. Ubiquitin-like with PHD and RING Finger domains 1 (UHRF1) is a potent oncogene overexpressed in various solid and haematological tumors and its high expression levels are associated with decreased expression of several TSGs including p16INK4A, BRCA1, PPARG and KiSS1. Using its several functional domains, UHRF1 creates a strong coordinated dialogue between DNA methylation and histone post-translation modification changes causing the epigenetic silencing of TSGs which allows cancer cells to escape apoptosis. To ensure the silencing of TSGs during cell division, UHRF1 recruits several enzymes including histone deacetylase 1 (HDAC1), DNA methyltransferase 1 (DNMT1) and histone lysine methyltransferases G9a and Suv39H1 to the right place at the right moment. Several in vitro and in vivo works have reported the direct implication of the epigenetic player UHRF1 in tumorigenesis through the repression of TSGs expression and suggested UHRF1 as a promising target for cancer treatment. This review describes the molecular mechanisms underlying UHRF1 regulation in cancer and discusses its importance as a therapeutic target to induce the reactivation of TSGs and subsequent apoptosis.
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Affiliation(s)
- Mahmoud Alhosin
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia. .,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia. .,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia. .,Biochemistry Department, Faculty of Sciences, Cancer and Mutagenesis Unit, King Fahd Centre for Medical Research, King Abdulaziz University, P. O. Box 80203, Jeddah, 21589, Saudi Arabia.
| | - Ziad Omran
- College of Pharmacy, Umm Al-Qura University, 21955, Makkah, Kingdom of Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulrahman L Al-Malki
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marc Mousli
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Christian Bronner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.
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86
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Jin WL, Mao XY, Qiu GZ. Targeting Deubiquitinating Enzymes in Glioblastoma Multiforme: Expectations and Challenges. Med Res Rev 2016; 37:627-661. [PMID: 27775833 DOI: 10.1002/med.21421] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/06/2016] [Accepted: 09/25/2016] [Indexed: 12/16/2022]
Abstract
Glioblastoma (GBM) is regarded as the most common primary intracranial neoplasm. Despite standard treatment with tumor resection and radiochemotherapy, the outcome remains gloomy. It is evident that a combination of oncogenic gain of function and tumor-suppressive loss of function has been attributed to glioma initiation and progression. The ubiquitin-proteasome system is a well-orchestrated system that controls the fate of most proteins by striking a dynamic balance between ubiquitination and deubiquitination of substrates, having a profound influence on the modulation of oncoproteins, tumor suppressors, and cellular signaling pathways. In recent years, deubiquitinating enzymes (DUBs) have emerged as potential anti-cancer targets due to their targeting several key proteins involved in the regulation of tumorigenesis, apoptosis, senescence, and autophagy. This review attempts to summarize recent studies of GBM-associated DUBs, their roles in various cellular processes, and discuss the relation between DUBs deregulation and gliomagenesis, especially how DUBs regulate glioma stem cells pluripotency, microenvironment, and resistance of radiation and chemotherapy through core stem-cell transcriptional factors. We also review recent achievements and progress in the development of potent and selective reversible inhibitors of DUBs, and attempted to find a potential GBM treatment by DUBs intervention.
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Affiliation(s)
- Wei-Lin Jin
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, Key Laboratory for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electronic Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China.,National Centers for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xiao-Yuan Mao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, P. R. China
| | - Guan-Zhong Qiu
- Department of Neurosurgery, General Hospital of Jinan Military Command, Jinan, 250031, P. R. China
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87
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Papageorgiou DN, Karkoulia E, Amaral-Psarris A, Burda P, Kolodziej K, Demmers J, Bungert J, Stopka T, Strouboulis J. Distinct and overlapping DNMT1 interactions with multiple transcription factors in erythroid cells: Evidence for co-repressor functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1515-1526. [PMID: 27693117 DOI: 10.1016/j.bbagrm.2016.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 01/14/2023]
Abstract
DNMT1 is the maintenance DNA methyltransferase shown to be essential for embryonic development and cellular growth and differentiation in many somatic tissues in mammals. Increasing evidence has also suggested a role for DNMT1 in repressing gene expression through interactions with specific transcription factors. Previously, we identified DNMT1 as an interacting partner of the TR2/TR4 nuclear receptor heterodimer in erythroid cells, implicated in the developmental silencing of fetal β-type globin genes in the adult stage of human erythropoiesis. Here, we extended this work by using a biotinylation tagging approach to characterize DNMT1 protein complexes in mouse erythroleukemic cells. We identified novel DNMT1 interactions with several hematopoietic transcription factors with essential roles in erythroid differentiation, including GATA1, GFI-1b and FOG-1. We provide evidence for DNMT1 forming distinct protein subcomplexes with specific transcription factors and propose the existence of a "core" DNMT1 complex with the transcription factors ZBP-89 and ZNF143, which is also present in non-hematopoietic cells. Furthermore, we identified the short (17a.a.) PCNA Binding Domain (PBD) located near the N-terminus of DNMT1 as being necessary for mediating interactions with the transcription factors described herein. Lastly, we provide evidence for DNMT1 serving as a co-repressor of ZBP-89 and GATA1 acting through upstream regulatory elements of the PU.1 and GATA1 gene loci.
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Affiliation(s)
- Dimitris N Papageorgiou
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Elena Karkoulia
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Alexandra Amaral-Psarris
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Pavel Burda
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Katarzyna Kolodziej
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jeroen Demmers
- Proteomics Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Tomas Stopka
- Biocev, 1st Medical Faculty, Charles University, Prague, Czech Republic
| | - John Strouboulis
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece.
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88
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Khan I, Senthilkumar CS, Upadhyay N, Singh H, Sachdeva M, Jatawa SK, Tiwari A. In silico docking of methyl isocyanate (MIC) and its hydrolytic product (1, 3-dimethylurea) shows significant interaction with DNA Methyltransferase 1 suggests cancer risk in Bhopal-Gas- Tragedy survivors. Asian Pac J Cancer Prev 2016; 16:7663-70. [PMID: 26625778 DOI: 10.7314/apjcp.2015.16.17.7663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
DNA methyltransferase 1 (DNMT1) is a relatively large protein family responsible for maintenance of normal methylation, cell growth and survival in mammals. Toxic industrial chemical exposure associated methylation misregulation has been shown to have epigenetic influence. Such misregulation could effectively contribute to cancer development and progression. Methyl isocyanate (MIC) is a noxious industrial chemical used extensively in the production of carbamate pesticides. We here applied an in silico molecular docking approach to study the interaction of MIC with diverse domains of DNMT1, to predict cancer risk in the Bhopal population exposed to MIC during 1984. For the first time, we investigated the interaction of MIC and its hydrolytic product (1,3-dimethylurea) with DNMT1 interacting (such as DMAP1, RFTS, and CXXC) and catalytic (SAM, SAH, and Sinefungin) domains using computer simulations. The results of the present study showed a potential interaction of MIC and 1,3-dimethylurea with these domains. Obviously, strong binding of MIC with DNMT1 interrupting normal methylation will lead to epigenetic alterations in the exposed humans. We suggest therefore that the MIC- exposed individuals surviving after 1984 disaster have excess risk of cancer, which can be attributed to alterations in their epigenome. Our findings will help in better understanding the underlying epigenetic mechanisms in humans exposed to MIC.
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Affiliation(s)
- Inbesat Khan
- School of Biotechnology, Rajiv Gandhi Technological University, Bhopal, India E-mail :
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89
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Jeltsch A, Jurkowska RZ. Allosteric control of mammalian DNA methyltransferases - a new regulatory paradigm. Nucleic Acids Res 2016; 44:8556-8575. [PMID: 27521372 PMCID: PMC5062992 DOI: 10.1093/nar/gkw723] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/08/2016] [Indexed: 12/23/2022] Open
Abstract
In mammals, DNA methylation is introduced by the DNMT1, DNMT3A and DNMT3B methyltransferases, which are all large multi-domain proteins containing a catalytic C-terminal domain and an N-terminal part with regulatory functions. Recently, two novel regulatory principles of DNMTs were uncovered. It was shown that their catalytic activity is under allosteric control of N-terminal domains with autoinhibitory function, the RFT and CXXC domains in DNMT1 and the ADD domain in DNMT3. Moreover, targeting and activity of DNMTs were found to be regulated in a concerted manner by interactors and posttranslational modifications (PTMs). In this review, we describe the structures and domain composition of the DNMT1 and DNMT3 enzymes, their DNA binding, catalytic mechanism, multimerization and the processes controlling their stability in cells with a focus on their regulation and chromatin targeting by PTMs, interactors and chromatin modifications. We propose that the allosteric regulation of DNMTs by autoinhibitory domains acts as a general switch for the modulation of the function of DNMTs, providing numerous possibilities for interacting proteins, nucleic acids or PTMs to regulate DNMT activity and targeting. The combined regulation of DNMT targeting and catalytic activity contributes to the precise spatiotemporal control of DNMT function and genome methylation in cells.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry, Pfaffenwaldring 55, Faculty of Chemistry, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- BioMed X Innovation Center, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
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90
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Pinto-Fernandez A, Kessler BM. DUBbing Cancer: Deubiquitylating Enzymes Involved in Epigenetics, DNA Damage and the Cell Cycle As Therapeutic Targets. Front Genet 2016; 7:133. [PMID: 27516771 PMCID: PMC4963401 DOI: 10.3389/fgene.2016.00133] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/12/2016] [Indexed: 12/21/2022] Open
Abstract
Controlling cell proliferation is one of the hallmarks of cancer. A number of critical checkpoints ascertain progression through the different stages of the cell cycle, which can be aborted when perturbed, for instance by errors in DNA replication and repair. These molecular checkpoints are regulated by a number of proteins that need to be present at the right time and quantity. The ubiquitin system has emerged as a central player controlling the fate and function of such molecules such as cyclins, oncogenes and components of the DNA repair machinery. In particular, proteases that cleave ubiquitin chains, referred to as deubiquitylating enzymes (DUBs), have attracted recent attention due to their accessibility to modulation by small molecules. In this review, we describe recent evidence of the critical role of DUBs in aspects of cell cycle checkpoint control, associated DNA repair mechanisms and regulation of transcription, representing pathways altered in cancer. Therefore, DUBs involved in these processes emerge as potentially critical targets for the treatment of not only hematological, but potentially also solid tumors.
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Affiliation(s)
- Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford, UK
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91
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Abstract
DNA replication is both highly conserved and controlled. Problematic DNA replication can lead to genomic instability and therefore carcinogenesis. Numerous mechanisms work together to achieve this tight control and increasing evidence suggests that post-translational modifications (phosphorylation, ubiquitination, SUMOylation) of DNA replication proteins play a pivotal role in this process. Here we discuss such modifications in the light of a recent article that describes a novel role for the deubiquitinase (DUB) USP7/HAUSP in the control of DNA replication. USP7 achieves this function by an unusual and novel mechanism, namely deubiquitination of SUMOylated proteins at the replication fork, making USP7 also a SUMO DUB (SDUB). This work extends previous observations of increased levels of SUMO and low levels of ubiquitin at the on-going replication fork. Here, we discuss this novel study, its contribution to the DNA replication and genomic stability field and what questions arise from this work.
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Affiliation(s)
- Veronique A J Smits
- Unidad de Investigación, Hosptial Universitario de Canarias, Instituto de Tecnologías Biomédicas, La Laguna, Tenerife, Spain
| | - Raimundo Freire
- Unidad de Investigación, Hosptial Universitario de Canarias, Instituto de Tecnologías Biomédicas, La Laguna, Tenerife, Spain
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92
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Lai M, Liang L, Chen J, Qiu N, Ge S, Ji S, Shi T, Zhen B, Liu M, Ding C, Wang Y, Qin J. Multidimensional Proteomics Reveals a Role of UHRF2 in the Regulation of Epithelial-Mesenchymal Transition (EMT). Mol Cell Proteomics 2016; 15:2263-78. [PMID: 27114453 DOI: 10.1074/mcp.m115.057448] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 01/07/2023] Open
Abstract
UHRF1 is best known for its positive role in the maintenance of DNMT1-mediated DNA methylation and is implicated in a variety of tumor processes. In this paper, we provided evidence to demonstrate a role of UHRF2 in cell motility and invasion through the regulation of the epithelial-mesenchymal transition (EMT) process by acting as a transcriptional co-regulator of the EMT-transcription factors (TFs). We ectopically expressed UHRF2 in gastric cancer cell lines and performed multidimensional proteomics analyses. Proteome profiling analysis suggested a role of UHRF2 in repression of cell-cell adhesion; analysis of proteome-wide TF DNA binding activities revealed the up-regulation of many EMT-TFs in UHRF2-overexpressing cells. These data suggest that UHRF2 is a regulator of cell motility and the EMT program. Indeed, cell invasion experiments demonstrated that silencing of UHRF2 in aggressive cells impaired their abilities of migration and invasion in vitro Further ChIP-seq identified UHRF2 genomic binding motifs that coincide with several TF binding motifs including EMT-TFs, and the binding of UHRF2 to CDH1 promoter was validated by ChIP-qPCR. Moreover, the interactome analysis with IP-MS uncovered the interaction of UHRF2 with TFs including TCF7L2 and several protein complexes that regulate chromatin remodeling and histone modifications, suggesting that UHRF2 is a transcription co-regulator for TFs such as TCF7L2 to regulate the EMT process. Taken together, our study identified a role of UHRF2 in EMT and tumor metastasis and demonstrated an effective approach to obtain clues of UHRF2 function without prior knowledge through combining evidence from multidimensional proteomics analyses.
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Affiliation(s)
- Mi Lai
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (Beijing); National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Lizhu Liang
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (Beijing); National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Jiwei Chen
- §Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, College of Life Science, East China Normal University, Shanghai, China
| | - Naiqi Qiu
- §Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, College of Life Science, East China Normal University, Shanghai, China
| | - Sai Ge
- ¶Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Shuhui Ji
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (Beijing); National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Tieliu Shi
- §Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, College of Life Science, East China Normal University, Shanghai, China
| | - Bei Zhen
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (Beijing); National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Mingwei Liu
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (Beijing); National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Chen Ding
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (Beijing); National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Yi Wang
- ‖Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Jun Qin
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (Beijing); National Engineering Research Center for Protein Drugs, Beijing 102206, China; ‖Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
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93
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USP7 is a SUMO deubiquitinase essential for DNA replication. Nat Struct Mol Biol 2016; 23:270-7. [PMID: 26950370 DOI: 10.1038/nsmb.3185] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 02/04/2016] [Indexed: 12/15/2022]
Abstract
Post-translational modification of proteins by ubiquitin (Ub) and Ub-like modifiers regulates DNA replication. We have previously shown that chromatin around replisomes is rich in SUMO and poor in Ub, whereas mature chromatin exhibits an opposite pattern. How this SUMO-rich, Ub-poor environment is maintained at sites of DNA replication in mammalian cells remains unexplored. Here we identify USP7 as a replisome-enriched SUMO deubiquitinase that is essential for DNA replication. By acting on SUMO and SUMOylated proteins, USP7 counteracts their ubiquitination. Inhibition or genetic deletion of USP7 leads to the accumulation of Ub on SUMOylated proteins, which are displaced away from replisomes. Our findings provide a model explaining the differential accumulation of SUMO and Ub at replication forks and identify an essential role of USP7 in DNA replication that should be considered in the development of USP7 inhibitors as anticancer agents.
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94
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Kent B, Magnani E, Walsh MJ, Sadler KC. UHRF1 regulation of Dnmt1 is required for pre-gastrula zebrafish development. Dev Biol 2016; 412:99-113. [PMID: 26851214 DOI: 10.1016/j.ydbio.2016.01.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 12/16/2022]
Abstract
Landmark epigenetic events underlie early embryonic development, yet how epigenetic modifiers are regulated to achieve rapid epigenome re-patterning is not known. Uhrf1 and DNA methyltransferase 1 (Dnmt1) are known to largely mediate maintenance DNA methylation and Uhrf1 is also required for both Dnmt1 localization and stability. Here, we investigate how these two key epigenetic modifiers regulate early zebrafish development and characterize the developmental consequences of disrupting their homeostatic relationship. Unlike Uhrf1 knockdown, which causes developmental arrest and death prior to gastrulation, overexpression of human UHRF1 (WT-UHRF1) caused asymmetric epiboly, inefficient gastrulation and multi-systemic defects. UHRF1 phosphorylation was previously demonstrated as essential for zebrafish embryogenesis, and we found that penetrance of the asymmetric epiboly phenotype was significantly increased in embryos injected with mRNA encoding non-phosphorylatable UHRF1 (UHRF1(S661A)). Surprisingly, both WT-UHRF1 and UHRF1(S661A) overexpression caused DNA hypomethylation. However, since other approaches that caused an equivalent degree of DNA hypomethylation did not cause the asymmetric epiboly phenotype, we conclude that bulk DNA methylation is not the primary mechanism. Instead, UHRF1(S661A) overexpression resulted in accumulation of Dnmt1 protein and the overexpression of both WT and a catalytically inactive Dnmt1 phenocopied the assymetric epiboly phenotype. Dnmt1 knockdown suppressed the phenotype caused by UHRF1(S661A) overexpression, and Uhrf1 knockdown suppressed the effect of Dnmt1 overexpression. Therefore, we conclude that the interaction between these two proteins is the mechanism underlying the gastrulation defects. This indicates that Dnmt1 stability requires UHRF1 phosphorylation and that crosstalk between the proteins is essential for the function of these two important epigenetic regulators during gastrulation.
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Affiliation(s)
- Brandon Kent
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States
| | - Elena Magnani
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States
| | - Martin J Walsh
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States
| | - Kirsten C Sadler
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States.
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95
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Long noncoding RNA UPAT promotes colon tumorigenesis by inhibiting degradation of UHRF1. Proc Natl Acad Sci U S A 2016; 113:1273-8. [PMID: 26768845 DOI: 10.1073/pnas.1500992113] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Many long noncoding RNAs (lncRNAs) are reported to be dysregulated in human cancers and play critical roles in tumor development and progression. Furthermore, it has been reported that many lncRNAs regulate gene expression by recruiting chromatin remodeling complexes to specific genomic loci or by controlling transcriptional or posttranscriptional processes. Here we show that an lncRNA termed UPAT [ubiquitin-like plant homeodomain (PHD) and really interesting new gene (RING) finger domain-containing protein 1 (UHRF1) Protein Associated Transcript] is required for the survival and tumorigenicity of colorectal cancer cells. UPAT interacts with and stabilizes the epigenetic factor UHRF1 by interfering with its β-transducin repeat-containing protein (TrCP)-mediated ubiquitination. Furthermore, we demonstrate that UHRF1 up-regulates Stearoyl-CoA desaturase 1 and Sprouty 4, which are required for the survival of colon tumor cells. Our study provides evidence for an lncRNA that regulates protein ubiquitination and degradation and thereby plays a critical role in the survival and tumorigenicity of tumor cells. Our results suggest that UPAT and UHRF1 may be promising molecular targets for the therapy of colon cancer.
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96
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Zhang H, Liu H, Chen Y, Yang X, Wang P, Liu T, Deng M, Qin B, Correia C, Lee S, Kim J, Sparks M, Nair AA, Evans DL, Kalari KR, Zhang P, Wang L, You Z, Kaufmann SH, Lou Z, Pei H. A cell cycle-dependent BRCA1-UHRF1 cascade regulates DNA double-strand break repair pathway choice. Nat Commun 2016; 7:10201. [PMID: 26727879 PMCID: PMC4728409 DOI: 10.1038/ncomms10201] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/13/2015] [Indexed: 01/07/2023] Open
Abstract
BRCA1 is an important mediator of the DNA damage response, which promotes homologous recombination (HR) and antagonizes 53BP1-dependent non-homologous end joining in S/G2 phase. But how this is achieved remains unclear. Here, we report that the E3 ubiquitin ligase UHRF1 (Ubiquitin-like, with PHD and RING finger domains 1) directly participates in the interplay between BRCA1 and 53BP1. Mechanistically, UHRF1 is recruited to DNA double-strand breaks (DSBs) by BRCA1 in S phase, which requires the BRCT domain of BRCA1 and phosphorylated Ser674 of UHRF1. Subsequently, UHRF1 mediates K63-linked polyubiquitination of RIF1, and results in its dissociation from 53BP1 and DSBs thereby facilitating HR initiation. Thus, UHRF1 is a key regulator of DSB repair choice, which is separate from its role in heterochromatin formation and epigenetic regulator. BRCA1 is a key regulator of DNA double-strand break repair, functioning to promote homologous recombination and repress non-homologous end-joining. Here the authors show that the ubiquitin ligase UHRF1 is recruited to breaks by BRCA1, where it targets RIF1 and thereby facilitates recombination.
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Affiliation(s)
- Haoxing Zhang
- School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hailong Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yali Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xu Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Panfei Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Tongzheng Liu
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Min Deng
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Bo Qin
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Cristina Correia
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Seungbaek Lee
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Jungjin Kim
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Melanie Sparks
- Department of Cell Biology and Physiology, Washington University, St Louis, Missouri 63130, USA
| | - Asha A Nair
- BSI-Genetics &Bioinformatics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Debra L Evans
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Krishna R Kalari
- BSI-Genetics &Bioinformatics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Pumin Zhang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Liewei Wang
- Molecular Pharmacology and Experimental therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University, St Louis, Missouri 63130, USA
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China.,Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA.,Molecular Pharmacology and Experimental therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Huadong Pei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
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97
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Dan J, Chen T. Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:123-150. [PMID: 27826837 DOI: 10.1007/978-3-319-43624-1_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cytosine methylation at the C5-position, generating 5-methylcytosine (5mC), is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80 %) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation levels and patterns are associated with various human diseases, including cancer and developmental disorders. DNA methylation is mediated by three active DNA methyltransferases (Dnmts), namely, Dnmt1, Dnmt3a, and Dnmt3b, in mammals. Over the last two decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and X-chromosome inactivation.
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Affiliation(s)
- Jiameng Dan
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Graduate School of Biomedical Sciences at Houston, Houston, TX, 77030, USA.
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98
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Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:87-122. [PMID: 27826836 DOI: 10.1007/978-3-319-43624-1_5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is currently one of the hottest topics in basic and biomedical research. Despite tremendous progress in understanding the structures and biochemical properties of the mammalian DNA nucleotide methyltransferases (DNMTs), principles of their regulation in cells have only begun to be uncovered. In mammals, DNA methylation is introduced by the DNMT1, DNMT3A, and DNMT3B enzymes, which are all large multi-domain proteins. These enzymes contain a catalytic C-terminal domain with a characteristic cytosine-C5 methyltransferase fold and an N-terminal part with different domains that interacts with other proteins and chromatin and is involved in targeting and regulation of the DNMTs. The subnuclear localization of the DNMT enzymes plays an important role in their biological function: DNMT1 is localized to replicating DNA via interaction with PCNA and UHRF1. DNMT3 enzymes bind to heterochromatin via protein multimerization and are targeted to chromatin by their ADD and PWWP domains. Recently, a novel regulatory mechanism has been discovered in DNMTs, as latest structural and functional data demonstrated that the catalytic activities of all three enzymes are under tight allosteric control of their N-terminal domains having autoinhibitory functions. This mechanism provides numerous possibilities for the precise regulation of the methyltransferases via controlling the binding and release of autoinhibitory domains by protein factors, noncoding RNAs, or by posttranslational modifications of the DNMTs. In this chapter, we summarize key enzymatic properties of DNMTs, including their specificity and processivity, and afterward we focus on the regulation of their activity and targeting via allosteric processes, protein interactors, and posttranslational modifications.
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Affiliation(s)
- Renata Z Jurkowska
- BioMed X Innovation Center, Im Neuenheimer Feld 583, Heidelberg, D-69120, Germany.
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, Stuttgart, D-70569, Germany.
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99
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Chernyavskaya Y, Kent B, Sadler KC. Zebrafish Discoveries in Cancer Epigenetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:169-97. [PMID: 27165354 DOI: 10.1007/978-3-319-30654-4_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cancer epigenome is fundamentally different than that of normal cells. How these differences arise in and contribute to carcinogenesis is not known, and studies using model organisms such as zebrafish provide an opportunity to address these important questions. Modifications of histones and DNA comprise the complex epigenome, and these influence chromatin structure, genome stability and gene expression, all of which are fundamental to the cellular changes that cause cancer. The cancer genome atlas covers the wide spectrum of genetic changes associated with nearly every cancer type, however, this catalog is currently uni-dimensional. As the pattern of epigenetic marks and chromatin structure in cancer cells is described and overlaid on the mutational landscape, the map of the cancer genome becomes multi-dimensional and highly complex. Two major questions remain in the field: (1) how the epigenome becomes repatterned in cancer and (2) which of these changes are cancer-causing. Zebrafish provide a tractable in vivo system to monitor the epigenome during transformation and to identify epigenetic drivers of cancer. In this chapter, we review principles of cancer epigenetics and discuss recent work using zebrafish whereby epigenetic modifiers were established as cancer driver genes, thus providing novel insights into the mechanisms of epigenetic reprogramming in cancer.
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Affiliation(s)
- Yelena Chernyavskaya
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA
| | - Brandon Kent
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA
- School of Biomedical Science, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA
| | - Kirsten C Sadler
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA.
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA.
- School of Biomedical Science, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA.
- Biology Program, New York University Abu Dhabi, Saadiyat Campus, 129188, Abu Dhabi, United Arab Emirates.
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100
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Tajima S, Suetake I, Takeshita K, Nakagawa A, Kimura H. Domain Structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:63-86. [PMID: 27826835 DOI: 10.1007/978-3-319-43624-1_4] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In mammals, three DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b, have been identified. Dnmt3a and Dnmt3b are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. Dnmt3-like (Dnmt3l), which is a member of the Dnmt3 family but does not possess DNA methylation activity, was reported to be indispensable for global methylation in germ cells. Once the DNA methylation patterns are established, maintenance-type DNA methyltransferase Dnmt1 faithfully propagates them to the next generation via replication. All Dnmts possess multiple domains, and in this chapter, the structures and functions of these domains are described.
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Affiliation(s)
- Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Isao Suetake
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- CREST/AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Kohei Takeshita
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- PRESTO/JST, Saitama, 332-0012, Japan
| | - Atsushi Nakagawa
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hironobu Kimura
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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