1
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Zhao H, Feng L, Cheng R, Wu M, Bai X, Fan L, Liu Y. miR-29c-3p acts as a tumor promoter by regulating β-catenin signaling through suppressing DNMT3A, TET1 and HBP1 in ovarian carcinoma. Cell Signal 2024; 113:110936. [PMID: 37925048 DOI: 10.1016/j.cellsig.2023.110936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023]
Abstract
Ovarian Carcinoma (OvCa) is characterized by rapid and sustained growth, activated invasion and metastasis. Studies have shown that microRNAs recruit and alter the expression of key regulators to modulate carcinogenesis. Here, we find that miR-29c-3p is increased in benign OvCa and malignant OvCa compared to normal ovary. Univariate and multivariate analyses report that miR-29c-3p overexpression is associated with poor prognosis in OvCa. Furthermore, we investigate that expression of miR-29c-3p is inversely correlated to DNA methyltransferase (DNMT) 3 A and Ten-Eleven-Translocation enzyme TET1. The high-throughput mRNA sequencing, bioinformatics analysis and pharmacological studies confirm that aberrant miR-29c-3p modulates tumorigenesis in OvCa cells, including epithelial-mesenchymal transition (EMT), proliferation, migration, and invasion. This modulation occurs through the regulation of β-catenin signaling by directly targeting 3'UTR of DNMT3A, TET1 and the HMG box transcription factor HBP1 and suppressing their expression. The further 3D spheres assay clearly shows the regulatory effects of miR-29c-3p on OvCa tumorigenesis. Additionally, the receiver operating characteristic (ROC) curve analysis of miR-29c-3p and the clinical detection/diagnostic biomarker CA125 suggests that miR-29c-3p may be conducive for clinical diagnosis or co-diagnosis of OvCa. These findings support miR-29c-3p functions as a tumor promoter by targeting its functional targets, providing new potential biomarker (s) for precision medicine strategies in OvCa.
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Affiliation(s)
- Haile Zhao
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, State Key Laboratory of Reproductive Regulation & Breeding of Grassland livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China
| | - Lijuan Feng
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, State Key Laboratory of Reproductive Regulation & Breeding of Grassland livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China
| | - Rui Cheng
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, State Key Laboratory of Reproductive Regulation & Breeding of Grassland livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China
| | - Man Wu
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, State Key Laboratory of Reproductive Regulation & Breeding of Grassland livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China
| | - Xiaozhou Bai
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, State Key Laboratory of Reproductive Regulation & Breeding of Grassland livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China
| | - Lifei Fan
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, State Key Laboratory of Reproductive Regulation & Breeding of Grassland livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010020, PR China.
| | - Yaping Liu
- Department of Gynecology and Obstetrics, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 010050, PR China.
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2
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Wang J, Catania S, Wang C, de la Cruz MJ, Rao B, Madhani HD, Patel DJ. Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance. Mol Cell 2022; 82:1186-1198.e6. [PMID: 35202575 PMCID: PMC8956514 DOI: 10.1016/j.molcel.2022.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 10/19/2022]
Abstract
Epigenetic evolution occurs over million-year timescales in Cryptococcus neoformans and is mediated by DNMT5, the first maintenance type cytosine methyltransferase identified in the fungal or protist kingdoms, the first dependent on adenosine triphosphate (ATP), and the most hemimethyl-DNA-specific enzyme known. To understand these novel properties, we solved cryo-EM structures of CnDNMT5 in three states. These studies reveal an elaborate allosteric cascade in which hemimethylated DNA binding first activates the SNF2 ATPase domain by a large rigid body rotation while the target cytosine partially flips out of the DNA duplex. ATP binding then triggers striking structural reconfigurations of the methyltransferase catalytic pocket to enable cofactor binding, completion of base flipping, and catalysis. Bound unmethylated DNA does not open the catalytic pocket and is instead ejected upon ATP binding, driving high fidelity. This unprecedented chaperone-like, enzyme-remodeling role of the SNF2 ATPase domain illuminates how energy is used to enable faithful epigenetic memory.
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Affiliation(s)
- Juncheng Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Sandra Catania
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chongyuan Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - M Jason de la Cruz
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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3
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Haggerty C, Kretzmer H, Riemenschneider C, Kumar AS, Mattei AL, Bailly N, Gottfreund J, Giesselmann P, Weigert R, Brändl B, Giehr P, Buschow R, Galonska C, von Meyenn F, Pappalardi MB, McCabe MT, Wittler L, Giesecke-Thiel C, Mielke T, Meierhofer D, Timmermann B, Müller FJ, Walter J, Meissner A. Dnmt1 has de novo activity targeted to transposable elements. Nat Struct Mol Biol 2021; 28:594-603. [PMID: 34140676 PMCID: PMC8279952 DOI: 10.1038/s41594-021-00603-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 05/10/2021] [Indexed: 02/06/2023]
Abstract
DNA methylation plays a critical role during development, particularly in repressing retrotransposons. The mammalian methylation landscape is dependent on the combined activities of the canonical maintenance enzyme Dnmt1 and the de novo Dnmts, 3a and 3b. Here, we demonstrate that Dnmt1 displays de novo methylation activity in vitro and in vivo with specific retrotransposon targeting. We used whole-genome bisulfite and long-read Nanopore sequencing in genetically engineered methylation-depleted mouse embryonic stem cells to provide an in-depth assessment and quantification of this activity. Utilizing additional knockout lines and molecular characterization, we show that the de novo methylation activity of Dnmt1 depends on Uhrf1, and its genomic recruitment overlaps with regions that enrich for Uhrf1, Trim28 and H3K9 trimethylation. Our data demonstrate that Dnmt1 can catalyze DNA methylation in both a de novo and maintenance context, especially at retrotransposons, where this mechanism may provide additional stability for long-term repression and epigenetic propagation throughout development.
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Affiliation(s)
- Chuck Haggerty
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Christina Riemenschneider
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Abhishek Sampath Kumar
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandra L Mattei
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Nina Bailly
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Judith Gottfreund
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Pay Giesselmann
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Raha Weigert
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Björn Brändl
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Christian-Albrechts-Universität zu Kiel, Department of Psychiatry and Psychotherapy, Kiel, Germany
| | - Pascal Giehr
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - René Buschow
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Christina Galonska
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Spatial Transcriptomics, Part of 10x Genomics Inc, Stockholm, Sweden
| | | | | | - Michael T McCabe
- Epigenetics Research Unit, Oncology R&D, GlaxoSmithKline, Collegeville, PA, USA
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Claudia Giesecke-Thiel
- Flow Cytometry Joint Facilities Scientific Service, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Joint Facilities Scientific Service, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Franz-Josef Müller
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Christian-Albrechts-Universität zu Kiel, Department of Psychiatry and Psychotherapy, Kiel, Germany
| | - Jörn Walter
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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4
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Das AB, Seddon AR, O'Connor KM, Hampton MB. Regulation of the epigenetic landscape by immune cell oxidants. Free Radic Biol Med 2021; 170:131-149. [PMID: 33444713 DOI: 10.1016/j.freeradbiomed.2020.12.453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
Excessive production of microbicidal oxidants by neutrophils can damage host tissue. The short-term response of cells to oxidative stress is well understood, but the mechanisms behind long-term consequences require further clarification. Epigenetic pathways mediate cellular adaptation, and are therefore a potential target of oxidative stress. Indeed, there is evidence that many proteins and metabolites involved in epigenetic pathways are redox sensitive. In this review we provide an overview of the epigenetic landscape and discuss the potential for redox regulation. Using this information, we highlight specific examples where neutrophil oxidants react with epigenetic pathway components. We also use published data from redox proteomics to map out known intersections between oxidative stress and epigenetics that may signpost helpful directions for future investigation. Finally, we discuss the role neutrophils play in adaptive pathologies with a focus on tumour initiation and progression. We hope this information will stimulate further discourse on the emerging field of redox epigenomics.
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Affiliation(s)
- Andrew B Das
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Annika R Seddon
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Karina M O'Connor
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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5
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Lu Y, Chan YT, Tan HY, Li S, Wang N, Feng Y. Epigenetic regulation in human cancer: the potential role of epi-drug in cancer therapy. Mol Cancer 2020; 19:79. [PMID: 32340605 PMCID: PMC7184703 DOI: 10.1186/s12943-020-01197-3] [Citation(s) in RCA: 225] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
Epigenetics is dynamic and heritable modifications to the genome that occur independently of DNA sequence. It requires interactions cohesively with various enzymes and other molecular components. Aberrant epigenetic alterations can lead to inappropriate onset of genetic expressions and promote tumorigenesis. As the epigenetic modifiers are susceptible to extrinsic factors and reversible, they are becoming promising targets in multiple cancer therapies. Recently, various epi-drugs have been developed and implicated in clinical use. The use of epi-drugs alone, or in combination with chemotherapy or immunotherapy, has shown compelling outcomes, including augmentation of anti-tumoral effects, overcoming drug resistance, and activation of host immune response.
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Affiliation(s)
- Yuanjun Lu
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Yau-Tuen Chan
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Hor-Yue Tan
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Sha Li
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Ning Wang
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China.
| | - Yibin Feng
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China.
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6
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Lin X, Pavani KC, Smits K, Deforce D, Heindryckx B, Van Soom A, Peelman L. Bta-miR-10b Secreted by Bovine Embryos Negatively Impacts Preimplantation Embryo Quality. Front Genet 2019; 10:757. [PMID: 31507632 PMCID: PMC6713719 DOI: 10.3389/fgene.2019.00757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/17/2019] [Indexed: 01/02/2023] Open
Abstract
In a previous study, we found miR-10b to be more abundant in a conditioned culture medium of degenerate embryos compared to that of blastocysts. Here, we show that miR-10b mimics added to the culture medium can be taken up by embryos. This uptake results in an increase in embryonic cell apoptosis and aberrant expression of DNA methyltransferases (DNMTs). Using several algorithms, Homeobox A1 (HOXA1) was identified as one of the potential miR-10b target genes and dual-luciferase assay confirmed HOXA1 as a direct target of miR-10b. Microinjection of si-HOXA1 into embryos also resulted in an increase in embryonic cell apoptosis and downregulation of DNMTs. Cell progression analysis using Madin–Darby bovine kidney cells (MDBKs) showed that miR-10b overexpression and HOXA1 knockdown results in suppressed cell cycle progression and decreased cell viability. Overall, this work demonstrates that miR-10b negatively influences embryo quality and might do this through targeting HOXA1 and/or influencing DNA methylation.
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Affiliation(s)
- Xiaoyuan Lin
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | | | - Katrien Smits
- Reproduction, Obstetrics and Herd Health, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Björn Heindryckx
- Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Ann Van Soom
- Reproduction, Obstetrics and Herd Health, Ghent University, Ghent, Belgium
| | - Luc Peelman
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
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7
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Wang QM, Lian GY, Song Y, Peng ZD, Xu SH, Gong Y. Downregulation of miR-152 contributes to DNMT1-mediated silencing of SOCS3/SHP-1 in non-Hodgkin lymphoma. Cancer Gene Ther 2018; 26:195-207. [PMID: 30470842 DOI: 10.1038/s41417-018-0057-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/30/2018] [Accepted: 09/14/2018] [Indexed: 12/16/2022]
Abstract
Understanding the molecular mechanisms for the development of non-Hodgkin lymphoma (NHL) will improve our ability to cure the patients. qRT-PCR was applied for the examination of the efficiency of shRNA for DNMT1, the expression of suppressor genes, miRNA-152. The MTT analysis, cell cycle analysis, clonal formation, and apoptotic analysis were used to examine the functions of DNMT1 and miR-152 in lymphoma cells. Methylation-specific polymerase chain reaction (MSP) was used to examine the methylation of tumor suppressor genes. The dual luciferase assay and western blot were used to validate if DNMT1 is the target of miR-152. For the in vivo experiments, the lymphoma cells were injected into the nude mice for quantification of the tumor growth after transfection of miR-152 mimics. Knockdown of DNMT1 by shRNA (sh-DNMT1) in OCI-Ly10 and Granta-159 cells significantly upregulated the expression of tumor suppressor genes (SOCS3, BCL2L10, p16, p14, and SHP-1) via decreasing their methylation level. At the cellular level, we found sh-DNMT1 inhibited the proliferation, clonal formation and cell cycle progression and induced the cell apoptosis of lymphoma cells. Furthermore, we found miR-152 can downregulates the expression of DNMT1 via directly targeting the gene. Overexpression of miR-152 also increased the expression of tumor suppressor genes SOCS3 and SHP-1. And miR-152 also can inhibit the cell proliferation and induce the cell apoptosis. Moreover, we found overexpression of miR-152 significantly repressed the tumor growth with decreased DNMT1 expression and increased expression of tumor suppressor genes in vivo. Our study demonstrates that miR-152 can inhibit lymphoma growth via suppressing DNMT1-mediated silencing of SOCS3 and SHP-1. These data demonstrate a new mechanism for the development of NHL and this may provide a new therapeutic target for NHL.
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Affiliation(s)
- Qing-Ming Wang
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
| | - Guang-Yu Lian
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuan Song
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Zhi-Da Peng
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Sheng-Hua Xu
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Yi Gong
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
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8
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Liu X, Li C, Zhang R, Xiao W, Niu X, Ye X, Li Z, Guo Y, Tan J, Li Y. The EZH2- H3K27me3-DNMT1 complex orchestrates epigenetic silencing of the wwc1 gene, a Hippo/YAP pathway upstream effector, in breast cancer epithelial cells. Cell Signal 2018; 51:243-256. [PMID: 30121333 DOI: 10.1016/j.cellsig.2018.08.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 02/06/2023]
Abstract
It is well known that epithelial-mesenchymal transition (EMT) can confer cancer cells with invasive and migratory capabilities associated with distant metastasis. As a key upstream factor in the Hippo pathway, Kibra (wwc1 gene) has been shown to suppress EMT in breast cancer cells, and we have found that its expression is reduced or lost completely in both human breast cancer cell lines and clinical tissue samples, particularly in triple negative breast cancer (TNBC). Unfortunately, the molecular mechanisms underlying this progression-associated event remain to be elucidated. Epigenetic gene silencing is one of the most common causes of suppressed expression of tumor suppressor genes. Furthermore, recent studies have demonstrated that EZH2 can recruit DNA methyltransferases, resulting in DNA methylation and subsequent gene silencing in certain circumstances. Thus, we hypothesized that there may exist a link between EZH2 and DNA methylation in association with wwc1 silencing in breast cancer. To test this hypothesis, we performed bisulfite sequencing, shRNA, co-IP, ChIP, MeDIP and ChIP-qPCR. As expected, RG108 or 5-Aza treatment improved the wwc1 gene transcription and Kibra protein expression. Both bisulfite sequencing and MeDIP demonstrated higher CpG methylation of the wwc1 promoter the TNBC cells (MDA-MB-231) than in luminal breast cancer cells (MCF7). It is noteworthy that ChIP and co-IP assays showed that EZH2, H3K27me3 and DNMT1 are enriched at the wwc1 promoter, and there exist physiologically relevant protein-protein interactions between them. We also found that EZH2 knockdown leads to a partial increase in Kibra expression and a considerable reduction in H3K27 and DNMT1 trimethylation. Moreover, ChIP-qPCR revealed more DNA fragments containing the wwc1 promoter in MDA-MB-231 than in MCF7 cells after immunoprecipitation with EZH2, DNMT1 and H3K27me3 antibodies. Collectively, our results reveal crosstalk between H3K27me3 inhibition catalyzed by EZH2 and CpG island methylation mediated by DNMT1 within the wwc1 promoter, which synergistically silence wwc1 gene expression in TNBC. Based on these results, we conclude that EZH2 shows promise as a potential anti-tumor target.
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Affiliation(s)
- Xiong Liu
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China; Present address: Shenzhen Key Lab of Neuropsychiatric Modulation and Collaborative Innovation Center for Brain Science, Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Center for Excellence in Brain Science and Intelligence Technology, The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chun Li
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China; Department of Pathology, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Rendong Zhang
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Wenjun Xiao
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Xia Niu
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Xiajun Ye
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Zijia Li
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Yuxian Guo
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Junyu Tan
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Yaochen Li
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China.
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9
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Li B, Zhao J, Ma JX, Li GM, Zhang Y, Xing GS, Liu J, Ma XL. Overexpression of DNMT1 leads to hypermethylation of H19 promoter and inhibition of Erk signaling pathway in disuse osteoporosis. Bone 2018; 111:82-91. [PMID: 29555308 DOI: 10.1016/j.bone.2018.03.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 12/28/2022]
Abstract
Disuse osteoporosis (DOP) is a common complication of the lack of mechanical loading. The precise mechanism underlying DOP remains unknown, although epigenetic modifications may be a major cause. Recently, cumulative research has revealed that DNA methyltransferase (DNMT) proteins can catalyze the conversion of cytosine to 5-methylcytosine (5mC), altering the epigenetic state of DNA. Here, we report that DNMT1 expression and lncRNA-H19 methylation are upregulated in the femoral tissues of DOP rats, accompanied with inhibited Erk signaling pathway. Overexpression of DNMT1 in UMR-106 cells mimics 5mC enrichment in the H19 promoter, inhibition of Erk signaling and impairment of osteogenesis, which can be rescued by 5'-aza-deoxycytidine (5'-Aza) treatment. Moreover, local intramedullary injection of Dnmt1 siRNA (siDNMT1) in Sprague-Dawley (SD) rats abrogated disuse lncRNA-H19 (H19) downregulation, Erk signaling inhibition, histopathological changes, and bone microstructure declines in the distal femur in vivo. Therefore, our data identify for the first time a new signaling cascade in DOP: mechanical unloading causes upregulation of DNMT1 and hypermethylation of H19 promoter, which subsequently leads to downregulation of lncRNA-H19 and inhibition of the ERK signaling, suggesting a new potential therapeutic target.
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Affiliation(s)
- Bing Li
- Joint Department, Tianjin Hospital, Tianjin 300211, People's Republic of China
| | - Jie Zhao
- Orthopedic Department, Tianjin Hospital, Tianjin 300211, People's Republic of China
| | - Jian-Xiong Ma
- Orthopedic Research Institute, Tianjin Hospital, Tianjin 300050, People's Republic of China
| | - Guo-Min Li
- Graduate School, Tianjin Medical University, Tianjin 300070, People's Republic of China
| | - Yang Zhang
- Orthopedic Research Institute, Tianjin Hospital, Tianjin 300050, People's Republic of China
| | - Guo-Sheng Xing
- Orthopedic Research Institute, Tianjin Hospital, Tianjin 300050, People's Republic of China
| | - Jun Liu
- Joint Department, Tianjin Hospital, Tianjin 300211, People's Republic of China.
| | - Xin-Long Ma
- Joint Department, Tianjin Hospital, Tianjin 300211, People's Republic of China; Orthopedic Research Institute, Tianjin Hospital, Tianjin 300050, People's Republic of China.
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10
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Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A. Global delay in nascent strand DNA methylation. Nat Struct Mol Biol 2018; 25:327-332. [PMID: 29531288 PMCID: PMC5889353 DOI: 10.1038/s41594-018-0046-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/05/2018] [Indexed: 12/12/2022]
Abstract
Cytosine methylation is widespread among organisms and essential for mammalian development. In line with early postulations of an epigenetic role in gene regulation, symmetric CpG methylation can be mitotically propagated over many generations with extraordinarily high fidelity. Here, we combine BrdU labeling and immunoprecipitation with genome-wide bisulfite sequencing to explore the inheritance of cytosine methylation onto newly replicated DNA in human cells. Globally, we observe a pronounced lag between the copying of genetic and epigenetic information in embryonic stem cells that is reconsolidated within hours to accomplish faithful mitotic transmission. Populations of arrested cells show a global reduction of lag-induced intermediate CpG methylation when compared to proliferating cells, whereas sites of transcription factor engagement appear cell-cycle invariant. Alternatively, the cancer cell line HCT116 preserves global epigenetic heterogeneity independently of cell-cycle arrest. Taken together, our data suggest that heterogeneous methylation largely reflects asynchronous proliferation, but is intrinsic to actively engaged cis-regulatory elements and cancer.
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Affiliation(s)
- Jocelyn Charlton
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Timothy L Downing
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Engineering, University of California-Irvine, Irvine, CA, USA
| | - Zachary D Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kendell Clement
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramona Pop
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Veronika Akopian
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sven Klages
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David P Santos
- The Ken & Ruth Davee Department of Neurology, Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alexander M Tsankov
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bernd Timmermann
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michael J Ziller
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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2-HG Inhibits Necroptosis by Stimulating DNMT1-Dependent Hypermethylation of the RIP3 Promoter. Cell Rep 2017; 19:1846-1857. [DOI: 10.1016/j.celrep.2017.05.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/31/2017] [Accepted: 05/02/2017] [Indexed: 01/07/2023] Open
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12
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Gao X, Hicks KC, Neumann P, Patel TB. Hypoxia inducible factors regulate the transcription of the sprouty2 gene and expression of the sprouty2 protein. PLoS One 2017; 12:e0171616. [PMID: 28196140 PMCID: PMC5308774 DOI: 10.1371/journal.pone.0171616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/23/2017] [Indexed: 12/15/2022] Open
Abstract
Receptor Tyrosine Kinase (RTK) signaling plays a major role in tumorigenesis and normal development. Sprouty2 (Spry2) attenuates RTK signaling and inhibits processes such as angiogenesis, cell proliferation, migration and survival, which are all upregulated in tumors. Indeed in cancers of the liver, lung, prostate and breast, Spry2 protein levels are markedly decreased correlating with poor patient prognosis and shorter survival. Thus, it is important to understand how expression of Spry2 is regulated. While prior studies have focused on the post-translation regulation of Spry2, very few studies have focused on the transcriptional regulation of SPRY2 gene. Here, we demonstrate that in the human hepatoma cell line, Hep3B, the transcription of SPRY2 is inhibited by the transcription regulating hypoxia inducible factors (HIFs). HIFs are composed of an oxygen regulated alpha subunit (HIF1α or HIF2α) and a beta subunit (HIF1β). Intriguingly, silencing of HIF1α and HIF2α elevates SPRY2 mRNA and protein levels suggesting HIFs reduce the transcription of the SPRY2 promoter. In silico analysis identified ten hypoxia response elements (HREs) in the proximal promoter and first intron of SPRY2. Using chromatin immunoprecipitation (ChIP), we show that HIF1α/2α bind near the putative HREs in the proximal promoter and intron of SPRY2. Our studies demonstrated that not only is the SPRY2 promoter methylated, but silencing HIF1α/2α reduced the methylation. ChIP assays also showed DNA methyltransferase1 (DNMT1) binding to the proximal promoter and first intron of SPRY2 and silencing HIF1α/2α decreased this association. Additionally, silencing of DNMT1 mimicked the HIF1α/2α silencing-mediated increase in SPRY2 mRNA and protein. While simultaneous silencing of HIF1α/2α and DNMT1 increased SPRY2 mRNA a little more, the increase was not additive suggesting a common mechanism by which DNMT1 and HIF1α/2α regulate SPRY2 transcription. Together these data suggest that the transcription of SPRY2 is inhibited by HIFs, in part, via DNMT1- mediated methylation.
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Affiliation(s)
- Xianlong Gao
- Department of Surgery, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Kristin C. Hicks
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, United States of America
| | - Paul Neumann
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, United States of America
| | - Tarun B. Patel
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, United States of America
- * E-mail:
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13
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Wu BK, Mei SC, Brenner C. RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation. Cell Cycle 2015; 13:3222-31. [PMID: 25485502 DOI: 10.4161/15384101.2014.950886] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Site-specific hypermethylation of tumor suppressor genes accompanied by genome-wide hypomethylation are epigenetic hallmarks of malignancy. However, the molecular mechanisms that drive these linked changes in DNA methylation remain obscure. DNA methyltransferase 1 (DNMT1), the principle enzyme responsible for maintaining methylation patterns is commonly dysregulated in tumors. Replication foci targeting sequence (RFTS) is an N-terminal domain of DNMT1 that inhibits DNA-binding and catalytic activity, suggesting that RFTS deletion would result in a gain of DNMT1 function. However, a substantial body of data suggested that RFTS is required for DNMT1 activity. Here, we demonstrate that deletion of RFTS alters DNMT1-dependent DNA methylation during malignant transformation. Compared to full-length DNMT1, ectopic expression of hyperactive DNMT1-ΔRFTS caused greater malignant transformation and enhanced promoter methylation with condensed chromatin structure that silenced DAPK and DUOX1 expression. Simultaneously, deletion of RFTS impaired DNMT1 chromatin association with pericentromeric Satellite 2 (SAT2) repeat sequences and produced DNA demethylation at SAT2 repeats and globally. To our knowledge, RFTS-deleted DNMT1 is the first single factor that can reprogram focal hypermethylation and global hypomethylation in parallel during malignant transformation. Our evidence suggests that the RFTS domain of DNMT1 is a target responsible for epigenetic changes in cancer.
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Affiliation(s)
- Bo-Kuan Wu
- a Department of Biochemistry; Carver College of Medicine ; University of Iowa ; Iowa City , IA USA
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14
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Zhang ZM, Liu S, Lin K, Luo Y, Perry JJ, Wang Y, Song J. Crystal Structure of Human DNA Methyltransferase 1. J Mol Biol 2015; 427:2520-2531. [PMID: 26070743 DOI: 10.1016/j.jmb.2015.06.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/26/2015] [Accepted: 06/04/2015] [Indexed: 02/05/2023]
Abstract
DNMT1 (DNA methyltransferase 1) is responsible for propagating the DNA methylation patterns during DNA replication. DNMT1 contains, in addition to a C-terminal methyltransferase domain, a large N-terminal regulatory region that is composed of an RFTS (replication foci targeting sequence) domain, a CXXC zinc finger domain and a pair of BAH (bromo adjacent homology) domains. The regulatory domains of DNMT1 mediate a network of protein-protein and protein-DNA interactions to control the recruitment and enzymatic activity of DNMT1. Here we report the crystal structure of human DNMT1 with all the structural domains (hDNMT1, residues 351-1600) in complex with S-adenosyl-l-homocysteine at 2.62Å resolution. The RFTS domain directly associates with the methyltransferase domain, thereby inhibiting the substrate binding of hDNMT1. Through structural analysis, mutational, biochemical and enzymatic studies, we further identify that a linker sequence between the CXXC and BAH1 domains, aside from its role in the CXXC domain-mediated DNMT1 autoinhibition, serves as an important regulatory element in the RFTS domain-mediated autoinhibition. In comparison with the previously determined structure of mouse DNMT1, this study also reveals a number of distinct structural features that may underlie subtle functional diversity observed for the two orthologues. In addition, this structure provides a framework for understanding the functional consequence of disease-related hDNMT1 mutations.
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Affiliation(s)
- Zhi-Min Zhang
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Shuo Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA; Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Krystal Lin
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Youfu Luo
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, PR China
| | | | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA; Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
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15
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Dysregulated transcriptional and post-translational control of DNA methyltransferases in cancer. Cell Biosci 2014; 4:46. [PMID: 25949795 PMCID: PMC4422219 DOI: 10.1186/2045-3701-4-46] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/01/2014] [Indexed: 01/29/2023] Open
Abstract
Cancer is a leading cause of death worldwide. Aberrant promoter hypermethylation of CpG islands associated with tumor suppressor genes can lead to transcriptional silencing and result in tumorigenesis. DNA methyltransferases (DNMTs) are the enzymes responsible for DNA methylation and have been reported to be over-expressed in various cancers. This review highlights the current status of transcriptional and post-translational regulation of the DNMT expression and activity with a focus on dysregulation involved in tumorigenesis. The transcriptional up-regulation of DNMT gene expression can be induced by Ras-c-Jun signaling pathway, Sp1 and Sp3 zinc finger proteins and virus oncoproteins. Transcriptional repression on DNMT genes has also been reported for p53, RB and FOXO3a transcriptional regulators and corepressors. In addition, the low expressions of microRNAs 29 family, 143, 148a and 152 are associated with DNMTs overexpression in various cancers. Several important post-translational modifications including acetylation and phosphorylation have been reported to mediate protein stability and activity of the DNMTs especially DNMT1. In this review, we also discuss drugs targeting DNMT protein expression and activation for therapeutic strategy against cancer.
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16
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Jasnos L, Sawado T. Determining cell division symmetry through the dissection of dividing cells using single-cell expression analysis. Nat Protoc 2014; 9:505-16. [PMID: 24504476 DOI: 10.1038/nprot.2014.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Symmetric cell divisions give rise to two sister cells that are identical to each other, whereas asymmetric divisions produce two sister cells with distinctive phenotypes. Although cell division symmetry is usually determined on the basis of a few markers or biological functions, the overall similarity between sister cells has not been thoroughly examined at a molecular level. Here we provide a protocol to separate sister embryonic stem cells (ESCs) and to conduct multiplexed gene expression analyses at the single-cell level by using 48 ESC genes. The procedure includes the dissection of dividing, paired sister cells by micromanipulation, followed by cell lysis, reverse transcription, gene-specific cDNA amplification and multiplexed quantitative PCR analyses. This protocol can be completed in 10 d, and it can be readily adapted to other cell types that are able to grow in suspension culture.
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Affiliation(s)
- Lukasz Jasnos
- Haemato-Oncology Research Unit, Division of Molecular Pathology, Division of Cancer Biology, The Institute of Cancer Research (ICR), Sutton, UK
| | - Tomoyuki Sawado
- Haemato-Oncology Research Unit, Division of Molecular Pathology, Division of Cancer Biology, The Institute of Cancer Research (ICR), Sutton, UK
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17
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Gros C, Chauvigné L, Poulet A, Menon Y, Ausseil F, Dufau I, Arimondo PB. Development of a universal radioactive DNA methyltransferase inhibition test for high-throughput screening and mechanistic studies. Nucleic Acids Res 2013; 41:e185. [PMID: 23980028 PMCID: PMC3799459 DOI: 10.1093/nar/gkt753] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/15/2013] [Accepted: 07/30/2013] [Indexed: 12/24/2022] Open
Abstract
DNA methylation is an important epigenetic mark in eukaryotes, and aberrant pattern of this modification is involved in numerous diseases such as cancers. Interestingly, DNA methylation is reversible and thus is considered a promising therapeutic target. Therefore, there is a need for identifying new small inhibitors of C5 DNA methyltransferases (DNMTs). Despite the development of numerous in vitro DNMT assays, there is a lack of reliable tests suitable for high-throughput screening, which can also give insights into inhibitor mechanisms of action. We developed a new test based on scintillation proximity assay meeting these requirements. After optimizing our assay on human DNMT1 and calibrating it with two known inhibitors, we carried out S-Adenosyl-l-Methionine and DNA competition studies on three inhibitors and were able to determine each mechanism of action. Finally, we showed that our test was applicable to 3 other methyltransferases sources: human DNMT3A, bacterial M.SssI and cellular extracts as well.
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Affiliation(s)
| | | | | | | | | | - Isabelle Dufau
- CNRS-Pierre Fabre USR n° 3388 ETaC, CRDPF, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Paola B. Arimondo
- CNRS-Pierre Fabre USR n° 3388 ETaC, CRDPF, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
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18
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DNA methylation inhibitors in cancer: recent and future approaches. Biochimie 2012; 94:2280-96. [PMID: 22967704 DOI: 10.1016/j.biochi.2012.07.025] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 07/30/2012] [Indexed: 12/14/2022]
Abstract
This review presents the different human DNA methyltransferases (DNMTs), their biological roles, their mechanisms of action and their role in cancer. The description of assays for detecting DNMT inhibitors (DNMTi) follows. The different known DNMTi are reported along with their advantages, drawbacks and clinical trials. A discussion on the features of the future DNMT inhibitors will conclude this review.
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19
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Bai X, Song Z, Fu Y, Yu Z, Zhao L, Zhao H, Yao W, Huang D, Mi X, Wang E, Zheng Z, Wei M. Clinicopathological significance and prognostic value of DNA methyltransferase 1, 3a, and 3b expressions in sporadic epithelial ovarian cancer. PLoS One 2012; 7:e40024. [PMID: 22768205 PMCID: PMC3386927 DOI: 10.1371/journal.pone.0040024] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 05/30/2012] [Indexed: 12/19/2022] Open
Abstract
Altered DNA methylation of tumor suppressor gene promoters plays a role in human carcinogenesis and DNA methyltransferases (DNMTs) are responsible for it. This study aimed to determine aberrant expression of DNMT1, DNMT3a, and DNMT3b in benign and malignant ovarian tumor tissues for their association with clinicopathological significance and prognostic value. A total of 142 ovarian cancers and 44 benign ovarian tumors were recruited for immunohistochemical analysis of their expression. The data showed that expression of DNMT1, DNMT3a, and DNMT3b was observed in 76 (53.5%), 92 (64.8%) and 79 (55.6%) of 142 cases of ovarian cancer tissues, respectively. Of the serious tumors, DNMT3a protein expression was significantly higher than that in benign tumor samples (P = 0.001); DNMT3b was marginally significant down regulated in ovarian cancers compared to that of the benign tumors (P = 0.054); DNMT1 expression has no statistical difference between ovarian cancers and benign tumor tissues (P = 0.837). Of the mucious tumors, the expression of DNMT3a, DNMT3b, and DNMT1 was not different between malignant and benign tumors. Moreover, DNMT1 expression was associated with DNMT3b expression (P = 0.020, r = 0.195). DNMT1 expression was associated with age of the patients, menopause status, and tumor localization, while DNMT3a expression was associated with histological types and serum CA125 levels and DNMT3b expression was associated with lymph node metastasis. In addition, patients with DNMT1 or DNMT3b expression had a trend of better survival than those with negative expression. Co-expression of DNMT1 and DNMT3b was significantly associated with better overall survival (P = 0.014). The data from this study provided the first evidence for differential expression of DNMTs proteins in ovarian cancer tissues and their associations with clinicopathological and survival data in sporadic ovarian cancer patients.
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Affiliation(s)
- Xuefeng Bai
- Department of Pharmacology, China Medical University, Shenyang, Liaoning, China
| | - Zhiguo Song
- Department of Pharmacology, China Medical University, Shenyang, Liaoning, China
| | - Yingzi Fu
- Department of Pharmacology, China Medical University, Shenyang, Liaoning, China
| | - Zhaojin Yu
- Department of Pharmacology, China Medical University, Shenyang, Liaoning, China
| | - Lin Zhao
- Department of Pharmacology, China Medical University, Shenyang, Liaoning, China
| | - Haishan Zhao
- Department of Pharmacology, China Medical University, Shenyang, Liaoning, China
| | - Weifan Yao
- Department of Pharmacology, China Medical University, Shenyang, Liaoning, China
| | - Desheng Huang
- Department of Mathematics, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Xiaoyi Mi
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
- Institute of Pathophysiology, China Medical University, Shenyang, Liaoning, China
| | - Enhua Wang
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
- Institute of Pathophysiology, China Medical University, Shenyang, Liaoning, China
| | - Zhihong Zheng
- Institute of Pathophysiology, China Medical University, Shenyang, Liaoning, China
| | - Minjie Wei
- Department of Pharmacology, China Medical University, Shenyang, Liaoning, China
- Institute of Pathophysiology, China Medical University, Shenyang, Liaoning, China
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20
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Verbrugge I, Johnstone RW, Bots M. Promises and challenges of anticancer drugs that target the epigenome. Epigenomics 2012; 3:547-65. [PMID: 22126246 DOI: 10.2217/epi.11.82] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The occurrence of epigenetic aberrations in cancer and their role in promoting tumorigenesis has led to the development of various small molecule inhibitors that target epigenetic enzymes. In preclinical settings, many epigenetic inhibitors demonstrate promising activity against a variety of both hematological and solid tumors. The therapeutic efficacy of those inhibitors that have entered the clinic however, is restricted predominantly to hematological malignancies. Here we outline the observed epigenetic aberrations in various types of cancer and the clinical responses to epigenetic drugs. We furthermore discuss strategies to improve the responsiveness of both hematological and solid malignancies to epigenetic drugs.
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Affiliation(s)
- Inge Verbrugge
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne 3002, Victoria, Australia
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21
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Malygin EG, Hattman S. DNA methyltransferases: mechanistic models derived from kinetic analysis. Crit Rev Biochem Mol Biol 2012; 47:97-193. [PMID: 22260147 DOI: 10.3109/10409238.2011.620942] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The sequence-specific transfer of methyl groups from donor S-adenosyl-L-methionine (AdoMet) to certain positions of DNA-adenine or -cytosine residues by DNA methyltransferases (MTases) is a major form of epigenetic modification. It is virtually ubiquitous, except for some notable exceptions. Site-specific methylation can be regarded as a means to increase DNA information capacity and is involved in a large spectrum of biological processes. The importance of these functions necessitates a deeper understanding of the enzymatic mechanism(s) of DNA methylation. DNA MTases fall into one of two general classes; viz. amino-MTases and [C5-cytosine]-MTases. Amino-MTases, common in prokaryotes and lower eukaryotes, catalyze methylation of the exocyclic amino group of adenine ([N6-adenine]-MTase) or cytosine ([N4-cytosine]-MTase). In contrast, [C5-cytosine]-MTases methylate the cyclic carbon-5 atom of cytosine. Characteristics of DNA MTases are highly variable, differing in their affinity to their substrates or reaction products, their kinetic parameters, or other characteristics (order of substrate binding, rate limiting step in the overall reaction). It is not possible to present a unifying account of the published kinetic analyses of DNA methylation because different authors have used different substrate DNAs and/or reaction conditions. Nevertheless, it would be useful to describe those kinetic data and the mechanistic models that have been derived from them. Thus, this review considers in turn studies carried out with the most consistently and extensively investigated [N6-adenine]-, [N4-cytosine]- and [C5-cytosine]-DNA MTases.
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Affiliation(s)
- Ernst G Malygin
- Institute of Molecular Biology, State Research Center of Virology and Biotechnology Vector, Novosibirsk, Russia
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22
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Pichler G, Wolf P, Schmidt CS, Meilinger D, Schneider K, Frauer C, Fellinger K, Rottach A, Leonhardt H. Cooperative DNA and histone binding by Uhrf2 links the two major repressive epigenetic pathways. J Cell Biochem 2011; 112:2585-93. [PMID: 21598301 PMCID: PMC3569875 DOI: 10.1002/jcb.23185] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Gene expression is regulated by DNA as well as histone modifications but the crosstalk and mechanistic link between these epigenetic signals are still poorly understood. Here we investigate the multi-domain protein Uhrf2 that is similar to Uhrf1, an essential cofactor of maintenance DNA methylation. Binding assays demonstrate a cooperative interplay of Uhrf2 domains that induces preference for hemimethylated DNA, the substrate of maintenance methylation, and enhances binding to H3K9me3 heterochromatin marks. FRAP analyses revealed that localization and binding dynamics of Uhrf2 in vivo require an intact tandem Tudor domain and depend on H3K9 trimethylation but not on DNA methylation. Besides the cooperative DNA and histone binding that is characteristic for Uhrf2, we also found an opposite expression pattern of uhrf1 and uhrf2 during differentiation. While uhrf1 is mainly expressed in pluripotent stem cells, uhrf2 is upregulated during differentiation and highly expressed in differentiated mouse tissues. Ectopic expression of Uhrf2 in uhrf1−/− embryonic stem cells did not restore DNA methylation at major satellites indicating functional differences. We propose that the cooperative interplay of Uhrf2 domains may contribute to a tighter epigenetic control of gene expression in differentiated cells.
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Affiliation(s)
- Garwin Pichler
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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23
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Svedružić ŽM. Dnmt1 structure and function. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:221-54. [PMID: 21507353 DOI: 10.1016/b978-0-12-387685-0.00006-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dnmt1, the principal DNA methyltransferase in mammalian cells, is a large and a highly dynamic enzyme with multiple regulatory features that can control DNA methylation in cells. This chapter highlights how insights into Dnmt1 structure and function can advance our understanding of DNA methylation in cells. The allosteric site(s) on Dnmt1 can regulate processes of de novo and maintenance DNA methylation in cells. Remaining open questions include which molecules, by what mechanism, bind at the allosteric site(s) in cells? Different phosphorylation sites on Dnmt1 can change its activity or ability to bind DNA target sites. Thirty-one different molecules are currently known to have physical and/or functional interaction with Dnmt1 in cells. The Dnmt1 structure and enzymatic mechanism offer unique insights into those interactions. The interacting molecules are involved in chromatin organization, DNA repair, cell cycle regulation, and apoptosis and also include RNA polymerase II, some RNA-binding proteins, and some specific Dnmt1-inhibitory RNA molecules. Combined insights from studies of different enzymatic features of Dnmt1 offer novel ideas for development of drug candidates, and can be used in selection of promising drug candidates from more than 15 different compounds that have been identified as possible inhibitors of DNA methylation in cells.
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Affiliation(s)
- Željko M Svedružić
- Medical Biochemistry, PB Rab, Faculty of Medicine, University of Rijeka, Rab, Croatia
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24
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Amara K, Ziadi S, Hachana M, Soltani N, Korbi S, Trimeche M. DNA methyltransferase DNMT3b protein overexpression as a prognostic factor in patients with diffuse large B-cell lymphomas. Cancer Sci 2010; 101:1722-30. [PMID: 20398054 PMCID: PMC11159814 DOI: 10.1111/j.1349-7006.2010.01569.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Diffuse large B-cell lymphomas (DLBCL) are the most common type of aggressive lymphomas, with considerable heterogeneity in clinical presentation, molecular characteristics, and outcome. Previous studies have showed significant correlations between DNA methyltransferase (DNMT) overexpression and unfavorable prognosis in human cancers. Therefore, we investigated in this study the biological and prognostic significance of DNMT1, DNMT3a, and DNMT3b protein expression in DLBCL. DNA methyltransferase (DNMT) expression was analyzed by immunohistochemistry in 81 DLBCL cases and correlated with clinicopathological parameters. Kaplan-Meier curves were used to estimate survival rates, and the Cox proportional hazard regression model was used to evaluate the prognostic impact of DNMT expression. Our results showed that overexpression of DNMT1, DNMT3a, and DNMT3b were detected in 48%, 13%, and 45% of investigated cases, respectively. DNA methyltransferase 1 (DNMT1) and DNMT3b overexpression was significantly correlated with advanced clinical stages (P = 0.028 and P = 0.016, respectively). Moreover, concomitant expression of DNMT1 and DNMT3b was significantly correlated with resistance to treatment (P = 0.015). With regard to survival rates, although data was available only for 40 patients, DNMT3b overexpression was significantly correlated with shorter overall survival (P = 0.006) and progression-free survival (P = 0.016). Interestingly, multivariate analysis demonstrated that DNMT3b overexpression was an independent prognostic factor for predicting shortened overall survival (P = 0.004) and progression-free survival (P = 0.024). In conclusion, DNMT3b overexpression was identified as an independent prognostic factor for predicting shortened survival of patients with DLBCL and could be, therefore, useful in identifying patients who would benefit from aggressive therapy.
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Affiliation(s)
- Khaled Amara
- Department of Pathology, Farhat-Hached Hospital, Sousse, Tunisia
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Rottach A, Frauer C, Pichler G, Bonapace IM, Spada F, Leonhardt H. The multi-domain protein Np95 connects DNA methylation and histone modification. Nucleic Acids Res 2009; 38:1796-804. [PMID: 20026581 PMCID: PMC2847221 DOI: 10.1093/nar/gkp1152] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
DNA methylation and histone modifications play a central role in the epigenetic regulation of gene expression and cell differentiation. Recently, Np95 (also known as UHRF1 or ICBP90) has been found to interact with Dnmt1 and to bind hemimethylated DNA, indicating together with genetic studies a central role in the maintenance of DNA methylation. Using in vitro binding assays we observed a weak preference of Np95 and its SRA (SET- and Ring-associated) domain for hemimethylated CpG sites. However, the binding kinetics of Np95 in living cells was not affected by the complete loss of genomic methylation. Investigating further links with heterochromatin, we could show that Np95 preferentially binds histone H3 N-terminal tails with trimethylated (H3K9me3) but not acetylated lysine 9 via a tandem Tudor domain. This domain contains three highly conserved aromatic amino acids that form an aromatic cage similar to the one binding H3K9me3 in the chromodomain of HP1ß. Mutations targeting the aromatic cage of the Np95 tandem Tudor domain (Y188A and Y191A) abolished specific H3 histone tail binding. These multiple interactions of the multi-domain protein Np95 with hemimethylated DNA and repressive histone marks as well as with DNA and histone methyltransferases integrate the two major epigenetic silencing pathways.
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Affiliation(s)
- Andrea Rottach
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany
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Yaish MWF, Peng M, Rothstein SJ. AtMBD9 modulates Arabidopsis development through the dual epigenetic pathways of DNA methylation and histone acetylation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:123-135. [PMID: 19419532 DOI: 10.1111/j.1365-313x.2009.03860.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mutations within the Arabidopsis METHYL-CpG BINDING DOMAIN 9 gene (AtMBD9) cause pleotropic phenotypes including early flowering and multiple lateral branches. Early flowering was previously attributed to the repression of flowering locus C (FLC) due to a reduction in histone acetylation. However, the reasons for other phenotypic variations remained obscure. Recent studies suggest an important functional correlation between DNA methylation and histone modifications. By investigating this relationship, we found that the global genomic DNA of atmbd9 was over-methylated, including the FLC gene region. Recombinant AtMBD9 does not have detectable DNA demethylation activity in vitro, but instead has histone acetylation activity. Ectopic over-expression of AtMBD9 and transient DNA demethylation promotes flowering and causes partial recovery of the normal branching phenotype. Co-immunoprecipitation assays suggest that AtMBD9 interacts in vivo with some regions of the FLC gene and binds to histone 4 (H4). Gene expression profile analysis revealed earlier up-regulation of some flower-specific transcriptional factors and alteration of potential hormonal and signal transducer axillary branching regulatory genes. In accordance with this result, AtMBD9 itself was found to be localized in the nucleus and expressed in the flower and axillary buds. Together, these results suggest that AtMBD9 controls flowering time and axillary branching by modulating gene expression through DNA methylation and histone acetylation, and reveal another component of the epigenetic mechanism controlling gene expression.
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Affiliation(s)
- Mahmoud W F Yaish
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
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Guil S, Esteller M. DNA methylomes, histone codes and miRNAs: tying it all together. Int J Biochem Cell Biol 2008; 41:87-95. [PMID: 18834952 DOI: 10.1016/j.biocel.2008.09.005] [Citation(s) in RCA: 236] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 12/12/2022]
Abstract
Our current knowledge of the deregulation that occurs during the onset and progression of cancer and other diseases leads us to recognize both genetic and epigenetic alterations as being at the core of the pathological state. The epigenetic landscape includes a variety of covalent modifications that affect the methylation status of DNA but also the post-translational modifications of histones, and determines the structural features of chromatin that ultimately control the transcriptional outcome of the cell to accommodate developmental, proliferative or environmental requirements. MicroRNAs are small non-coding RNAs that regulate the expression of complementary messenger RNAs and function as key controllers in a myriad of cellular processes, including proliferation, differentiation and apoptosis. In the last few years, increasing evidence has indicated that a substantial number of microRNA genes are subjected to epigenetic alterations, resulting in aberrant patterns of expression upon the occurrence of cancer. In this review we discuss microRNA genes that are epigenetically modified in cancer cells, and the role that microRNAs themselves can have as chromatin modifiers.
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Affiliation(s)
- Sònia Guil
- Institut d'Investigacio Biomedica de Bellvitge, 08907 L'Hospitalet, Barcelona, Catalonia, Spain
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28
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Fabbri M, Garzon R, Cimmino A, Liu Z, Zanesi N, Callegari E, Liu S, Alder H, Costinean S, Fernandez-Cymering C, Volinia S, Guler G, Morrison CD, Chan KK, Marcucci G, Calin GA, Huebner K, Croce CM. MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc Natl Acad Sci U S A 2007; 104:15805-10. [PMID: 17890317 PMCID: PMC2000384 DOI: 10.1073/pnas.0707628104] [Citation(s) in RCA: 1248] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that regulate expression of many genes. Recent studies suggest roles of miRNAs in carcinogenesis. We and others have shown that expression profiles of miRNAs are different in lung cancer vs. normal lung, although the significance of this aberrant expression is poorly understood. Among the reported down-regulated miRNAs in lung cancer, the miRNA (miR)-29 family (29a, 29b, and 29c) has intriguing complementarities to the 3'-UTRs of DNA methyltransferase (DNMT)3A and -3B (de novo methyltransferases), two key enzymes involved in DNA methylation, that are frequently up-regulated in lung cancer and associated with poor prognosis. We investigated whether miR-29s could target DNMT3A and -B and whether restoration of miR-29s could normalize aberrant patterns of methylation in non-small-cell lung cancer. Here we show that expression of miR-29s is inversely correlated to DNMT3A and -3B in lung cancer tissues, and that miR-29s directly target both DNMT3A and -3B. The enforced expression of miR-29s in lung cancer cell lines restores normal patterns of DNA methylation, induces reexpression of methylation-silenced tumor suppressor genes, such as FHIT and WWOX, and inhibits tumorigenicity in vitro and in vivo. These findings support a role of miR-29s in epigenetic normalization of NSCLC, providing a rationale for the development of miRNA-based strategies for the treatment of lung cancer.
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Affiliation(s)
- Muller Fabbri
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | - Ramiro Garzon
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | - Amelia Cimmino
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
- Department of Biochemistry and Biophysics “F. Cedrangolo,” Medical School, Second University of Naples, 80138 Naples, Italy
| | - Zhongfa Liu
- Comprehensive Cancer Center, and
- College of Pharmacy, Ohio State University, Columbus, OH 43210
| | - Nicola Zanesi
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | - Elisa Callegari
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | - Shujun Liu
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | - Hansjuerg Alder
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | - Stefan Costinean
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | | | - Stefano Volinia
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | - Gulnur Guler
- Department of Pathology, Hacettepe University, Ankara 06100, Turkey; and
| | - Carl D. Morrison
- Department of Pathology, Roswell Park Center Institute, Buffalo, NY 14263
| | - Kenneth K. Chan
- Comprehensive Cancer Center, and
- College of Pharmacy, Ohio State University, Columbus, OH 43210
| | - Guido Marcucci
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | - George A. Calin
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | - Kay Huebner
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
| | - Carlo M. Croce
- *Department of Molecular Virology, Immunology, and Medical Genetics
- Comprehensive Cancer Center, and
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Schermelleh L, Haemmer A, Spada F, Rösing N, Meilinger D, Rothbauer U, Cardoso MC, Leonhardt H. Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation. Nucleic Acids Res 2007; 35:4301-12. [PMID: 17576694 PMCID: PMC1934996 DOI: 10.1093/nar/gkm432] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Postreplicative maintenance of genomic methylation patterns was proposed to depend largely on the binding of DNA methyltransferase 1 (Dnmt1) to PCNA, a core component of the replication machinery. We investigated how the slow and discontinuous DNA methylation could be mechanistically linked with fast and processive DNA replication. Using photobleaching and quantitative live cell imaging we show that Dnmt1 binding to PCNA is highly dynamic. Activity measurements of a PCNA-binding-deficient mutant with an enzyme-trapping assay in living cells showed that this interaction accounts for a 2-fold increase in methylation efficiency. Expression of this mutant in mouse dnmt1-/- embryonic stem (ES) cells restored CpG island methylation. Thus association of Dnmt1 with the replication machinery enhances methylation efficiency, but is not strictly required for maintaining global methylation. The transient nature of this interaction accommodates the different kinetics of DNA replication and methylation while contributing to faithful propagation of epigenetic information.
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Affiliation(s)
- Lothar Schermelleh
- Ludwig Maximilians University Munich (LMU), Department of Biology II, 82152 Martinsried, Germany and Max Delbrück Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Andrea Haemmer
- Ludwig Maximilians University Munich (LMU), Department of Biology II, 82152 Martinsried, Germany and Max Delbrück Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Fabio Spada
- Ludwig Maximilians University Munich (LMU), Department of Biology II, 82152 Martinsried, Germany and Max Delbrück Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Nicole Rösing
- Ludwig Maximilians University Munich (LMU), Department of Biology II, 82152 Martinsried, Germany and Max Delbrück Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Daniela Meilinger
- Ludwig Maximilians University Munich (LMU), Department of Biology II, 82152 Martinsried, Germany and Max Delbrück Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Ulrich Rothbauer
- Ludwig Maximilians University Munich (LMU), Department of Biology II, 82152 Martinsried, Germany and Max Delbrück Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - M. Cristina Cardoso
- Ludwig Maximilians University Munich (LMU), Department of Biology II, 82152 Martinsried, Germany and Max Delbrück Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Heinrich Leonhardt
- Ludwig Maximilians University Munich (LMU), Department of Biology II, 82152 Martinsried, Germany and Max Delbrück Center for Molecular Medicine (MDC), 13125 Berlin, Germany
- *To whom correspondence should be addressed. +49-89-2180-74232+49-89-2180-74236
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30
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Lin RK, Hsu HS, Chang JW, Chen CY, Chen JT, Wang YC. Alteration of DNA methyltransferases contributes to 5'CpG methylation and poor prognosis in lung cancer. Lung Cancer 2006; 55:205-13. [PMID: 17140695 DOI: 10.1016/j.lungcan.2006.10.022] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Revised: 07/29/2006] [Accepted: 10/19/2006] [Indexed: 01/13/2023]
Abstract
Overexpression of DNA methyltransferases DNMT1, DNMT3a and DNMT3b has been reported in various cancers. However, physical binding of DNA methyltransferase (DNMT) to the hypermethylated promoter of tumor suppressor genes (TSGs) has never been demonstrated in tumor tissues. In addition, alteration of DNMT at the protein level has never been reported in the same series of cancer patients. By immunohistochemical analysis, we demonstrated that DNMT1, DNMT3a and DNMT3b proteins were highly expressed in a coordinate manner in lung tumors, particularly in smokers (P=0.037, by the Fisher exact test). Patients with DNMT1 overexpression had a trend of poorer prognosis than those without such overexpression, and this prognostic significance was apparent in squamous carcinoma (SQ) patients (P=0.041, by the log-rank test). Both DNMT1 and DNMT3b overexpressions correlated with hypermethylation in the TSG promoters, especially among smoking SQ patients (P=0.012). To further explore the molecular mechanisms between altered TSGs promoter methylation and overexpression of DNMTs protein, we performed a tissue chromatin-immunoprecipitation polymerase chain reaction assay for lung tumors and showed that the methylated FHIT, p16(INK4a) and RARbeta promoters were bound by both DNMT protein and methyl-CpG-binding protein 2. These data suggest that overexpression and strong binding of various DNMTs may result in promoter hypermethylation of multiple TSGs and ultimately lead to lung tumorigenesis and poor prognosis.
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Affiliation(s)
- Ruo-Kai Lin
- Department of Life Sciences, National Taiwan Normal University, Taipei, Taiwan, ROC
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31
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Soma T, Kaganoi J, Kawabe A, Kondo K, Imamura M, Shimada Y. Nicotine induces the fragile histidine triad methylation in human esophageal squamous epithelial cells. Int J Cancer 2006; 119:1023-7. [PMID: 16570269 DOI: 10.1002/ijc.21948] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The fragile histidine triad (FHIT) gene has been proposed to have an important role in very early carcinogenesis. Methylation of the FHIT gene is associated with transcriptional inactivation in esophageal squamous cell carcinoma, and FHIT inactivation has been linked to smoking-related carcinogenesis. In this study, we confirmed methylation of the FHIT gene in human esophageal squamous epithelial cells (HEECs) and examined whether nicotine induced alteration of FHIT. Methylation status in the promoter region of the FHIT gene and p16(INK4A) gene was determined by methylation-specific PCR in HEECs exposed to nicotine under various conditions. Methylation status of the FHIT gene was confirmed by DNA-sequencing analysis. Protein expression of Fhit and the DNA methyltransferases (DNMTs) DNMT1 and DNMT3a were assessed by immunoblot analysis. In the absence of nicotine, methylation of the FHIT gene and attenuation of Fhit protein were not detected in HEECs. Nicotine induced the methylation of FHIT gene and attenuated Fhit protein in association with increased expression of DNMT3a. Reexpression of Fhit protein in HEECs was found after cessation of moderate- to long-term exposure to nicotine. Our results show that nicotine induces methylation of the FHIT gene followed by loss of Fhit protein expression in HEECs. Continuous smoking may thus increase the risk of esophageal cancer.
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Affiliation(s)
- Toshiya Soma
- Department of Surgery and Surgical Basic Science, Kyoto University, Sakyo-ku, Japan
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32
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Brero A, Leonhardt H, Cardoso MC. Replication and Translation of Epigenetic Information. Curr Top Microbiol Immunol 2006; 301:21-44. [PMID: 16570844 DOI: 10.1007/3-540-31390-7_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most cells in multicellular organisms contain identical genetic information but differ in their epigenetic information. The latter is encoded at the molecular level by post-replicative methylation of certain DNA bases (in mammals 5-methyl cytosine at CpG sites) and multiple histone modifications in chromatin. In addition, higher-order chromatin structures are generated during differentiation, which might impact on genome expression and stability. The epigenetic information needs to be "translated" in order to define specific cell types with specific sets of active and inactive genes, collectively called the epigenome. Once established, the epigenome needs to be "replicated" at each cell division cycle, i.e., both genetic and epigenetic information have to be faithfully duplicated, which implies a tight coordination between the DNA replication machinery and epigenetic regulators. In this review, we focus on the molecules and mechanisms responsible for the replication and translation of DNA methylation in mammals as one of the central epigenetic marks.
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Affiliation(s)
- A Brero
- Max Delbrück Center for Molecular Medicine, FVK, Berlin, Germany
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Abstract
DNA methylation is an essential modification of DNA in mammals that is involved in gene regulation, development, genome defence and disease. In mammals 3 families of DNA methyltransferases (MTases) comprising (so far) 4 members have been found: Dnmt1, Dnmt2, Dnmt3A and Dnmt3B. In addition, Dnmt3L has been identified as a stimulator of the Dnmt3A and Dnmt3B enzymes. In this review the enzymology of the mammalian DNA MTases is described, starting with a depiction of the catalytic mechanism that involves covalent catalysis and base flipping. Subsequently, important mechanistic features of the mammalian enzyme are discussed including the specificity of Dnmt1 for hemimethylated target sites, the target sequence specificity of Dnmt3A, Dnmt3B and Dnmt2 and the flanking sequence preferences of Dnmt3A and Dnmt3B. In addition, the processivity of the methylation reaction by Dnmt1, Dnmt3A and Dnmt3B is reviewed. Finally, the control of the catalytic activity of mammalian MTases is described that includes the regulation of the activity of Dnmtl by its N-terminal domain and the interaction of Dnmt3A and Dnmt3B with Dnmt3L. The allosteric activation of Dnmt1 for methylation at unmodified sites is described. Wherever possible, correlations between the biochemical properties of the enzymes and their physiological functions in the cell are indicated.
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Affiliation(s)
- A Jeltsch
- School of Engineering and Science, International University Bremen, Germany.
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Dean W, Lucifero D, Santos F. DNA methylation in mammalian development and disease. ACTA ACUST UNITED AC 2005; 75:98-111. [PMID: 16035040 DOI: 10.1002/bdrc.20037] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetic modification of the cytosine base of DNA by its methylation introduced the possibility that beyond the inherent information contained within the nucleotide sequence there was an additional layer of information added to the underlying genetic code. DNA methylation has been implicated in a wide range of biological functions, including an essential developmental role in the reprogramming of germ cells and early embryos, the repression of endogenous retrotransposons, and a generalized role in gene expression. Special functions of DNA methylation include the marking of one of the parental alleles of many imprinted genes, a group of genes essential for growth and development in mammals with a unique parent-of-origin expression pattern, a role in stabilizing X-chromosome inactivation, and centromere function. In this regard, it is not surprising that errors in establishing or maintaining patterns of methylation are associated with a diverse group of human diseases and syndromes.
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Affiliation(s)
- Wendy Dean
- Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Babraham Research Campus, Cambridge CB2 4AT, UK.
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Hsieh CL. The de novo methylation activity of Dnmt3a is distinctly different than that of Dnmt1. BMC BIOCHEMISTRY 2005; 6:6. [PMID: 15799776 PMCID: PMC1084342 DOI: 10.1186/1471-2091-6-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Accepted: 03/30/2005] [Indexed: 12/31/2022]
Abstract
Background Though Dnmt1 is considered the primary maintenance methyltransferase and Dnmt3a and Dnmt3b are considered de novo methyltransferases in mammals, these three enzymes may work together in maintaining as well as establishing DNA methylation patterns. It has been proposed that Dnmt1 may carry out de novo methylation at sites in the genome with transient single-stranded regions, such as replication origins, and then spread methylation from these nucleation sites in vivo, even though such activity has not been reported. Results In this study, we show that Dnmt3a does not act on single-stranded substrates in vitro, indicating that Dnmt3a is not likely to initiate DNA methylation at such proposed nucleation sites. Dnmt3a shows similar methylation activity on unmethylated and hemimethylated duplex DNA, though with some substrate preference. Unlike Dnmt1, pre-existing cytosine methylation at CpG sites or non-CpG sites does not stimulate Dnmt3a activity in vitro and in vivo. Conclusion The fact that Dnmt3a does not act on single stranded DNA and is not stimulated by pre-existing cytosine methylation indicates that the de novo methylation activity of Dnmt3a is quite different from that of Dnmt1. These findings are consistent with a model in which Dnmt3a initiates methylation on one of the DNA strands of duplex DNA, and these hemimethylated sites then stimulate Dnmt1 activity for further methylation.
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Affiliation(s)
- Chih-Lin Hsieh
- Department of Urology, University of Southern California, 1441 Eastlake Ave,, Rm 5420, Norris Cancer Center, Los Angeles, CA 90033, USA.
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36
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Ko YG, Nishino K, Hattori N, Arai Y, Tanaka S, Shiota K. Stage-by-stage change in DNA methylation status of Dnmt1 locus during mouse early development. J Biol Chem 2005; 280:9627-34. [PMID: 15634679 DOI: 10.1074/jbc.m413822200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methylation of DNA is involved in tissue-specific gene control, and establishment of DNA methylation pattern in the genome is thought to be essential for embryonic development. Three isoforms of Dnmt1 (DNA methyltransferase 1) transcripts, Dnmt1s, Dnmt1o, and Dnmt1p, are produced by alternative usage of multiple first exons. Dnmt1s is expressed in somatic cells. Dnmt1p is found only in pachytene spermatocytes, whereas Dnmt1o is specific to oocytes and preimplantation embryos. Here we determined that there is a tissue-dependent differentially methylated region (T-DMR) in the 5' region of Dnmt1o but not in that of the Dnmt1s/1p. The methylation status of the Dnmt1o T-DMR was distinctively different in the oocyte from that in the sperm and adult somatic tissues and changed at each stage from fertilization to blastocyst stage, suggesting that active methylation and demethylation occur during preimplantation development. The T-DMR was highly methylated in somatic cells and embryonic stem cells. Analysis using Dnmt-deficient embryonic stem cell lines revealed that Dnmt1, Dnmt3a, and Dnmt3b are each partially responsible for maintenance of methylation of Dnmt1o T-DMR. In particular, there are compensatory and cooperative roles between Dnmt3a and Dnmt3b. Thus, the regulatory region of Dnmt1o, but not of Dnmt1s/1p, appeared to be a target of DNA methylation. The present study also suggested that the DNA methylation status of the gene region dynamically changes during embryogenesis independently of the change in the bulk DNA methylation status.
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Affiliation(s)
- Yeoung-Gyu Ko
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, Japan 113-8657
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37
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Vilkaitis G, Suetake I, Klimasauskas S, Tajima S. Processive Methylation of Hemimethylated CpG Sites by Mouse Dnmt1 DNA Methyltransferase. J Biol Chem 2005; 280:64-72. [PMID: 15509558 DOI: 10.1074/jbc.m411126200] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA methyltransferase Dnmt1 ensures clonal transmission of lineage-specific DNA methylation patterns in a mammalian genome during replication. Dnmt1 is targeted to replication foci, interacts with PCNA, and favors methylating the hemimethylated form of CpG sites. To understand the underlying mechanism of its maintenance function, we purified recombinant forms of full-length Dnmt1, a truncated form of Dnmt1-(291-1620) lacking the binding sites for PCNA and DNA and examined their processivity using a series of long unmethylated and hemimethylated DNA substrates. Direct analysis of methylation patterns using bisulfite-sequencing and hairpin-PCR techniques demonstrated that full-length Dnmt1 methylates hemimethylated DNA with high processivity and a fidelity of over 95%, but unmethylated DNA with much less processivity. The truncated form of Dnmt1 showed identical properties to full-length Dnmt1 indicating that the N-terminal 290-amino acid residue region of Dnmt1 is not required for preferential activity toward hemimethylated sites or for processivity of the enzyme. Remarkably, our analyses also revealed that Dnmt1 methylates hemimethylated CpG sites on one strand of double-stranded DNA during a single processive run. Our findings suggest that these inherent enzymatic properties of Dnmt1 play an essential role in the faithful and efficient maintenance of methylation patterns in the mammalian genome.
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Affiliation(s)
- Giedrius Vilkaitis
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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38
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Patnaik D, Chin HG, Estève PO, Benner J, Jacobsen SE, Pradhan S. Substrate specificity and kinetic mechanism of mammalian G9a histone H3 methyltransferase. J Biol Chem 2004; 279:53248-58. [PMID: 15485804 DOI: 10.1074/jbc.m409604200] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lysine-specific murine histone H3 methyltransferase, G9a, was expressed and purified in a baculovirus expression system. The primary structure of the recombinant enzyme is identical to the native enzyme. Enzymatic activity was favorable at alkaline conditions (>pH 8) and low salt concentration and virtually unchanged between 25 and 42 degrees C. Purified G9a was used for substrate specificity and steady-state kinetic analysis with peptides representing un- or dimethylated lysine 9 histone H3 tails with native lysine 4 or with lysine 4 changed to alanine (K4AK9). In vitro methylation of the H3 tail peptide resulted in trimethylation of Lys-9 and the reaction is processive. The turnover number (k(cat)) for methylation was 88 and 32 h(-1) on the wild type and K4AK9 histone H3 tail, respectively. The Michaelis constants for wild type and K4AK9 ((K(m)(pep))) were 0.9 and 1.0 microM and for S-adenosyl-L-methionine (K(m)(AdoMet)) were 1.8 and 0.6 microM, respectively. Comparable kinetic constants were obtained for recombinant histone H3. The conversion of K4AK9 di- to trimethyl-lysine was 7-fold slower than methyl group addition to unmethylated peptide. Preincubation studies showed that G9a-AdoMet and G9a-peptide complexes are catalytically active. Initial velocity data with peptide and S-adenosyl-L-methionine (AdoMet) and product inhibition studies with S-adenosyl-L-homocysteine were performed to assess the kinetic mechanism of the reaction. Double reciprocal plots and preincubation studies revealed S-adenosyl-L-homocysteine as a competitive inhibitor to AdoMet and mixed inhibitor to peptide. Trimethylated peptides acted as a competitive inhibitor to substrate peptide and mixed inhibitor to AdoMet suggesting a random mechanism in a Bi Bi reaction for recombinant G9a where either substrate can bind first to the enzyme, and either product can release first.
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39
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Abstract
Abstract
Several alternatively spliced variants of DNA methyltransferase (DNMT) 3b have been described. Here, we identified new murine Dnmt3b mRNA isoforms and found that mouse embryonic stem (ES) cells expressed only Dnmt3b transcripts that contained exons 10 and 11, whereas the Dnmt3b transcripts in somatic cells lacked these exons, suggesting that this region is important for embryonic development. DNMT3b2 and 3b3 were the major isoforms expressed in human cell lines and the mRNA levels of these isoforms closely correlated with their protein levels. Although DNMT3b3 may be catalytically inactive, it still may be biologically important because D4Z4 and satellites 2 and 3 repeat sequences, all known DNMT3b target sequences, were methylated in cells that predominantly expressed DNMT3b3. Treatment of cells with the mechanism-based inhibitor 5-aza-2′-deoxycytidine (5-Aza-CdR) caused a complete depletion of DNMT1, 3a, 3b1, and 3b2 proteins. Human DNMT3b3 and the murine Dnmt3b3-like isoform, Dnmt3b6, were also depleted although less efficiently, suggesting that DNMT3b3 also may be capable of DNA binding. Moreover, de novo methylation of D4Z4 in T24 cancer cells after 5-Aza-CdR treatment only occurred when DNMT3b3 was expressed, reinforcing its role as a contributing factor of DNA methylation. The expression of either DNMT3b2 or 3b3, however, was not sufficient to explain the abnormal methylation of DNMT3b target sequences in human cancers, which may therefore be dependent on factors that affect DNMT3b targeting. Methylation analyses of immunodeficiency, chromosomal instabilities, and facial abnormalities cells revealed that an Alu repeat sequence was highly methylated, suggesting that Alu sequences are not DNMT3b targets.
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40
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Zardo G, Reale A, De Matteis G, Buontempo S, Caiafa P. A role for poly(ADP-ribosyl)ation in DNA methylation. Biochem Cell Biol 2003; 81:197-208. [PMID: 12897854 DOI: 10.1139/o03-050] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The aberrant DNA methylation of promoter regions of housekeeping genes leads to gene silencing. Additional epigenetic events, such as histone methylation and acetylation, also play a very important role in the definitive repression of gene expression by DNA methylation. If the aberrant DNA methylation of promoter regions is the starting or the secondary event leading to the gene silencing is still debated. Mechanisms controlling DNA methylation patterns do exist although they have not been ultimately proven. Our data suggest that poly(ADP-ribosyl)ation might be part of this control mechanism. Thus an additional epigenetic modification seems to be involved in maintaining tissue and cell-type methylation patterns that when formed during embryo development, have to be rigorously conserved in adult organisms.
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Affiliation(s)
- Giuseppe Zardo
- Department of Cellular Biotechnologies and Hematology, University of Rome La Sapienza, Italy
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41
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Weisenberger DJ, Velicescu M, Preciado-Lopez MA, Gonzales FA, Tsai YC, Liang G, Jones PA. Identification and characterization of alternatively spliced variants of DNA methyltransferase 3a in mammalian cells. Gene 2002; 298:91-9. [PMID: 12406579 DOI: 10.1016/s0378-1119(02)00976-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
CpG methylation is mediated by the functions of at least three active DNA methyltransferases (DNMTs). While DNMT1 is thought to perform maintenance methylation, the more recently discovered DNMT3a and DNMT3b enzymes are thought to facilitate de novo methylation. Murine Dnmt3a and 3b are developmentally regulated and a new Dnmt3a isoform, Dnmt3a2, has been recently shown to be expressed preferentially in mouse embryonic stem (ES) cells. Here we have characterized four alternatively spliced variants of human and mouse DNMT3a. These transcripts included a novel exon 1 (1beta) that was spliced into the same exon 2 acceptor splice site used by the original exon 1 (1alpha). Cloning and sequencing of the 5' region of the human DNMT3a gene revealed that exon 1beta was situated upstream of exon 1alpha and that the entire region was contained within a CpG island. We also identified other alternatively spliced species containing intron 4 inclusions that were associated with either exon 1alpha or 1beta. These were expressed at low levels in mouse and human cells. All transcripts were highly conserved between human and mouse. The levels of Dnmt3a mRNA containing exon 1beta were 3-25-fold greater in mouse ES cells than in various somatic cells as determined by semiquantitative reverse transcription-polymerase chain reaction analysis, while the levels of exon 1alpha-containing transcripts were slightly higher in human and mouse somatic cells. The preferential expression of the beta transcript in ES cells suggests that this transcript, in addition to Dnmt3a2, may also be important for de novo methylation during development.
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Affiliation(s)
- Daniel J Weisenberger
- Urologic Cancer Research Laboratory, Department of Biochemistry and Molecular Biology, University of Southern California/Norris Comprehensive Cancer Center, Keck School of Medicine, 1441 Eastlake Avenue, Room 8302L, Los Angeles, CA 90089-9181, USA
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42
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Jørgensen HF, Bird A. MeCP2 and other methyl-CpG binding proteins. MENTAL RETARDATION AND DEVELOPMENTAL DISABILITIES RESEARCH REVIEWS 2002; 8:87-93. [PMID: 12112733 DOI: 10.1002/mrdd.10021] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
DNA methylation is an epigenetic modification that is implicated in transcriptional silencing. Recently, it has become increasingly clear that both correct levels and proper interpretation of methylation are important factors for normal development and function of the human organism. One example is the neurological disorder Rett syndrome (RTT), which affects approximately one in 10,000 girls. RTT is caused by mutations in MeCP2, a protein that was identified by its ability to bind specifically to CpG-methylated DNA. Furthermore, MeCP2 represses transcription in a methylation-dependent manner, and it is the founding member of the family of methyl-CpG binding domain (MBD) proteins.
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Affiliation(s)
- Helle Faerk Jørgensen
- The Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, United Kingdom
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43
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Abstract
Methylation of cytosines within the CpG dinucleotide by DNA methyltransferases is involved in regulating transcription and chromatin structure, controlling the spread of parasitic elements, maintaining genome stability in the face of vast amounts of repetitive DNA, and X chromosome inactivation. Cellular DNA methylation is highly compartmentalized over the mammalian genome and this compartmentalization is essential for embryonic development. When the complicated mechanisms that control which DNA sequences become methylated go awry, a number of inherited genetic diseases and cancer may result. Much new information has recently come to light regarding how cellular DNA methylation patterns may be established during development and maintained in somatic cells. Emerging evidence indicates that various chromatin states such as histone modifications (acetylation and methylation) and nucleosome positioning (modulated by ATP-dependent chromatin remodeling machines) determine DNA methylation patterning. Additionally, various regulatory factors interacting with the DNA methyltransferases may direct them to specific DNA sequences, regulate their enzymatic activity, and allow their use as transcriptional repressors. Continued studies of the connections between DNA methylation and chromatin structure and the DNA methyltransferase-associated proteins, will likely reveal that many, if not all, epigenetic modifications of the genome are directly connected. Such studies should also yield new insights into treating diseases involving aberrant DNA methylation.
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Affiliation(s)
- Keith D Robertson
- Epigenetic Gene Regulation and Cancer Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, MD 20892, USA.
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Kim GD, Ni J, Kelesoglu N, Roberts RJ, Pradhan S. Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases. EMBO J 2002; 21:4183-95. [PMID: 12145218 PMCID: PMC126147 DOI: 10.1093/emboj/cdf401] [Citation(s) in RCA: 258] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2002] [Revised: 06/10/2002] [Accepted: 06/10/2002] [Indexed: 11/13/2022] Open
Abstract
Three different families of DNA (cytosine-5) methyltransferases, DNMT1, DUMT2, DNMT3a and DNMT3b, participate in establishing and maintaining genomic methylation patterns during mammalian development. These enzymes have a large N-terminal domain fused to a catalytic domain. The catalytic domain is homologous to prokaryotic (cytosine-5) methyltransferases and contains the catalytic PC dipeptide, while the N-terminus acts as a transcriptional repressor by recruiting several chromatin remodeling proteins. Here, we show that the human de novo enzymes hDNMT3a and hDNMT3b form complexes with the major maintenance enzyme hDNMT1. Antibodies against hDNMT1 pull down both the de novo enzymes. Furthermore, the N-termini of the enzymes are involved in protein-protein interactions. Immunocytochemical staining revealed mostly nuclear co-localization of the fusion proteins, with the exception of hDNMT3a, which is found either exclusively in cytoplasm or in both nucleus and cytoplasm. Pre-methylated substrate DNAs exhibited differential methylation by de novo and maintenance enzymes. In vivo co-expression of hDNMT1 and hDNMT3a or hDNMT3b leads to methylation spreading in the genome, suggesting co-operation between de novo and maintenance enzymes during DNA methylation.
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Affiliation(s)
- Gun-Do Kim
- New England Biolabs, 32 Tozer Road, Beverly, MA 01915 and Cell Signaling Technology Inc., 166B Cummings Center, Beverly, MA 01915, USA Present address: Korea Research Institute of Chemical Technology, Yusung, Taejon 305-600, South Korea Present address: Celera Genomics Inc., 45 West Gude Drive, Rockville, MD 20850, USA Corresponding author e-mail:
| | - Jingwei Ni
- New England Biolabs, 32 Tozer Road, Beverly, MA 01915 and Cell Signaling Technology Inc., 166B Cummings Center, Beverly, MA 01915, USA Present address: Korea Research Institute of Chemical Technology, Yusung, Taejon 305-600, South Korea Present address: Celera Genomics Inc., 45 West Gude Drive, Rockville, MD 20850, USA Corresponding author e-mail:
| | - Nicole Kelesoglu
- New England Biolabs, 32 Tozer Road, Beverly, MA 01915 and Cell Signaling Technology Inc., 166B Cummings Center, Beverly, MA 01915, USA Present address: Korea Research Institute of Chemical Technology, Yusung, Taejon 305-600, South Korea Present address: Celera Genomics Inc., 45 West Gude Drive, Rockville, MD 20850, USA Corresponding author e-mail:
| | - Richard J. Roberts
- New England Biolabs, 32 Tozer Road, Beverly, MA 01915 and Cell Signaling Technology Inc., 166B Cummings Center, Beverly, MA 01915, USA Present address: Korea Research Institute of Chemical Technology, Yusung, Taejon 305-600, South Korea Present address: Celera Genomics Inc., 45 West Gude Drive, Rockville, MD 20850, USA Corresponding author e-mail:
| | - Sriharsa Pradhan
- New England Biolabs, 32 Tozer Road, Beverly, MA 01915 and Cell Signaling Technology Inc., 166B Cummings Center, Beverly, MA 01915, USA Present address: Korea Research Institute of Chemical Technology, Yusung, Taejon 305-600, South Korea Present address: Celera Genomics Inc., 45 West Gude Drive, Rockville, MD 20850, USA Corresponding author e-mail:
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45
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Brank AS, Van Bemmel DM, Christman JK. Optimization of baculovirus-mediated expression and purification of hexahistidine-tagged murine DNA (cytosine-C5)-methyltransferase-1 in Spodoptera frugiperda 9 cells. Protein Expr Purif 2002; 25:31-40. [PMID: 12071696 DOI: 10.1006/prep.2001.1606] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Enzymatic DNA methylation of carbon 5 of cytosines is an epigenetic modification that plays a role in regulating gene expression, differentiation, and tumorigenesis. DNA (cytosine-C5)-methyltransferase-1 is the enzyme responsible for maintaining established methylation patterns during replication in mammalian cells. It is composed of a large ( approximately 1100 amino acids (a.a.)) amino-terminal region containing many putative regulatory domains and a smaller ( approximately 500 a.a.) carboxy-terminal region containing conserved, catalytic domains. In this study, murine DNA (cytosine C5)-methyltransferase-1, fused to an amino-terminal hexahistidine tag, was expressed by infecting Spodoptera frugiperda cells for 46 h with a recombinant baculovirus carrying the DNA (cytosine-C5)-methyltransferase-1 cDNA. A total of 3 x 10(8) infected S. frugiperda cells yielded approximately 1 mg of full-length, hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1, which was purified approximately 450-fold from RNase-treated S. frugiperda cell extracts by nickel affinity chromatography. The characterization of hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1 through DNA methylation and inhibitor-binding assays indicated that the purified enzyme had at least a 30-fold higher catalytic efficiency with hemimethylated double-stranded oligodeoxyribonucleotide substrates than unmethylated substrates and was most active with small oligodeoxyribonucleotide substrates with a capacity for forming stem-loop structures. The expression and purification procedures reported here differ significantly from the original reports of baculovirus-mediated hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1 expression and purification by nickel affinity chromatography and provide a consistent yield of active enzyme.
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Affiliation(s)
- Adam S Brank
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
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46
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Yokochi T, Robertson KD. Preferential methylation of unmethylated DNA by Mammalian de novo DNA methyltransferase Dnmt3a. J Biol Chem 2002; 277:11735-45. [PMID: 11821381 DOI: 10.1074/jbc.m106590200] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA methylation is an epigenetic modification of DNA. There are currently three catalytically active mammalian DNA methyltransferases, DNMT1, -3a, and -3b. DNMT1 has been shown to have a preference for hemimethylated DNA and has therefore been termed the maintenance methyltransferase. Although previous studies on DNMT3a and -3b revealed that they act as functional enzymes during development, there is little biochemical evidence about how new methylation patterns are established and maintained. To study this mechanism we have cloned and expressed Dnmt3a using a baculovirus expression system. The substrate specificity of Dnmt3a and molecular mechanism of its methylation reaction were then analyzed using a novel and highly reproducible assay. We report here that Dnmt3a is a true de novo methyltransferase that prefers unmethylated DNA substrates more than 3-fold to hemimethylated DNA. Furthermore, Dnmt3a binds DNA nonspecifically, regardless of the presence of CpG dinucleotides in the DNA substrate. Kinetic analysis supports an Ordered Bi Bi mechanism for Dnmt3a, where DNA binds first, followed by S-adenosyl-l-methionine.
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Affiliation(s)
- Tomoki Yokochi
- Epigenetic Gene Regulation and Cancer Section, Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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47
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Davis CD, Uthus EO. Dietary selenite and azadeoxycytidine treatments affect dimethylhydrazine-induced aberrant crypt formation in rat colon and DNA methylation in HT-29 cells. J Nutr 2002; 132:292-7. [PMID: 11823593 DOI: 10.1093/jn/132.2.292] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Several observations implicate a role for altered DNA methylation in cancer pathogenesis. The global level of DNA methylation is generally lower; however, DNA methyltransferase (Dnmt1) activity is usually higher in tumor cells than in normal cells. The purpose of this study was to investigate whether the Dnmt1 inhibitor, 5-aza-2'-deoxycytidine (aza-dC) would alter the effect of dietary selenium on the formation of aberrant crypts. Weanling rats (n = 60) were fed three concentrations of selenium (deficient, 0.1 and 2.0 mg/kg diet) in a Torula yeast-based diet. Half of the rats were injected weekly with aza-dC (1 mg/kg, subcutaneously) and half were injected with the vehicle control (PBS). After 3.5 wk of consuming the experimental diets, the rats were given two injections of dimethylhydrazine (DMH; 25 mg/kg, intraperitoneally). Rats fed the selenium-deficient diet and injected with PBS had significantly (P < 0.006) more aberrant crypts than rats fed 0.1 or 2.0 mg selenium/kg diet (244 +/- 21 vs. 165 +/- 9 and 132 +/- 14, respectively). In contrast, when rats were injected with aza-dC, there was a significant (P < 0.0001) reduction in aberrant crypt formation and dietary selenium had no effect (62 +/- 8 vs. 77 +/- 13 vs. 54 +/- 8, in rats fed 0, 0.1 and 2.0 mg selenium/kg diet, respectively). HT-29 cells cultured in the absence of selenium had significantly hypomethylated DNA but significantly more Dnmt1 protein expression than cells cultured in the presence of 1 or 2 micromol/L selenium. These results suggest that aza-dC treatment may protect selenium-deficient rats against carcinogen-induced aberrant crypt formation.
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Affiliation(s)
- Cindy D Davis
- U.S. Department of Agriculture, Grand Forks Human Nutrition Research Center, Grand Forks, ND 58202-9034, USA.
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48
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Lin IG, Han L, Taghva A, O'Brien LE, Hsieh CL. Murine de novo methyltransferase Dnmt3a demonstrates strand asymmetry and site preference in the methylation of DNA in vitro. Mol Cell Biol 2002; 22:704-23. [PMID: 11784849 PMCID: PMC133553 DOI: 10.1128/mcb.22.3.704-723.2002] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2001] [Accepted: 10/23/2001] [Indexed: 11/20/2022] Open
Abstract
CpG methylation is involved in a wide range of biological processes in vertebrates as well as in plants and fungi. To date, three enzymes, Dnmt1, Dnmt3a, and Dnmt3b, are known to have DNA methyltransferase activity in mouse and human. It has been proposed that de novo methylation observed in early embryos is predominantly carried out by the Dnmt3a and Dnmt3b methyltransferases, while Dntm1 is believed to be responsible for maintaining the established methylation patterns upon replication. Analysis of the sites methylated in vivo using the bisulfite genomic sequencing method confirms the previous finding that some regions of the plasmid are much more methylated by Dnmt3a than other regions on the same plasmid. However, the preferred targets of the enzyme cannot be determined due to the presence of other methylases, DNA binding proteins, and chromatin structure. To discern the DNA targets of Dnmt3a without these compounding factors, sites methylated by Dnmt3a in vitro were analyzed. These analyses revealed that the two cDNA strands have distinctly different methylation patterns. Dnmt3a prefers CpG sites on a strand in which it is flanked by pyrimidines over CpG sites flanked by purines in vitro. These findings indicate that, unlike Dnmt1, Dnmt3a most likely methylates one strand of DNA without concurrent methylation of the CpG site on the complementary strand. These findings also indicate that Dnmt3a may methylate some CpG sites more frequently than others, depending on the sequence context. Methylation of each DNA strand independently and with possible sequence preference is a novel feature among the known DNA methyltransferases.
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Affiliation(s)
- Iping G Lin
- Department of Urology, University of Southern California, Norris Cancer Center, Los Angeles, California 90033, USA
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49
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Müller-Tidow C, Kügler K, Diederichs S, Klümpen S, Möller M, Vogt U, Metzger R, Schneider PM, Berdel WE, Serve H. Loss of expression of HDAC-recruiting methyl-CpG-binding domain proteins in human cancer. Br J Cancer 2001; 85:1168-74. [PMID: 11710831 PMCID: PMC2375156 DOI: 10.1054/bjoc.2001.2041] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dysregulation of CpG-methylation is a common feature of many human cancers and tumour suppressor genes can be silenced by hypermethylation. Recently, 2 methyl-CpG-binding domain proteins have been linked to gene inactivation by their ability to recruit co-repressors and HDAC-activity to methylated gene promoters. Here, we have analysed mRNA expression of these genes, MeCP2 and MBD2, in a wide variety of primary human tumours. In solid tumours, expression levels of MBD2 (57/71) and MeCP2 (64/71) were significantly reduced in the majority of primary tumours as detected by quantitative real-time RT-PCR. Western blot analyses of MeCP2 in matched tumour-normal samples of patients with non-small-cell lung cancer (NSCLC) indicated reduced protein in a significant percentage of patients. In acute myelogenous leukaemia (n = 26), expression levels were only slightly reduced and did not differ between samples analysed at diagnosis or at the time of relapse. In early-stage NSCLC (n = 70) expression of MeCP2 and MBD2 was significantly lower in squamous cell carcinoma than in adenocarcinoma or large cell carcinoma (P = 0.03 and P = 0.01). To further elucidate the mechanisms of gene regulation, we analysed MeCP2 and MBD2 regulation during haematopoietic differentiation. No significant changes in MeCP2 or MBD2 expression were found when NB4 cells were differentiated toward granulocytes suggesting that neither differentiation nor cell cycle status were relevant for the reduced expression of these genes in human cancer. In conclusion, the significant loss of MeCP2 and MBD2 expression in human cancers suggests a potential role of this phenomenon in the development of solid human tumours.
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Affiliation(s)
- C Müller-Tidow
- Department of Medicine, Hematology and Oncology, University of Münster, Germany
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50
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Fatemi M, Hermann A, Pradhan S, Jeltsch A. The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA. J Mol Biol 2001; 309:1189-99. [PMID: 11399088 DOI: 10.1006/jmbi.2001.4709] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mammalian DNA methyltransferase Dnmt1 is responsible for the maintenance of the pattern of DNA methylation in vivo. It is a large multidomain enzyme comprising 1620 amino acid residues. We have purified and characterized individual domains of Dnmt1 (NLS-containing domain, NlsD, amino acid residues: 1-343; replication foci-directing domain, 350-609; Zn-binding domain (ZnD), 613-748; polybromo domain, 746-1110; and the catalytic domain (CatD), 1124-1620). CatD, ZnD and NlsD bind to DNA, demonstrating the existence of three independent DNA-binding sites in Dnmt1. CatD shows a preference for binding to hemimethylated CpG-sites; ZnD prefers methylated CpGs; and NlsD specifically binds to CpG-sites, but does not discriminate between unmethylated and methylated DNA. These results are not compatible with the suggestion that the target recognition domain of Dnmt1 resides in the N terminus of the enzyme. We show by protein-protein interaction assays that ZnD and CatD interact with each other. The isolated catalytic domain does not methylate DNA, neither alone nor in combination with other domains. Full-length Dnmt1 was purified from baculovirus-infected insect cells. Under the experimental conditions, Dnmt1 has a strong (50-fold) preference for hemimethylated DNA. Dnmt1 is stimulated to methylate unmodified CpG sites by the addition of fully methylated DNA. This effect is dependent on Zn, suggesting that binding of methylated DNA to ZnD triggers the allosteric activation of the catalytic center of Dnmt1. The allosteric activation model can explain kinetic data obtained by others. It suggests that Dnmt1 might be responsible for spreading of methylation, a process that is observed during aging and carcenogenesis but may be important for de novo methylation of DNA.
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Affiliation(s)
- M Fatemi
- Institut für Biochemie Fachbereich 8, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, Giessen, 35392, Germany
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