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Dar MS, Mensah IK, He M, McGovern S, Sohal IS, Whitlock HC, Bippus NE, Ceminsky M, Emerson ML, Tan HJ, Hall MC, Gowher H. Dnmt3bas coordinates transcriptional induction and alternative exon inclusion to promote catalytically active Dnmt3b expression. Cell Rep 2023; 42:112587. [PMID: 37294637 PMCID: PMC10592478 DOI: 10.1016/j.celrep.2023.112587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 06/11/2023] Open
Abstract
Embryonic expression of DNMT3B is critical for establishing de novo DNA methylation. This study uncovers the mechanism through which the promoter-associated long non-coding RNA (lncRNA) Dnmt3bas controls the induction and alternative splicing of Dnmt3b during embryonic stem cell (ESC) differentiation. Dnmt3bas recruits the PRC2 (polycomb repressive complex 2) at cis-regulatory elements of the Dnmt3b gene expressed at a basal level. Correspondingly, Dnmt3bas knockdown enhances Dnmt3b transcriptional induction, whereas overexpression of Dnmt3bas dampens it. Dnmt3b induction coincides with exon inclusion, switching the predominant isoform from the inactive Dnmt3b6 to the active Dnmt3b1. Intriguingly, overexpressing Dnmt3bas further enhances the Dnmt3b1:Dnmt3b6 ratio, attributed to its interaction with hnRNPL (heterogeneous nuclear ribonucleoprotein L), a splicing factor that promotes exon inclusion. Our data suggest that Dnmt3bas coordinates alternative splicing and transcriptional induction of Dnmt3b by facilitating the hnRNPL and RNA polymerase II (RNA Pol II) interaction at the Dnmt3b promoter. This dual mechanism precisely regulates the expression of catalytically active DNMT3B, ensuring fidelity and specificity of de novo DNA methylation.
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Affiliation(s)
- Mohd Saleem Dar
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ikjot Singh Sohal
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Nina Elise Bippus
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Madison Ceminsky
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Martin L Emerson
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Hern J Tan
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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2
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Ma Y, Budde MW, Zhu J, Elowitz MB. Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density. bioRxiv 2023:2023.05.30.542205. [PMID: 37398290 PMCID: PMC10312471 DOI: 10.1101/2023.05.30.542205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Methylation of cytosines in CG dinucleotides (CpGs) within promoters has been shown to lead to gene silencing in mammals in natural contexts. Recently, engineered recruitment of methyltransferases (DNMTs) at specific loci was shown to be sufficient to silence synthetic and endogenous gene expression through this mechanism. A critical parameter for DNA methylation-based silencing is the distribution of CpGs within the target promoter. However, how the number or density of CpGs in the target promoter affects the dynamics of silencing by DNMT recruitment has remained unclear. Here we constructed a library of promoters with systematically varying CpG content, and analyzed the rate of silencing in response to recruitment of DNMT. We observed a tight correlation between silencing rate and CpG content. Further, methylation-specific analysis revealed a constant accumulation rate of methylation at the promoter after DNMT recruitment. We identified a single CpG site between TATA box and transcription start site (TSS) that accounted for a substantial part of the difference in silencing rates between promoters with differing CpG content, indicating that certain residues play disproportionate roles in controlling silencing. Together, these results provide a library of promoters for synthetic epigenetic and gene regulation applications, as well as insights into the regulatory link between CpG content and silencing rate.
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Affiliation(s)
- Yitong Ma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125, USA
| | - Mark W. Budde
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125, USA
- Primordium Labs, Arcadia, CA 91006, USA
| | - Junqin Zhu
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Michael B. Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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3
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So JY, Skrypek N, Yang HH, Merchant AS, Nelson GW, Chen WD, Ishii H, Chen JM, Hu G, Achyut BR, Yoon EC, Han L, Huang C, Cam MC, Zhao K, Lee MP, Yang L. Induction of DNMT3B by PGE2 and IL6 at Distant Metastatic Sites Promotes Epigenetic Modification and Breast Cancer Colonization. Cancer Res 2020; 80:2612-2627. [PMID: 32265226 PMCID: PMC7299749 DOI: 10.1158/0008-5472.can-19-3339] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/26/2020] [Accepted: 03/27/2020] [Indexed: 11/16/2022]
Abstract
Current cancer treatments are largely based on the genetic characterization of primary tumors and are ineffective for metastatic disease. Here we report that DNA methyltransferase 3B (DNMT3B) is induced at distant metastatic sites and mediates epigenetic reprogramming of metastatic tumor cells. Multiomics analysis and spontaneous metastatic mouse models revealed that DNMT3B alters multiple pathways including STAT3, NFκB, PI3K/Akt, β-catenin, and Notch signaling, which are critical for cancer cell survival, apoptosis, proliferation, invasion, and colonization. PGE2 and IL6 were identified as critical inflammatory mediators in DNMT3B induction. DNMT3B expression levels positively correlated with human metastatic progression. Targeting IL6 or COX-2 reduced DNMT3B induction and improved chemo or PD1 therapy. We propose a novel mechanism linking the metastatic microenvironment with epigenetic alterations that occur at distant sites. These results caution against the "Achilles heel" in cancer therapies based on primary tumor characterization and suggests targeting DNMT3B induction as new option for treating metastatic disease. SIGNIFICANCE: These findings reveal that DNMT3B epigenetically regulates multiple pro-oncogenic signaling pathways via the inflammatory microenvironment at distant sites, cautioning the clinical approach basing current therapies on genetic characterization of primary tumors.
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Affiliation(s)
- Jae Young So
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Nicolas Skrypek
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Howard H Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Anand S Merchant
- Collaborative Bioinformatics Resource, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - George W Nelson
- Collaborative Bioinformatics Resource, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Wei-Dong Chen
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Hiroki Ishii
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Jennifer M Chen
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Gangqing Hu
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Bhagelu R Achyut
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Esther C Yoon
- Department of Pathology, New York Medical College, Valhalla, New York
| | - Liying Han
- Department of Pathology, New York Medical College, Valhalla, New York
| | - Chuanshu Huang
- Department of Environmental Medicine and Biochemistry and Molecular Pharmacology, New York University School of Medicine, Tuxedo, New York
| | - Margaret C Cam
- Collaborative Bioinformatics Resource, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Maxwell P Lee
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Li Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
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Chand V, Pandey A, Kopanja D, Guzman G, Raychaudhuri P. Opposing Roles of the Forkhead Box Factors FoxM1 and FoxA2 in Liver Cancer. Mol Cancer Res 2019; 17:1063-1074. [PMID: 30814128 PMCID: PMC6497570 DOI: 10.1158/1541-7786.mcr-18-0968] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/10/2018] [Accepted: 02/22/2019] [Indexed: 12/11/2022]
Abstract
The forkhead box transcription factor FoxM1 is essential for hepatocellular carcinoma (HCC) development, and its overexpression coincides with poor prognosis. Here, we show that the mechanisms by which FoxM1 drives HCC progression involve overcoming the inhibitory effects of the liver differentiation gene FoxA2. First, the expression patterns of FoxM1 and FoxA2 in human HCC are opposite. We show that FoxM1 represses expression of FoxA2 in G1 phase. Repression of FoxA2 in G1 phase is important, as it is capable of inhibiting expression of the pluripotency genes that are expressed mainly in S-G2 phases. Using a transgenic mouse model for oncogenic Ras-driven HCC, we provide genetic evidence for a repression of FoxA2 by FoxM1. Conversely, FoxA2 inhibits expression of FoxM1 and inhibits FoxM1-induced tumorigenicity. Also, FoxA2 inhibits Ras-induced HCC progression that involves FoxM1. IMPLICATIONS: The observations provide strong genetic evidence for an opposing role of FoxM1 and FoxA2 in HCC progression. Moreover, FoxM1 drives high-grade HCC progression partly by inhibiting the hepatocyte differentiation gene FoxA2.
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Affiliation(s)
- Vaibhav Chand
- Department of Biochemistry and Molecular Genetics, University of Illinois, College of Medicine, Chicago, Illinois
| | - Akshay Pandey
- Department of Biochemistry and Molecular Genetics, University of Illinois, College of Medicine, Chicago, Illinois
| | - Dragana Kopanja
- Department of Biochemistry and Molecular Genetics, University of Illinois, College of Medicine, Chicago, Illinois
| | - Grace Guzman
- Department of Pathology, University of Illinois, College of Medicine, Chicago, Illinois
| | - Pradip Raychaudhuri
- Department of Biochemistry and Molecular Genetics, University of Illinois, College of Medicine, Chicago, Illinois.
- Jesse Brown VA Medical Center, Chicago, Illinois
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5
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Lin L, Liu Y, Xu F, Huang J, Daugaard TF, Petersen TS, Hansen B, Ye L, Zhou Q, Fang F, Yang L, Li S, Fløe L, Jensen KT, Shrock E, Chen F, Yang H, Wang J, Liu X, Xu X, Bolund L, Nielsen AL, Luo Y. Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience 2018; 7:1-19. [PMID: 29635374 PMCID: PMC5888497 DOI: 10.1093/gigascience/giy011] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/29/2017] [Accepted: 02/12/2018] [Indexed: 12/31/2022] Open
Abstract
Background Fusion of DNA methyltransferase domains to the nuclease-deficient clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 9 (dCas9) has been used for epigenome editing, but the specificities of these dCas9 methyltransferases have not been fully investigated. Findings We generated CRISPR-guided DNA methyltransferases by fusing the catalytic domain of DNMT3A or DNMT3B to the C terminus of the dCas9 protein from Streptococcus pyogenes and validated its on-target and global off-target characteristics. Using targeted quantitative bisulfite pyrosequencing, we prove that dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B can efficiently methylate the CpG dinucleotides flanking its target sites at different genomic loci (uPA and TGFBR3) in human embryonic kidney cells (HEK293T). Furthermore, we conducted whole genome bisulfite sequencing (WGBS) to address the specificity of our dCas9 methyltransferases. WGBS revealed that although dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B did not cause global methylation changes, a substantial number (more than 1000) of the off-target differentially methylated regions (DMRs) were identified. The off-target DMRs, which were hypermethylated in cells expressing dCas9 methyltransferase and guide RNAs, were predominantly found in promoter regions, 5΄ untranslated regions, CpG islands, and DNase I hypersensitivity sites, whereas unexpected hypomethylated off-target DMRs were significantly enriched in repeated sequences. Through chromatin immunoprecipitation with massive parallel DNA sequencing analysis, we further revealed that these off-target DMRs were weakly correlated with dCas9 off-target binding sites. Using quantitative polymerase chain reaction, RNA sequencing, and fluorescence reporter cells, we also found that dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B can mediate transient inhibition of gene expression, which might be caused by dCas9-mediated de novo DNA methylation as well as interference with transcription. Conclusion Our results prove that dCas9 methyltransferases cause efficient RNA-guided methylation of specific endogenous CpGs. However, there is significant off-target methylation indicating that further improvements of the specificity of CRISPR-dCas9 based DNA methylation modifiers are required.
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Affiliation(s)
- Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Danish Regenerative Engineering Alliance for Medicine, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Yong Liu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jinrong Huang
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Bettina Hansen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Qing Zhou
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
| | - Fang Fang
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
| | - Ling Yang
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
| | - Shengting Li
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Lasse Fløe
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Ellen Shrock
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fang Chen
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Danish Regenerative Engineering Alliance for Medicine, Department of Biomedicine, Aarhus University, Aarhus, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
- BGI-Qingdao, 2877 Tuanjie Road, Sino-German Ecopark, Qingdao, 266000, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, China
| | | | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Danish Regenerative Engineering Alliance for Medicine, Department of Biomedicine, Aarhus University, Aarhus, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China
- BGI-Qingdao, 2877 Tuanjie Road, Sino-German Ecopark, Qingdao, 266000, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, China
- BrainStem - Stem Cell Center of Excellence in Neurology, Copenhagen, Denmark
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6
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Zhou C, Huang C, Wang J, Huang H, Li J, Xie Q, Liu Y, Zhu J, Li Y, Zhang D, Zhu Q, Huang C. LncRNA MEG3 downregulation mediated by DNMT3b contributes to nickel malignant transformation of human bronchial epithelial cells via modulating PHLPP1 transcription and HIF-1α translation. Oncogene 2017; 36:3878-3889. [PMID: 28263966 PMCID: PMC5525547 DOI: 10.1038/onc.2017.14] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/11/2016] [Accepted: 12/27/2016] [Indexed: 02/08/2023]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as key factors in various fundamental cellular biological processes, and many of them are likely to have functional roles in tumorigenesis. Maternally expressed gene 3 (MEG3) is an imprinted gene located at 14q32 that encodes a lncRNA, and the decreased MEG3 expression has been reported in multiple cancer tissues. However, nothing is known about the alteration and role of MEG3 in environmental carcinogen-induced lung tumorigenesis. Our present study, for the first time to the best of our knowledge, discovered that environmental carcinogen nickel exposure led to MEG3 downregulation, consequently initiating c-Jun-mediated PHLPP1 transcriptional inhibition and hypoxia-inducible factor-1α (HIF-1α) protein translation upregulation, in turn resulting in malignant transformation of human bronchial epithelial cells. Mechanistically, MEG3 downregulation was attributed to nickel-induced promoter hypermethylation via elevating DNMT3b expression, whereas PHLPP1 transcriptional inhibition was due to the decreasing interaction of MEG3 with its inhibitory transcription factor c-Jun. Moreover, HIF-1α protein translation was upregulated via activating the Akt/p70S6K/S6 axis resultant from PHLPP1 inhibition in nickel responses. Collectively, we uncover that nickel exposure results in DNMT3b induction and MEG3 promoter hypermethylation and expression inhibition, further reduces its binding to c-Jun and in turn increasing c-Jun inhibition of PHLPP1 transcription, leading to the Akt/p70S6K/S6 axis activation, and HIF-1α protein translation, as well as malignant transformation of human bronchial epithelial cells. Our studies provide a significant insight into understanding the alteration and role of MEG3 in nickel-induced lung tumorigenesis.
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MESH Headings
- Adenocarcinoma/enzymology
- Adenocarcinoma/pathology
- Adenocarcinoma of Lung
- Bronchi/pathology
- Carcinogens/toxicity
- Carcinoma, Squamous Cell/enzymology
- Carcinoma, Squamous Cell/pathology
- Cell Line
- Cell Transformation, Neoplastic/chemically induced
- Cell Transformation, Neoplastic/metabolism
- DNA (Cytosine-5-)-Methyltransferases/physiology
- Down-Regulation
- Epithelial Cells/enzymology
- Gene Expression Regulation, Neoplastic
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Lung Neoplasms/enzymology
- Lung Neoplasms/pathology
- Nickel/toxicity
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phosphoprotein Phosphatases/genetics
- Phosphoprotein Phosphatases/metabolism
- Promoter Regions, Genetic
- Protein Biosynthesis
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Transcription, Genetic
- DNA Methyltransferase 3B
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Affiliation(s)
- Chengfan Zhou
- Department of Occupational and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
| | - Chao Huang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
| | - Jingjing Wang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jingxia Li
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
| | - Qipeng Xie
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yu Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Junlan Zhu
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
| | - Yang Li
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
| | - Dongyun Zhang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
| | - Qixing Zhu
- Department of Occupational and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
| | - Chuanshu Huang
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
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7
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Rajabi H, Tagde A, Alam M, Bouillez A, Pitroda S, Suzuki Y, Kufe D. DNA methylation by DNMT1 and DNMT3b methyltransferases is driven by the MUC1-C oncoprotein in human carcinoma cells. Oncogene 2016; 35:6439-6445. [PMID: 27212035 PMCID: PMC5121097 DOI: 10.1038/onc.2016.180] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/25/2016] [Accepted: 04/12/2016] [Indexed: 12/23/2022]
Abstract
Aberrant expression of the DNA methyltransferases (DNMTs) and disruption of DNA methylation patterns are associated with carcinogenesis and cancer cell survival. The oncogenic MUC1-C protein is aberrantly overexpressed in diverse carcinomas; however, there is no known link between MUC1-C and DNA methylation. Our results demonstrate that MUC1-C induces the expression of DNMT1 and DNMT3b, but not DNMT3a, in breast and other carcinoma cell types. We show that MUC1-C occupies the DNMT1 and DNMT3b promoters in complexes with NF-κB p65 and drives DNMT1 and DNMT3b transcription. In this way, MUC1-C controls global DNA methylation as determined by analysis of LINE-1 repeat elements. The results further demonstrate that targeting MUC1-C downregulates DNA methylation of the CDH1 tumor suppressor gene in association with induction of E-cadherin expression. These findings provide compelling evidence that MUC1-C is of functional importance to induction of DNMT1 and DNMT3b and, in turn, changes in DNA methylation patterns in cancer cells.
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Affiliation(s)
- H Rajabi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - A Tagde
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - M Alam
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - A Bouillez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - S Pitroda
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
| | - Y Suzuki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - D Kufe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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8
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Abstract
Published data on the association between DNA methyltransferase (DNMT) 3B -149C/T polymorphism and cancer risk remain inconclusive. To derive a more precise estimation for this association, we performed a meta-analysis of 5,903 cancer cases and 8,132 controls from 22 published case-control studies. We used odds ratios (ORs) with 95 % confidence intervals (CIs) to assess the strength of the association. Our meta-analysis suggested that DNMT3B -149C/T polymorphism was associated with the risk of head and neck cancer under heterozygote comparison (OR 0.73, 95 % CI 0.59-0.90) and dominant model (OR 1.75, 95 % CI 0.62-0.92), although no evidence of association between DNMT3B -149C/T polymorphism and cancer risk was observed as we compared in the pooled analyses (homozygote comparison: OR 0.96, 95 % CI 0.86-1.09; heterozygote comparison: OR 1.07, 95 % CI 0.86-0.32; dominant model: OR 1.03, 95 % CI 0.85-1.25; recessive model: OR 0.93, 95 % CI 0.8-1.08). More studies are needed to detect DNMT3B -149C/T polymorphism and its association with cancer in different ethnic populations incorporated with environment exposures in the susceptibility of different kinds of cancer.
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Affiliation(s)
- Jing Zhu
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Three Gorges University, Yichang, 443000 China
| | - Songtao Du
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
| | - Jiaqi Zhang
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
| | - Yingnan Wang
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
| | - Qiaoling Wu
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
| | - Jixiang Ni
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yichang, 2# Jiefang Road, Yichang, 443000 Hubei Province China
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Three Gorges University, Yichang, 443000 China
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9
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Yang X, Han H, De Carvalho DD, Lay FD, Jones PA, Liang G. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell 2014; 26:577-90. [PMID: 25263941 PMCID: PMC4224113 DOI: 10.1016/j.ccr.2014.07.028] [Citation(s) in RCA: 774] [Impact Index Per Article: 77.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 03/18/2014] [Accepted: 07/29/2014] [Indexed: 02/08/2023]
Abstract
DNA methylation in promoters is well known to silence genes and is the presumed therapeutic target of methylation inhibitors. Gene body methylation is positively correlated with expression, yet its function is unknown. We show that 5-aza-2'-deoxycytidine treatment not only reactivates genes but decreases the overexpression of genes, many of which are involved in metabolic processes regulated by c-MYC. Downregulation is caused by DNA demethylation of the gene bodies and restoration of high levels of expression requires remethylation by DNMT3B. Gene body methylation may, therefore, be an unexpected therapeutic target for DNA methylation inhibitors, resulting in the normalization of gene overexpression induced during carcinogenesis. Our results provide direct evidence for a causal relationship between gene body methylation and transcription.
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Affiliation(s)
- Xiaojing Yang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Han Han
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel D De Carvalho
- The Princess Margaret Cancer Centre, University Health Network, Toronto ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto ON M5G 2M9, Canada
| | - Fides D Lay
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter A Jones
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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10
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Wongtrakoongate P, Li J, Andrews PW. Aza-deoxycytidine induces apoptosis or differentiation via DNMT3B and targets embryonal carcinoma cells but not their differentiated derivatives. Br J Cancer 2014; 110:2131-8. [PMID: 24603304 PMCID: PMC3992495 DOI: 10.1038/bjc.2014.128] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Teratocarcinoma is a malignant male germ cell tumour, which contains stem cells and differentiated cancer tissues. DNMT3B has been shown to be highly expressed in human teratocarcinoma stem cells, and to mediate cytotoxicity of Aza-deoxycytidine (Aza-dC) in a pluripotent stem cell line NTERA2. METHODS We have established DNMT3B or POU5F1 (hereafter referred to as OCT4) knockdown in teratocarcinoma stem cells N2102Ep and TERA1 and in the pluripotent NTERA2 by a doxycycline-inducible system, and tested the cytotoxicity induced by Aza-dC. RESULTS Silencing of DNMT3B led to apoptosis of human teratocarcinoma stem cells N2102Ep and TERA1. Further, we found that induction of apoptosis or differentiation in NTERA2 and human embryonic stem cells by Aza-dC requires DNMT3B. To test whether Aza-dC inhibits proliferation of differentiated teratocarcinoma cells, we depleted OCT4 expression in N2102Ep and TERA1 cells treated with Aza-dC. Treatment with Aza-dC reduced cell number of differentiated cells to a lesser extent than their undifferentiated parental stem cells. Moreover, in contrast to the stem cells, Aza-dC failed to induce apoptosis of differentiated cells. CONCLUSIONS Our finding suggests that DNMT3B acts as an antiapoptotic gene in teratocarcinoma stem cells, and mediates apoptosis and differentiation of human pluripotent stem cells induced by Aza-dC, and that Aza-dC specifically induces apoptosis of teratocarcinoma stem cells.
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Affiliation(s)
- P Wongtrakoongate
- Centre for Stem Cell Biology, University of Sheffield, Sheffield S10 2TN, UK
| | - J Li
- Centre for Stem Cell Biology, University of Sheffield, Sheffield S10 2TN, UK
| | - P W Andrews
- Centre for Stem Cell Biology, University of Sheffield, Sheffield S10 2TN, UK
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11
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Horii T, Tamura D, Morita S, Kimura M, Hatada I. Generation of an ICF syndrome model by efficient genome editing of human induced pluripotent stem cells using the CRISPR system. Int J Mol Sci 2013; 14:19774-81. [PMID: 24084724 PMCID: PMC3821585 DOI: 10.3390/ijms141019774] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 09/11/2013] [Accepted: 09/17/2013] [Indexed: 12/22/2022] Open
Abstract
Genome manipulation of human induced pluripotent stem (iPS) cells is essential to achieve their full potential as tools for regenerative medicine. To date, however, gene targeting in human pluripotent stem cells (hPSCs) has proven to be extremely difficult. Recently, an efficient genome manipulation technology using the RNA-guided DNase Cas9, the clustered regularly interspaced short palindromic repeats (CRISPR) system, has been developed. Here we report the efficient generation of an iPS cell model for immunodeficiency, centromeric region instability, facial anomalies syndrome (ICF) syndrome using the CRISPR system. We obtained iPS cells with mutations in both alleles of DNA methyltransferase 3B (DNMT3B) in 63% of transfected clones. Our data suggest that the CRISPR system is highly efficient and useful for genome engineering of human iPS cells.
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Affiliation(s)
- Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (T.H.); (D.T.); (S.M.); (M.K.)
| | - Daiki Tamura
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (T.H.); (D.T.); (S.M.); (M.K.)
| | - Sumiyo Morita
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (T.H.); (D.T.); (S.M.); (M.K.)
| | - Mika Kimura
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (T.H.); (D.T.); (S.M.); (M.K.)
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (T.H.); (D.T.); (S.M.); (M.K.)
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12
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Wiley KL, Treadwell E, Manigaba K, Word B, Lyn-Cook BD. Ethnic differences in DNA methyltransferases expression in patients with systemic lupus erythematosus. J Clin Immunol 2013; 33:342-8. [PMID: 23054340 PMCID: PMC3573322 DOI: 10.1007/s10875-012-9803-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 09/16/2012] [Indexed: 11/26/2022]
Abstract
PURPOSE Systemic lupus erythematous (SLE) is a systemic autoimmune inflammatory disease with both genetic and epigenetic etiologies. Evidence suggests that deregulation of specific genes through epigenetic mechanisms may be a contributing factor to SLE pathology. There is increasing evidence that DNA methyltransferase activity may be involved. This study demonstrated modulation in expression of DNA methyltransferases (DNMTs) according to ethnicity in patients diagnosed with SLE. Furthermore, differential expression in one of the DNMTs was found in a subset of lupus patients on dehydroepiandrosterone (DHEA) therapy. METHODS Real-time PCR analyses of DNMT1, DNMT3A and DNMT3B in peripheral blood mononuclear cells from a cohort of African American and European American lupus and non-lupus women were conducted. Also, global DNA methylation was assessed using the MethylFlash(TM) methylated quantification colorimetric assay. RESULTS Significant increase in DNMT3A (p < 0.001) was shown in lupus patients when compared to age-matched healthy controls. This increase was associated with a higher SLEDI index. More striking was that expression levels for African American (AA) women were higher than European American women in the lupus populations. A subset of AA women on DHEA therapy showed a significant decrease (p < 0.05) in DNMT3A expression in comparison to lupus patients not on the therapy. DHEA is an androgenic steroid found in low levels in the serum of lupus patients. Supplementation of this hormone has been shown to be beneficial to some lupus patients. DHEA was not shown to effect DNMT1 or DNMT3B expression. Increased expression was also noted in DNMT3B (p < 0.05) in lupus patients compared to age-matched healthy controls. However, no significant difference was noted in DNMT1 (p = 0.2148) expression between lupus patients and healthy controls. Although increases were detected in de novo methyltransferases, a global decrease (p < 0.001) in 5-methycytosine was observed in lupus patients when compared to age-matched healthy controls. CONCLUSION These findings suggest that epigenetic changes may play a critical role in the manifestations of the disease observed among ethnic groups, particularly African American women who often have a higher incidence of lupus. DHEA therapy effects on DNMT3A expression in AA women warrant further investigation in a larger population.
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Affiliation(s)
- Kenneth L. Wiley
- FDA-National Center for Toxicological Research, 3900 NCTR Rd, Jefferson, AR 72079 USA
| | | | - Kayihura Manigaba
- FDA-National Center for Toxicological Research, 3900 NCTR Rd, Jefferson, AR 72079 USA
| | - Beverly Word
- FDA-National Center for Toxicological Research, 3900 NCTR Rd, Jefferson, AR 72079 USA
| | - Beverly D. Lyn-Cook
- FDA-National Center for Toxicological Research, 3900 NCTR Rd, Jefferson, AR 72079 USA
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13
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Ostler KR, Yang Q, Looney TJ, Zhang L, Vasanthakumar A, Tian Y, Kocherginsky M, Raimondi SL, DeMaio JG, Salwen HR, Gu S, Chlenski A, Naranjo A, Gill A, Peddinti R, Lahn BT, Cohn SL, Godley LA. Truncated DNMT3B isoform DNMT3B7 suppresses growth, induces differentiation, and alters DNA methylation in human neuroblastoma. Cancer Res 2012; 72:4714-23. [PMID: 22815530 PMCID: PMC3445765 DOI: 10.1158/0008-5472.can-12-0886] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Epigenetic changes in pediatric neuroblastoma may contribute to the aggressive pathophysiology of this disease, but little is known about the basis for such changes. In this study, we examined a role for the DNA methyltransferase DNMT3B, in particular, the truncated isoform DNMT3B7, which is generated frequently in cancer. To investigate if aberrant DNMT3B transcripts alter DNA methylation, gene expression, and phenotypic character in neuroblastoma, we measured DNMT3B expression in primary tumors. Higher levels of DNMT3B7 were detected in differentiated ganglioneuroblastomas compared to undifferentiated neuroblastomas, suggesting that expression of DNMT3B7 may induce a less aggressive clinical phenotype. To test this hypothesis, we investigated the effects of enforced DNMT3B7 expression in neuroblastoma cells, finding a significant inhibition of cell proliferation in vitro and angiogenesis and tumor growth in vivo. DNMT3B7-positive cells had higher levels of total genomic methylation and a dramatic decrease in expression of the FOS and JUN family members that comprise AP1 transcription factors. Consistent with an established antagonistic relationship between AP1 expression and retinoic acid receptor activity, increased differentiation was seen in the DNMT3B7-expressing neuroblastoma cells following treatment with all-trans retinoic acid (ATRA) compared to controls. Our results indicate that DNMT3B7 modifies the epigenome in neuroblastoma cells to induce changes in gene expression, inhibit tumor growth, and increase sensitivity to ATRA.
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Affiliation(s)
- Kelly R. Ostler
- Department of Medicine, The University of Chicago, Chicago, IL
| | - Qiwei Yang
- Department of Pediatrics, The University of Chicago, Chicago, IL
- Department of Pediatrics, The University of Illinois at Chicago, Chicago, IL
| | - Timothy J. Looney
- Department of Human Genetics and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL
| | - Li Zhang
- Department of Human Genetics and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL
| | | | - Yufeng Tian
- Department of Pediatrics, The University of Chicago, Chicago, IL
| | | | - Stacey L. Raimondi
- Department of Medicine, The University of Chicago, Chicago, IL
- Department of Biology, Elmhurst College, Elmhurst, IL
| | - Jessica G. DeMaio
- Department of Medicine, The University of Chicago, Chicago, IL
- Department of Biology, Elmhurst College, Elmhurst, IL
| | - Helen R. Salwen
- Department of Pediatrics, The University of Chicago, Chicago, IL
| | - Song Gu
- Department of Pediatrics, The University of Chicago, Chicago, IL
- Department of Pediatric Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University
| | | | - Arlene Naranjo
- Children’s Oncology Group (COG), University of Florida, Gainesville, FL
| | - Amy Gill
- Department of Pediatrics, The University of Chicago, Chicago, IL
| | - Radhika Peddinti
- Department of Pediatrics, The University of Chicago, Chicago, IL
| | - Bruce T. Lahn
- Department of Human Genetics and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL
| | - Susan L. Cohn
- Department of Pediatrics, The University of Chicago, Chicago, IL
| | - Lucy A. Godley
- Department of Medicine, The University of Chicago, Chicago, IL
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14
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Maekawa F, Shimba S, Takumi S, Sano T, Suzuki T, Bao J, Ohwada M, Ehara T, Ogawa Y, Nohara K. Diurnal expression of Dnmt3b mRNA in mouse liver is regulated by feeding and hepatic clockwork. Epigenetics 2012; 7:1046-56. [PMID: 22847467 PMCID: PMC3515014 DOI: 10.4161/epi.21539] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
DNA methyltransferase 3B (DNMT3B) is critically involved in de novo DNA methylation and genomic stability, while the regulatory mechanism in liver is largely unknown. We previously reported that diurnal variation occurs in the mRNA expression of Dnmt3b in adult mouse liver. The aim of this study was to determine the mechanism underlying the diurnal expression pattern. The highest level and the lowest level of Dnmt3b mRNA expression were confirmed to occur at dawn and in the afternoon, respectively, and the expression pattern of Dnmt3b closely coincided with that of Bmal1. Since the diurnal pattern of Dnmt3b mRNA expression developed at weaning and scheduled feeding to separate the feeding cycle from the light/dark cycle led to a phase-shift in the expression, it could be assumed that feeding plays a critical role as an entrainment signal. In liver-specific Bmal1 knockout (L-Bmal1 KO) mice, L-Bmal1 deficiency resulted in significantly higher levels of Dnmt3b at all measured time points, and the time when the expression was the lowest in wild-type mice was shifted to earlier. Investigation of global DNA methylation revealed a temporal decrease of 5-methyl-cytosine percentage in the genome of wild-type mice in late afternoon. By contrast, no such decrease in 5-methyl-cytosine percentage was detected in L-Bmal1 KO mice, suggesting that altered Dnmt3b expression affects the DNA methylation state. Taken together, the results suggest that the feeding and hepatic clockwork generated by the clock genes, including Bmal1, regulate the diurnal variation in Dnmt3b mRNA expression and the consequent dynamic changes in global DNA methylation.
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Affiliation(s)
- Fumihiko Maekawa
- Center for Environmental Health Sciences; National Institute for Environmental Studies; Tsukuba, Japan
| | - Shigeki Shimba
- Department of Health Science; School of Pharmacy; Nihon University; Funabashi, Japan
| | - Shota Takumi
- Center for Environmental Health Sciences; National Institute for Environmental Studies; Tsukuba, Japan
| | - Tomoharu Sano
- Center for Environmental Measurement and Analysis; National Institute for Environmental Studies; Tsukuba, Japan
| | - Takehiro Suzuki
- Center for Environmental Health Sciences; National Institute for Environmental Studies; Tsukuba, Japan
| | - Jinhua Bao
- Center for Environmental Health Sciences; National Institute for Environmental Studies; Tsukuba, Japan
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba, Japan
| | - Mika Ohwada
- Center for Environmental Health Sciences; National Institute for Environmental Studies; Tsukuba, Japan
| | - Tatsuya Ehara
- Department of Molecular Endocrinology and Metabolism; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo, Japan
| | - Yoshihiro Ogawa
- Department of Molecular Endocrinology and Metabolism; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo, Japan
| | - Keiko Nohara
- Center for Environmental Health Sciences; National Institute for Environmental Studies; Tsukuba, Japan
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba, Japan
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15
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SANDHU RUPNINDER, RIVENBARK ASHLEYG, COLEMAN WILLIAMB. Loss of post-transcriptional regulation of DNMT3b by microRNAs: a possible molecular mechanism for the hypermethylation defect observed in a subset of breast cancer cell lines. Int J Oncol 2012; 41:721-32. [PMID: 22664488 PMCID: PMC3982716 DOI: 10.3892/ijo.2012.1505] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/05/2012] [Indexed: 01/12/2023] Open
Abstract
A hypermethylation defect associated with DNMT hyperactivity and DNMT3b overexpression characterizes a subset of breast cancers and breast cancer cell lines. We analyzed breast cancer cell lines for differential expression of regulatory miRs to determine if loss of miR-mediated post-transcriptional regulation of DNMT3b represents the molecular mechanism that governs the overexpression of DNMT3b that drives the hypermethylation defect in breast cancer. MicroRNAs (miRs) that regulate (miR-29a, miR-29b, miR-29c, miR-148a, miR-148b) or are predicted (miR-26a, miR-26b, miR-203, miR-222) to regulate DNMT3b were examined among 10 hypermethylator and 6 non-hypermethylator breast cancer cell lines. Hypermethylator cell lines express diminished levels of miR-29c, miR-148a, miR-148b, miR-26a, miR-26b, and miR-203 compared to non-hypermethylator cell lines. miR expression patterns correlate inversely with methylation-sensitive gene expression (r=-0.66, p=0.0056) and directly with the methylation status of these genes (r=0.72, p=0.002). To determine the mechanistic role of specific miRs in the dysregulation of DNMT3b among breast cancer cell lines, miR levels were modulated by transfection of pre-miR precursors for miR-148b, miR-26b, and miR-29c into hypermethylator cell lines (Hs578T, HCC1937, SUM185) and transfection of antagomirs directed against miR-148b, miR-26b, and miR-29c into non-hypermethylator cell lines (BT20, MDA-MB-415, MDA-MB-468). Antagomir-mediated knock-down of miR-148b, miR-29c, and miR-26b significantly increased DNMT3b mRNA in non-hypermethylator cell lines, and re-expression of miR-148b, miR-29c, and miR-26b following transfection of pre-miR precursors significantly reduced DNMT3b mRNA in hypermethylator cell lines. These findings strongly suggest that: i) post-transcriptional regulation of DNMT3b is combinatorial, ii) diminished expression of regulatory miRs contributes to DNMT3b overexpression, iii) re-expression of regulatory miRs reduces DNMT3b mRNA levels in hypermethylator breast cancer cell lines, and iv) down-regulation of regulatory miRs increases DNMT3b mRNA levels in non-hypermethylator breast cancer cell lines. In conlcusion, the molecular mechanism governing the DNMT3b-mediated hypermethylation defect in breast cancer cell lines involves the loss of post-transcriptional regulation of DNMT3b by regulatory miRs.
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Affiliation(s)
- RUPNINDER SANDHU
- Department of Pathology and Laboratory Medicine
- Program in Translational Medicine
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC,
USA
| | - ASHLEY G. RIVENBARK
- Department of Pathology and Laboratory Medicine
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC,
USA
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Heyn H, Vidal E, Sayols S, Sanchez-Mut JV, Moran S, Medina I, Sandoval J, Simó-Riudalbas L, Szczesna K, Huertas D, Gatto S, Matarazzo MR, Dopazo J, Esteller M. Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient. Epigenetics 2012; 7:542-50. [PMID: 22595875 PMCID: PMC3398983 DOI: 10.4161/epi.20523] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The immunodeficiency, centromere instability and facial anomalies (ICF) syndrome is associated to mutations of the DNA methyl-transferase DNMT3B, resulting in a reduction of enzyme activity. Aberrant expression of immune system genes and hypomethylation of pericentromeric regions accompanied by chromosomal instability were determined as alterations driving the disease phenotype. However, so far only technologies capable to analyze single loci were applied to determine epigenetic alterations in ICF patients. In the current study, we performed whole-genome bisulphite sequencing to assess alteration in DNA methylation at base pair resolution. Genome-wide we detected a decrease of methylation level of 42%, with the most profound changes occurring in inactive heterochromatic regions, satellite repeats and transposons. Interestingly, transcriptional active loci and ribosomal RNA repeats escaped global hypomethylation. Despite a genome-wide loss of DNA methylation the epigenetic landscape and crucial regulatory structures were conserved. Remarkably, we revealed a mislocated activity of mutant DNMT3B to H3K4me1 loci resulting in hypermethylation of active promoters. Functionally, we could associate alterations in promoter methylation with the ICF syndrome immunodeficient phenotype by detecting changes in genes related to the B-cell receptor mediated maturation pathway.
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Affiliation(s)
- Holger Heyn
- Cancer Epigenetics and Biology Program (PEBC); Bellvitge Biomedical Research Institute (IDIBELL); L’Hospitalet de Llobregat; Barcelona, Catalonia, Spain
| | - Enrique Vidal
- Department of Bioinformatics; Centro de Investigación Príncipe Felipe (CIPF); Valencia, Spain
- CIBER de Enfermedades Raras (CIBERER); Valencia, Spain
| | - Sergi Sayols
- Cancer Epigenetics and Biology Program (PEBC); Bellvitge Biomedical Research Institute (IDIBELL); L’Hospitalet de Llobregat; Barcelona, Catalonia, Spain
| | - Jose V. Sanchez-Mut
- Cancer Epigenetics and Biology Program (PEBC); Bellvitge Biomedical Research Institute (IDIBELL); L’Hospitalet de Llobregat; Barcelona, Catalonia, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC); Bellvitge Biomedical Research Institute (IDIBELL); L’Hospitalet de Llobregat; Barcelona, Catalonia, Spain
| | - Ignacio Medina
- Department of Bioinformatics; Centro de Investigación Príncipe Felipe (CIPF); Valencia, Spain
- Functional Genomics Node (INB) at CIPF; Valencia, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC); Bellvitge Biomedical Research Institute (IDIBELL); L’Hospitalet de Llobregat; Barcelona, Catalonia, Spain
| | - Laia Simó-Riudalbas
- Cancer Epigenetics and Biology Program (PEBC); Bellvitge Biomedical Research Institute (IDIBELL); L’Hospitalet de Llobregat; Barcelona, Catalonia, Spain
| | - Karolina Szczesna
- Cancer Epigenetics and Biology Program (PEBC); Bellvitge Biomedical Research Institute (IDIBELL); L’Hospitalet de Llobregat; Barcelona, Catalonia, Spain
| | - Dori Huertas
- Cancer Epigenetics and Biology Program (PEBC); Bellvitge Biomedical Research Institute (IDIBELL); L’Hospitalet de Llobregat; Barcelona, Catalonia, Spain
| | - Sole Gatto
- Institute of Genetics and Biophysics ABT; CNR; Naples, Italy
| | | | - Joaquin Dopazo
- Department of Bioinformatics; Centro de Investigación Príncipe Felipe (CIPF); Valencia, Spain
- CIBER de Enfermedades Raras (CIBERER); Valencia, Spain
- Functional Genomics Node (INB) at CIPF; Valencia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC); Bellvitge Biomedical Research Institute (IDIBELL); L’Hospitalet de Llobregat; Barcelona, Catalonia, Spain
- Department of Physiological Sciences II; School of Medicine; University of Barcelona; Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA); Barcelona, Catalonia, Spain
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17
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Martins-Taylor K, Schroeder DI, LaSalle JM, Lalande M, Xu RH. Role of DNMT3B in the regulation of early neural and neural crest specifiers. Epigenetics 2012; 7:71-82. [PMID: 22207353 PMCID: PMC3329505 DOI: 10.4161/epi.7.1.18750] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/28/2011] [Accepted: 11/11/2011] [Indexed: 01/05/2023] Open
Abstract
The de novo DNA methyltransferase DNMT3B functions in establishing DNA methylation patterns during development. DNMT3B missense mutations cause immunodeficiency, centromere instability and facial anomalies (ICF) syndrome. The restriction of Dnmt3b expression to neural progenitor cells, as well as the mild cognitive defects observed in ICF patients, suggests that DNMT3B may play an important role in early neurogenesis. We performed RNAi knockdown of DNMT3B in human embryonic stem cells (hESCs) in order to investigate the mechanistic contribution of DNMT3B to DNA methylation and early neuronal differentiation. While DNMT3B was not required for early neuroepithelium specification, DNMT3B deficient neuroepithelium exhibited accelerated maturation with earlier expression, relative to normal hESCs, of mature neuronal markers (such as NEUROD1) and of early neuronal regional specifiers (such as those for the neural crest). Genome-wide analyses of DNA methylation by MethylC-seq identified novel regions of hypomethylation in the DNMT3B knockdowns along the X chromosome as well as pericentromeric regions, rather than changes to promoters of specific dysregulated genes. We observed a loss of H3K27me3 and the polycomb complex protein EZH2 at the promoters of early neural and neural crest specifier genes during differentiation of DNMT3B knockdown but not normal hESCs. Our results indicate that DNMT3B mediates large-scale methylation patterns in hESCs and that DNMT3B deficiency in the cells alters the timing of their neuronal differentiation and maturation.
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Affiliation(s)
- Kristen Martins-Taylor
- Department of Genetics and Developmental Biology; University of Connecticut Health Center; University of Connecticut Stem Cell Institute; Farmington, CT USA
| | - Diane I. Schroeder
- Medical Microbiology and Immunology; Genome Center; M.I.N.D. Institute; University of California; Davis, CA USA
| | - Janine M LaSalle
- Medical Microbiology and Immunology; Genome Center; M.I.N.D. Institute; University of California; Davis, CA USA
| | - Marc Lalande
- Department of Genetics and Developmental Biology; University of Connecticut Health Center; University of Connecticut Stem Cell Institute; Farmington, CT USA
| | - Ren-He Xu
- Department of Genetics and Developmental Biology; University of Connecticut Health Center; University of Connecticut Stem Cell Institute; Farmington, CT USA
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18
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Pawlak M, Jaenisch R. De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state. Genes Dev 2011; 25:1035-40. [PMID: 21576263 PMCID: PMC3093119 DOI: 10.1101/gad.2039011] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 03/18/2011] [Indexed: 12/16/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are generated from somatic cells by the transduction of defined transcription factors, and this process involves dynamic changes in DNA methylation. While the reprogramming of somatic cells is accompanied by demethylation of pluripotency genes, the functional importance of de novo DNA methylation has not been clarified. Here, using loss-of-function studies, we generated iPSCs from fibroblasts that were deficient in de novo DNA methylation mediated by Dnmt3a and Dnmt3b. These iPSCs reactivated pluripotency genes, underwent self-renewal, and showed restricted developmental potential that was rescued upon reintroduction of Dnmt3a and Dnmt3b. We conclude that de novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells.
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Affiliation(s)
- Mathias Pawlak
- The Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Rudolf Jaenisch
- The Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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19
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Shamay M, Greenway M, Liao G, Ambinder RF, Hayward SD. De novo DNA methyltransferase DNMT3b interacts with NEDD8-modified proteins. J Biol Chem 2010; 285:36377-86. [PMID: 20847044 PMCID: PMC2978566 DOI: 10.1074/jbc.m110.155721] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 09/08/2010] [Indexed: 01/09/2023] Open
Abstract
DNA methylation and histone modifications play an important role in transcription regulation. In cancer cells, many promoters become aberrantly methylated through the activity of the de novo DNA methyltransferases DNMT3a and DNMT3b and acquire repressive chromatin marks. NEDD8 is a ubiquitin-like protein modifier that is conjugated to target proteins, such as cullins, to regulate their activity, and cullin 4A (CUL4A) in its NEDD8-modified form is essential for repressive chromatin formation. We found that DNMT3b associates with NEDD8-modified proteins. Whereas DNMT3b interacts directly in vitro with NEDD8, conjugation of NEDD8 to target proteins enhances this interaction in vivo. DNMT3b immunoprecipitated two major bands of endogenously NEDDylated proteins at the size of NEDDylated cullins, and indeed DNMT3b interacted with CUL1, CUL2, CUL3, CUL4A, and CUL5. Moreover, DNMT3b preferentially immunoprecipitated the NEDDylated form of endogenous CUL4A. NEDD8 enhanced DNMT3b-dependent DNA methylation. Chromatin immunoprecipitation assays suggest that DNMT3b recruits CUL4A and NEDD8 to chromatin, whereas deletion of Dnmt3b reduces the association of CUL4A and NEDD8 at a repressed promoter in a cancer cell line.
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Affiliation(s)
- Meir Shamay
- Viral Oncology Program, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland 21231, USA.
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20
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Abstract
Werner syndrome (WS) is an autosomal recessive disorder, the hallmarks of which are premature aging and early onset of neoplastic diseases (Orren, 2006; Bohr, 2008). The gene, whose mutation underlies the WS phenotype, is called WRN. The protein encoded by the WRN gene, WRNp, has DNA helicase activity (Gray et al., 1997; Orren, 2006; Bohr, 2008; Opresko, 2008). Extensive evidence suggests that WRNp plays a role in DNA replication and DNA repair (Chen et al., 2003; Hickson, 2003; Orren, 2006; Turaga et al., 2007; Bohr, 2008). However, WRNp function is not yet fully understood. In this study, we show that WRNp is involved in de novo DNA methylation of the promoter of the Oct4 gene, which encodes a crucial stem cell transcription factor. We demonstrate that WRNp localizes to the Oct4 promoter during retinoic acid-induced differentiation of human pluripotent cells and associates with the de novo methyltransferase Dnmt3b in the chromatin of differentiating pluripotent cells. Depletion of WRNp does not affect demethylation of lysine 4 of the histone H3 at the Oct4 promoter, nor methylation of lysine 9 of H3, but it blocks the recruitment of Dnmt3b to the promoter and results in the reduced methylation of CpG sites within the Oct4 promoter. The lack of DNA methylation was associated with continued, albeit greatly reduced, Oct4 expression in WRN-deficient, retinoic acid-treated cells, which resulted in attenuated differentiation. The presented results reveal a novel function of WRNp and demonstrate that WRNp controls a key step in pluripotent stem cell differentiation.
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Affiliation(s)
- Johanna A. Smith
- Division of Infectious Diseases - Center for Human Virology, and Jefferson Center for Stem Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, U.S.A
| | - Abibatou M. N. Ndoye
- Division of Infectious Diseases - Center for Human Virology, and Jefferson Center for Stem Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, U.S.A
| | - Kyla Geary
- Division of Infectious Diseases - Center for Human Virology, and Jefferson Center for Stem Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, U.S.A
| | - Michael P. Lisanti
- Department of Stem Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, U.S.A
| | - Olga Igoucheva
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, U.S.A
| | - René Daniel
- Division of Infectious Diseases - Center for Human Virology, and Jefferson Center for Stem Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, U.S.A
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21
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Abstract
Both appropriate DNA methylation and histone modifications play a crucial role in the maintenance of normal cell function and cellular identity. In cancerous cells these "epigenetic belts" become massively perturbed, leading to significant changes in expression profiles which confer advantage to the development of a malignant phenotype. DNA (cytosine-5)-methyltransferase 1 (Dnmt1), Dnmt3a and Dnmt3b are the enzymes responsible for setting up and maintaining DNA methylation patterns in eukaryotic cells. Intriguingly, DNMTs were found to be overexpressed in cancerous cells, which is believed to partly explain the hypermethylation phenomenon commonly observed in tumors. However, several lines of evidence indicate that further layers of gene regulation are critical coordinators of DNMT expression, catalytic activity and target specificity. Splice variants of DNMT transcripts have been detected which seem to modulate methyltransferase activity. Also, the DNMT mRNA 3'UTR as well as the coding sequence harbors multiple binding sites for trans-acting factors guiding post-transcriptional regulation and transcript stabilization. Moreover, microRNAs targeting DNMT transcripts have recently been discovered in normal cells, yet expression of these microRNAs was found to be diminished in breast cancer tissues. In this review we summarize the current knowledge on mechanisms which potentially lead to the establishment of a DNA hypermethylome in cancer cells.
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Affiliation(s)
- Jürgen Veeck
- Cancer Epigenetics and Biology Program (PEBC), The Bellvitge Institute for Biomedical Research (IDIBELL), Hospital Duran i Reynals, Av. Gran Via de L’Hospitalet 199-203, 08907 L’Hospitalet de Llobregat, Barcelona, Catalonia Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), The Bellvitge Institute for Biomedical Research (IDIBELL), Hospital Duran i Reynals, Av. Gran Via de L’Hospitalet 199-203, 08907 L’Hospitalet de Llobregat, Barcelona, Catalonia Spain
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22
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Beyrouthy MJ, Garner KM, Hever MP, Freemantle SJ, Eastman A, Dmitrovsky E, Spinella MJ. High DNA methyltransferase 3B expression mediates 5-aza-deoxycytidine hypersensitivity in testicular germ cell tumors. Cancer Res 2009; 69:9360-6. [PMID: 19951990 PMCID: PMC2795063 DOI: 10.1158/0008-5472.can-09-1490] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Testicular germ cell tumors (TGCT) are the most common solid tumors of 15- to 35-year-old men. TGCT patients are frequently cured with cytotoxic cisplatin-based therapy. However, TGCT patients refractory to cisplatin-based chemotherapy have a poor prognosis, as do those having a late relapse. Pluripotent embryonal carcinomas (EC) are the malignant counterparts to embryonic stem cells and are considered the stem cells of TGCTs. Here, we show that human EC cells are highly sensitive to 5-aza-deoxycytidine (5-aza-CdR) compared with somatic solid tumor cells. Decreased proliferation and survival with low nanomolar concentrations of 5-aza-CdR is associated with ATM activation, H2AX phosphorylation, increased expression of p21, and the induction of genes known to be methylated in TGCTs (MGMT, RASSF1A, and HOXA9). Notably, 5-aza-CdR hypersensitivity is associated with markedly abundant expression of the pluripotency-associated DNA methyltransferase 3B (DNMT3B) compared with somatic tumor cells. Knockdown of DNMT3B in EC cells results in substantial resistance to 5-aza-CdR, strongly indicating that 5-aza-CdR sensitivity is mechanistically linked to high levels of DNMT3B. Intriguingly, cisplatin-resistant EC cells retain an exquisite sensitivity to low-dose 5-aza-CdR treatment, and pretreatment of 5-aza-CdR resensitizes these cells to cisplatin-mediated toxicity. This resensitization is also partially dependent on high DNMT3B levels. These novel findings indicate that high expression of DNMT3B, a likely byproduct of their pluripotency and germ cell origin, sensitizes TGCT-derived EC cells to low-dose 5-aza-CdR treatment.
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Affiliation(s)
- Maroun J. Beyrouthy
- Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, NH 03755
| | - Kristen M. Garner
- Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, NH 03755
| | - Mary P. Hever
- Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, NH 03755
| | - Sarah J. Freemantle
- Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, NH 03755
| | - Alan Eastman
- Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, NH 03755
- Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755
| | - Ethan Dmitrovsky
- Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, NH 03755
- Department of Medicine, Dartmouth Medical School, Hanover, NH 03755
- Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755
| | - Michael J. Spinella
- Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, NH 03755
- Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755
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Liu Z, Wang L, Wang LE, Sturgis EE, Wei Q. Polymorphisms of the DNMT3B gene and risk of squamous cell carcinoma of the head and neck: a case-control study. Cancer Lett 2008; 268:158-65. [PMID: 18455294 PMCID: PMC2646006 DOI: 10.1016/j.canlet.2008.03.034] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 03/25/2008] [Accepted: 03/26/2008] [Indexed: 12/01/2022]
Abstract
DNA-methyltransferase-3B (DNMT3B) may play an oncogenic role during tumorigenesis, and its genetic variants have been reportedly to be associated with risk of several cancers, but few studies have investigated their roles in squamous cell carcinoma of the head and neck cancer (SCCHN). Here we report a hospital-based case-control study with 832 SCCHN patients and 843 cancer-free controls of non-Hispanic whites that evaluated the association between two DNMT3B single nucleotide polymorphisms (SNPs) DNMT3B -149C>T (rs2424913) and DNMT3B -579G>T (rs2424909) in the promoter region and risk of SCCHN. We found that compared with C-allele carriers, the DNMT3B -149 TT genotype was statistically significantly associated with increased risk of SCCHN (adjusted OR, 1.35, 95% CI, 1.01-1.80, P=0.043), whereas the DNMT3B -579 TT genotype showed only a non-statistically significant risk compared with G-allele carriers. Further analysis of the effects of combined genotypes suggested that subjects with either DNMT3B -149 TT or DNMT3B -579 TT homozygous genotypes had statistically significantly increased risk of SCCHN (adjusted OR=1.36, 95% CI=1.07-1.73, P=0.013). Stratification analysis showed a more profound risk in the subgroups of the young (< or =57 years, the median age of the controls), males, current smokers, current drinkers, and patients with primary tumor sites of pharynx and larynx. This large study provides reliable risk estimates for associations between DNMT3B variants and SCCHN risk in non-Hispanic whites, and our findings are consistent with that of previously reported cancer case-control studies of other cancers. Further mechanistic studies are needed to unravel the underlying molecular mechanisms.
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Affiliation(s)
- Zhensheng Liu
- Departments of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Luo Wang
- Departments of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Li-E Wang
- Departments of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Erich E. Sturgis
- Departments of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX
- Departments of Head and Neck Surgery, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Qingyi Wei
- Departments of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX
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24
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Gowher H, Stuhlmann H, Felsenfeld G. Vezf1 regulates genomic DNA methylation through its effects on expression of DNA methyltransferase Dnmt3b. Genes Dev 2008; 22:2075-84. [PMID: 18676812 PMCID: PMC2492749 DOI: 10.1101/gad.1658408] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Accepted: 06/03/2008] [Indexed: 01/08/2023]
Abstract
The zinc finger protein vascular endothelial zinc finger 1 (Vezf1) has been implicated in the development of the blood vascular and lymphatic system in mice, and has been characterized as a transcriptional activator in some systems. The chicken homolog, BGP1, has binding sites in the beta-globin locus, including the upstream insulator element. We report that in a mouse embryonic stem cell line deletion of both copies of Vezf1 results in loss of DNA methylation at widespread sites in the genome, including Line1 elements and minor satellite repeats, some imprinted genes, and several CpG islands. Loss of methylation appears to arise from a substantial decrease in the abundance of the de novo DNA methyltransferase, Dnmt3b. These results suggest that naturally occurring mutations in Vezf1/BGP1 might have widespread effects on DNA methylation patterns and therefore on epigenetic regulation of gene expression.
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Affiliation(s)
- Humaira Gowher
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Heidi Stuhlmann
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York 10021, USA
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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25
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Duursma AM, Kedde M, Schrier M, le Sage C, Agami R. miR-148 targets human DNMT3b protein coding region. RNA 2008; 14:872-7. [PMID: 18367714 PMCID: PMC2327368 DOI: 10.1261/rna.972008] [Citation(s) in RCA: 433] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 02/06/2008] [Indexed: 05/24/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules of 20-24 nucleotides that regulate gene expression. In animals, miRNAs form imperfect interactions with sequences in the 3' Untranslated region (3'UTR) of mRNAs, causing translational inhibition and mRNA decay. In contrast, plant miRNAs mostly associate with protein coding regions. Here we show that human miR-148 represses DNA methyltransferase 3b (Dnmt3b) gene expression through a region in its coding sequence. This region is evolutionary conserved and present in the Dnmt3b splice variants Dnmt3b1, Dnmt3b2, and Dnmt3b4, but not in the abundantly expressed Dnmt3b3. Whereas overexpression of miR-148 results in decreased DNMT3b1 expression, short-hairpin RNA-mediated miR-148 repression leads to an increase in DNMT3b1 expression. Interestingly, mutating the putative miR-148 target site in Dnmt3b1 abolishes regulation by miR-148. Moreover, endogenous Dnmt3b3 mRNA, which lacks the putative miR-148 target site, is resistant to miR-148-mediated regulation. Thus, our results demonstrate that the coding sequence of Dnmt3b mediates regulation by the miR-148 family. More generally, we provide evidence that coding regions of human genes can be targeted by miRNAs, and that such a mechanism might play a role in determining the relative abundance of different splice variants.
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Affiliation(s)
- Anja M Duursma
- Division of Tumor Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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26
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Fan H, Liu DS, Zhang SH, Hu JB, Zhang F, Zhao ZJ. DNMT3B 579 G>T promoter polymorphism and risk of esophagus carcinoma in Chinese. World J Gastroenterol 2008; 14:2230-4. [PMID: 18407600 PMCID: PMC2703851 DOI: 10.3748/wjg.14.2230] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 02/04/2008] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the relationship between 579 G>T polymorphisms in the DNMT3B gene, which is involved in de novo methylation and associated with the risk of esophagus cancer (EC) in Chinese. METHODS DNMT3B 579 G>T genotypes were determined by PCR-RFLP in 194 EC patients and 210 healthy controls matched for age and sex, who did not receive radiotherapy or chemotherapy for newly diagnosed and histopathologically confirmed EC. RESULTS In control subjects, the frequency of T/T and G/T genotypes, and T and G alleles was 81.4%, 18.1%, 90.05% and 9.55%, respectively. The distribution of genotypes and allelotypes in the EC patients was not significantly different from that in the controls. When stratified by sex and age, there was still no significant association between the risks of EC and GT and GG genotypes. This study also showed a distinct difference in the distribution of DNMT3B and single nucleotide polymorphism (SNP) between Chinese and Koreans. CONCLUSION DNMT3B 579 G>T polymorphism may not be a stratification marker to predict the susceptibility to EC, at least in Chinese. DNMT3B promoter SNP is diverse in ethnic populations.
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27
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Linhart HG, Lin H, Yamada Y, Moran E, Steine EJ, Gokhale S, Lo G, Cantu E, Ehrich M, He T, Meissner A, Jaenisch R. Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing. Genes Dev 2007; 21:3110-22. [PMID: 18056424 PMCID: PMC2081977 DOI: 10.1101/gad.1594007] [Citation(s) in RCA: 210] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Accepted: 10/11/2007] [Indexed: 01/28/2023]
Abstract
Increased methylation of CpG islands and silencing of affected target genes is frequently found in human cancer; however, in vivo the question of causality has only been addressed by loss-of-function studies. To directly evaluate the role and mechanism of de novo methylation in tumor development, we overexpressed the de novo DNA methyltransferases Dnmt3a1 and Dnmt3b1 in Apc Min/+ mice. We found that Dnmt3b1 enhanced the number of colon tumors in Apc Min/+ mice approximately twofold and increased the average size of colonic microadenomas, whereas Dnmt3a1 had no effect. The overexpression of Dnmt3b1 caused loss of imprinting and increased expression of Igf2 as well as methylation and transcriptional silencing of the tumor suppressor genes Sfrp2, Sfrp4, and Sfrp5. Importantly, we found that Dnmt3b1 but not Dnmt3a1 efficiently methylates the same set of genes in tumors and in nontumor tissues, demonstrating that de novo methyltransferases can initiate methylation and silencing of specific genes in phenotypically normal cells. This suggests that DNA methylation patterns in cancer are the result of specific targeting of at least some tumor suppressor genes rather than of random, stochastic methylation followed by clonal selection due to a proliferative advantage caused by tumor suppressor gene silencing.
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Affiliation(s)
- Heinz G. Linhart
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Haijiang Lin
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Yasuhiro Yamada
- Department for Tumor Pathology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Eva Moran
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Eveline J. Steine
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Sumita Gokhale
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Grace Lo
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Erika Cantu
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Timothy He
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139, USA
| | - Alex Meissner
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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28
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Ostler KR, Davis EM, Payne SL, Gosalia BB, Expósito-Céspedes J, Le Beau MM, Godley LA. Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins. Oncogene 2007; 26:5553-63. [PMID: 17353906 PMCID: PMC2435620 DOI: 10.1038/sj.onc.1210351] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 01/17/2007] [Accepted: 01/17/2007] [Indexed: 12/21/2022]
Abstract
Cancer cells display an altered distribution of DNA methylation relative to normal cells. Certain tumor suppressor gene promoters are hypermethylated and transcriptionally inactivated, whereas repetitive DNA is hypomethylated and transcriptionally active. Little is understood about how the abnormal DNA methylation patterns of cancer cells are established and maintained. Here, we identify over 20 DNMT3B transcripts from many cancer cell lines and primary acute leukemia cells that contain aberrant splicing at the 5' end of the gene, encoding truncated proteins lacking the C-terminal catalytic domain. Many of these aberrant transcripts retain intron sequences. Although the aberrant transcripts represent a minority of the DNMT3B transcripts present, Western blot analysis demonstrates truncated DNMT3B isoforms in the nuclear protein extracts of cancer cells. To test if expression of a truncated DNMT3B protein could alter the DNA methylation patterns within cells, we expressed DNMT3B7, the most frequently expressed aberrant transcript, in 293 cells. DNMT3B7-expressing 293 cells have altered gene expression as identified by microarray analysis. Some of these changes in gene expression correlate with altered DNA methylation of corresponding CpG islands. These results suggest that truncated DNMT3B proteins could play a role in the abnormal distribution of DNA methylation found in cancer cells.
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Affiliation(s)
- KR Ostler
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - EM Davis
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - SL Payne
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - BB Gosalia
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - J Expósito-Céspedes
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - MM Le Beau
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
- University of Chicago Cancer Research Center, University of Chicago, Chicago, IL, USA
| | - LA Godley
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
- University of Chicago Cancer Research Center, University of Chicago, Chicago, IL, USA
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29
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Oda M, Yamagiwa A, Yamamoto S, Nakayama T, Tsumura A, Sasaki H, Nakao K, Li E, Okano M. DNA methylation regulates long-range gene silencing of an X-linked homeobox gene cluster in a lineage-specific manner. Genes Dev 2006; 20:3382-94. [PMID: 17182866 PMCID: PMC1698446 DOI: 10.1101/gad.1470906] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 10/30/2006] [Indexed: 12/31/2022]
Abstract
DNA methylation is a major epigenetic mechanism that has been suggested to control developmental gene regulation during embryogenesis, but its regulatory mechanisms remain unclear. In this report, we show that CpG islands associated with the X-linked homeobox gene cluster Rhox, which is highly expressed in the extraembryonic trophectoderm, are differentially methylated in a stage- and lineage-specific manner during the post-implantation development of mice. Inactivation of both Dnmt3a and Dnmt3b, DNA methyltransferases essential for the initiation of de novo DNA methylation, abolished the establishment of DNA methylation and the silencing of Rhox cluster genes in the embryo proper. The Dnmt3-dependent CpG-island methylation at the Rhox locus extended for a large genomic region ( approximately 1 Mb) containing the Rhox cluster and surrounding genes. Complementation experiments using embryonic stem (ES) cells deficient in the DNA methyltransferases suggested that the CpG-island methylation by Dnmt3a and Dnmt3b was restricted within this large genomic region, and did not affect the neighboring genes outside it, implicating the existence of region-specific boundaries. Our results suggest that DNA methylation plays important roles in both long-range gene silencing and lineage-specific silencing in embryogenesis.
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Affiliation(s)
- Masaaki Oda
- Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, Kobe, Hyogo, 650-0047, Japan
| | - Akiko Yamagiwa
- Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, Kobe, Hyogo, 650-0047, Japan
| | - Shinji Yamamoto
- Laboratory for Embryonic Induction, Center for Developmental Biology, RIKEN, Kobe, Hyogo, 650-0047, Japan
| | - Takao Nakayama
- Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, Kobe, Hyogo, 650-0047, Japan
- Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Akiko Tsumura
- Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, Kobe, Hyogo, 650-0047, Japan
| | - Hiroshi Sasaki
- Laboratory for Embryonic Induction, Center for Developmental Biology, RIKEN, Kobe, Hyogo, 650-0047, Japan
| | - Kazuki Nakao
- Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology, RIKEN, Kobe, Hyogo, 650-0047, Japan
| | - En Li
- Epigenetics Program, Novartis Institute for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Masaki Okano
- Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, Kobe, Hyogo, 650-0047, Japan
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