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Kubo N, Uehara R, Uemura S, Ohishi H, Shirane K, Sasaki H. Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells. Nat Commun 2024; 15:3266. [PMID: 38627502 PMCID: PMC11021467 DOI: 10.1038/s41467-024-47699-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
DNA methyltransferase 3A (DNMT3A) and its catalytically inactive cofactor DNA methyltransferase 3-Like (DNMT3L) proteins form functional heterotetramers to deposit DNA methylation in mammalian germ cells. While both proteins have an ATRX-DNMT3-DNMT3L (ADD) domain that recognizes histone H3 tail unmethylated at lysine-4 (H3K4me0), the combined and differential roles of the domains in the two proteins have not been fully defined in vivo. Here we investigate DNA methylation landscapes in female and male germ cells derived from mice with loss-of-function amino acid substitutions in the ADD domains of DNMT3A and/or DNMT3L. Mutations in either the DNMT3A-ADD or the DNMT3L-ADD domain moderately decrease global CG methylation levels, but to different degrees, in both germ cells. Furthermore, when the ADD domains of both DNMT3A and DNMT3L lose their functions, the CG methylation levels are much more reduced, especially in oocytes, comparable to the impact of the Dnmt3a/3L knockout. In contrast, aberrant accumulation of non-CG methylation occurs at thousands of genomic regions in the double mutant oocytes and spermatozoa. These results highlight the critical role of the ADD-H3K4me0 binding in proper CG and non-CG methylation in germ cells and the various impacts of the ADD domains of the two proteins.
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Affiliation(s)
- Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Ryuji Uehara
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shuhei Uemura
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Hiroaki Ohishi
- Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenjiro Shirane
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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Huang C, Aghaei-Zarch SM. From molecular pathogenesis to therapy: Unraveling non-coding RNAs/DNMT3A axis in human cancers. Biochem Pharmacol 2024; 222:116107. [PMID: 38438051 DOI: 10.1016/j.bcp.2024.116107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/03/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Cancer is a comprehensive classification encompassing more than 100 forms of malignancies that manifest in diverse tissues within the human body. Recent studies have provided evidence that aberrant epigenetic modifications are pivotal indicators of cancer. Epigenetics encapsulates DNA methyltransferases as a crucial class of modifiers. DNMTs, including DNMT3A, assume central roles in DNA methylation processes that orchestrate normal biological functions, such as gene transcription, predominantly in mammals. Typically, deviations in DNMT3A function engender distortions in factors that drive tumor growth and progression, thereby exacerbating the malignant phenotype of tumors. Consequently, such abnormalities pose significant challenges in cancer therapy because they impede treatment efficacy. Non-coding RNAs (ncRNAs) represent a group of RNA molecules that cannot encode functional proteins. Recent investigation attests to the crucial significance of regulatory ncRNAs in epigenetic regulation. Notably, recent reports have illuminated the complex interplay between ncRNA expression and epigenetic regulatory machinery, including DNMT3A, particularly in cancer. Recent findings have demonstrated that miRNAs, namely miR-770-5p, miR-101, and miR-145 exhibit the capability to target DNMT3A directly, and their aberration is implicated in diverse cellular abnormalities that predispose to cancer development. This review aims to articulate the interplay between DNMT3A and the ncRNAs, focusing on its impact on the development and progression of cancer, cancer therapy resistance, cancer stem cells, and prognosis. Importantly, the emergence of such reports that suggest a connection between DNMT3A and ncRNAs in several cancers indicates that this connecting axis offers a valuable target with significant therapeutic potential that might be exploited for cancer management.
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Affiliation(s)
- Chunjie Huang
- School of Medicine, Nantong University, Nantong 226001, China
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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3
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Bilgic Eltan S, Nain E, Catak MC, Ezen E, Sefer AP, Karimi N, Kiykim A, Kolukisa B, Baser D, Bulutoglu A, Kasap N, Yorgun Altunbas M, Yalcin Gungoren E, Kendir Demirkol Y, Kutlug S, Hancioglu G, Dilek F, Yildiran A, Ozen A, Karakoc-Aydiner E, Erman B, Baris S. Evaluation of Clinical and Immunological Alterations Associated with ICF Syndrome. J Clin Immunol 2023; 44:26. [PMID: 38129713 DOI: 10.1007/s10875-023-01620-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE Immunodeficiency with centromeric instability and facial anomalies (ICF) syndrome is a rare autosomal recessive combined immunodeficiency. The detailed immune responses are not explored widely. We investigated known and novel immune alterations in lymphocyte subpopulations and their association with clinical symptoms in a well-defined ICF cohort. METHODS We recruited the clinical findings from twelve ICF1 and ICF2 patients. We performed detailed immunological evaluation, including lymphocyte subset analyses, upregulation, and proliferation of T cells. We also determined the frequency of circulating T follicular helper (cTFH) and regulatory T (Treg) cells and their subtypes by flow cytometry. RESULTS There were ten ICF1 and two ICF2 patients. We identified two novel homozygous missense mutations in the ZBTB24 gene. Respiratory tract infections were the most common recurrent infections among the patients. Gastrointestinal system (GIS) involvements were observed in seven patients. All patients received intravenous immunoglobulin replacement therapy and antibacterial prophylaxis; two died during the follow-up period. Immunologically, CD4+ T-cell counts, percentages of recent thymic emigrant T cells, and naive CD4+ T decreased in two, five, and four patients, respectively. Impaired T-cell proliferation and reduced CD25 upregulation were detected in all patients. These changes were more prominent in CD8+ T cells. GIS involvements negatively correlated with CD3+ T-, CD3+CD4+ T-, CD16+CD56+ NK-cell counts, and CD4+/CD8+ T-cell ratios. Further, we observed expanded cTFH cells and reduced Treg and follicular regulatory T cells with a skewing to a TH2-like phenotype in all tested subpopulations. CONCLUSION The ICF syndrome encompasses various manifestations affecting multiple end organs. Perturbed T-cell responses with increased cTFH and decreased Treg cells may provide further insight into the immune aberrations observed in ICF syndrome.
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Affiliation(s)
- Sevgi Bilgic Eltan
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Ercan Nain
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Mehmet Cihangir Catak
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Ege Ezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Asena Pınar Sefer
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Nastaran Karimi
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayca Kiykim
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Burcu Kolukisa
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Dilek Baser
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Alper Bulutoglu
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Nurhan Kasap
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Melek Yorgun Altunbas
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Ezgi Yalcin Gungoren
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Yasemin Kendir Demirkol
- Division of Pediatric Genetics, Umraniye Education and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Seyhan Kutlug
- Division of Pediatric Immunology and Allergy, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Gonca Hancioglu
- Division of Pediatric Immunology and Allergy, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Fatih Dilek
- Department of Pediatrics, Faculty of Medicine, Atlas University, Istanbul, Turkey
| | - Alisan Yildiran
- Division of Pediatric Immunology and Allergy, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Ahmet Ozen
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Safa Baris
- Pediatric Allergy and Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey.
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.
- The Isil Berat Barlan Center for Translational Medicine, Division of Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey.
- Pediatric Allergy and Immunology, Marmara University Hospital, Istanbul, Turkey.
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4
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Gao L, Guo Y, Biswal M, Lu J, Yin J, Fang J, Chen X, Shao Z, Huang M, Wang Y, Wang GG, Song J. Structure of DNMT3B homo-oligomer reveals vulnerability to impairment by ICF mutations. Nat Commun 2022; 13:4249. [PMID: 35869095 PMCID: PMC9307851 DOI: 10.1038/s41467-022-31933-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 07/04/2022] [Indexed: 02/05/2023] Open
Abstract
DNA methyltransferase DNMT3B plays an essential role in establishment of DNA methylation during embryogenesis. Mutations of DNMT3B are associated with human diseases, notably the immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome. How ICF mutations affect DNMT3B activity is not fully understood. Here we report the homo-oligomeric structure of DNMT3B methyltransferase domain, providing insight into DNMT3B-mediated DNA methylation in embryonic stem cells where the functional regulator DNMT3L is dispensable. The interplay between one of the oligomer interfaces (FF interface) and the catalytic loop renders DNMT3B homo-oligomer a conformation and activity distinct from the DNMT3B-DNMT3L heterotetramer, and a greater vulnerability to certain ICF mutations. Biochemical and cellular analyses further reveal that the ICF mutations of FF interface impair the DNA binding and heterochromatin targeting of DNMT3B, leading to reduced DNA methylation in cells. Together, this study provides a mechanistic understanding of DNMT3B-mediated DNA methylation and its dysregulation in disease.
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Affiliation(s)
- Linfeng Gao
- Environmental Toxicology Graduate Program, University of California, Riverside, 92521, CA, USA
| | - Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, 27599, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Mahamaya Biswal
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, 92521, CA, USA
| | - Jian Fang
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Xinyi Chen
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Zengyu Shao
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Mengjiang Huang
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, 92521, CA, USA
- Department of Chemistry, University of California, Riverside, 92521, CA, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, 27599, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, 27599, NC, USA.
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, 27599, NC, USA.
| | - Jikui Song
- Environmental Toxicology Graduate Program, University of California, Riverside, 92521, CA, USA.
- Department of Biochemistry, University of California, Riverside, 92521, CA, USA.
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5
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Zhao H, Yu J, Weng G, Yu J, Wang E, Gao J, Liu H, Hou T, Wang Z, Kang Y. Structural view on the role of the TRD loop in regulating DNMT3A activity: a molecular dynamics study. Phys Chem Chem Phys 2022; 24:15791-15801. [PMID: 35758413 DOI: 10.1039/d2cp02031a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methyltransferase 3A (DNMT3A) has been regarded as a potential epigenetic target for the development of cancer therapeutics. A number of DNMT3A inhibitors have been reported, but most of them do not have good potency, high selectivity and/or low cytotoxicity. It has been suggested that a non-conserved region around the target recognition domain (TRD) loop is implicated in the DNMT3A activity under the allosteric regulation of the ATRX-DNMT3-DNMT3L (ADD) domain, but the molecular mechanism of the regulation of the TRD loop on the DNMT3A activity needs to be elucidated. In this study, based on the reported crystal structures, the dynamics of the TRD loop in different multimerization with/without the bound guest molecule, namely the ADD domain or the DNA molecule, was investigated using conventional molecular dynamics (MD) and umbrella sampling simulations. The simulation results illustrate that the TRD loop exhibits relatively higher flexibility than the other components in the whole catalytic domain (CD), which could be well stabilized into different local minima through the binding with either the ADD domain or the DNA molecule by forming tight hydrogen-bond and salt-bridge networks involving distinct residues. Moreover, the movement of the TRD loop away from the catalytic loop upon activation could be triggered simply by the detachment of the ADD domain, but not necessarily induced by the ADD domain relocation on the CD. All these dynamic structural details could be a supplement to the previously reported crystal structure, which underlines the importance of the structural flexibility for the critical residues in the TRD loop, arousing more interest in the rational design of novel DNMT3A inhibitors targeting this region.
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Affiliation(s)
- Hong Zhao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China. .,Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, China
| | - Jie Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Gaoqi Weng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Jiahui Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Ercheng Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Junbo Gao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao, SAR, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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6
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Mack A, Emperle M, Schnee P, Adam S, Pleiss J, Bashtrykov P, Jeltsch A. Preferential self-interaction of DNA methyltransferase DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence preferences. J Mol Biol 2022; 434:167482. [DOI: 10.1016/j.jmb.2022.167482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 11/30/2022]
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7
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Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:69-110. [DOI: 10.1007/978-3-031-11454-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Mensah IK, Norvil AB, AlAbdi L, McGovern S, Petell CJ, He M, Gowher H. Misregulation of the expression and activity of DNA methyltransferases in cancer. NAR Cancer 2021; 3:zcab045. [PMID: 34870206 PMCID: PMC8634572 DOI: 10.1093/narcan/zcab045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In mammals, DNA methyltransferases DNMT1 and DNMT3's (A, B and L) deposit and maintain DNA methylation in dividing and nondividing cells. Although these enzymes have an unremarkable DNA sequence specificity (CpG), their regional specificity is regulated by interactions with various protein factors, chromatin modifiers, and post-translational modifications of histones. Changes in the DNMT expression or interacting partners affect DNA methylation patterns. Consequently, the acquired gene expression may increase the proliferative potential of cells, often concomitant with loss of cell identity as found in cancer. Aberrant DNA methylation, including hypermethylation and hypomethylation at various genomic regions, therefore, is a hallmark of most cancers. Additionally, somatic mutations in DNMTs that affect catalytic activity were mapped in Acute Myeloid Leukemia cancer cells. Despite being very effective in some cancers, the clinically approved DNMT inhibitors lack specificity, which could result in a wide range of deleterious effects. Elucidating distinct molecular mechanisms of DNMTs will facilitate the discovery of alternative cancer therapeutic targets. This review is focused on: (i) the structure and characteristics of DNMTs, (ii) the prevalence of mutations and abnormal expression of DNMTs in cancer, (iii) factors that mediate their abnormal expression and (iv) the effect of anomalous DNMT-complexes in cancer.
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Affiliation(s)
- Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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9
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Emperle M, Bangalore DM, Adam S, Kunert S, Heil HS, Heinze KG, Bashtrykov P, Tessmer I, Jeltsch A. Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase. Nucleic Acids Res 2021; 49:8294-8308. [PMID: 34289056 PMCID: PMC8373138 DOI: 10.1093/nar/gkab600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023] Open
Abstract
DNMT3A/3L heterotetramers contain two active centers binding CpG sites at 12 bp distance, however their interaction with DNA not containing this feature is unclear. Using randomized substrates, we observed preferential co-methylation of CpG sites with 6, 9 and 12 bp spacing by DNMT3A and DNMT3A/3L. Co-methylation was favored by AT bases between the 12 bp spaced CpG sites consistent with their increased bending flexibility. SFM analyses of DNMT3A/3L complexes bound to CpG sites with 12 bp spacing revealed either single heterotetramers inducing 40° DNA bending as observed in the X-ray structure, or two heterotetramers bound side-by-side to the DNA yielding 80° bending. SFM data of DNMT3A/3L bound to CpG sites spaced by 6 and 9 bp revealed binding of two heterotetramers and 100° DNA bending. Modeling showed that for 6 bp distance between CpG sites, two DNMT3A/3L heterotetramers could bind side-by-side on the DNA similarly as for 12 bp distance, but with each CpG bound by a different heterotetramer. For 9 bp spacing our model invokes a tetramer swap of the bound DNA. These additional DNA interaction modes explain how DNMT3A and DNMT3A/3L overcome their structural preference for CpG sites with 12 bp spacing during the methylation of natural DNA.
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Affiliation(s)
- Max Emperle
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Disha M Bangalore
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Sabrina Adam
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Stefan Kunert
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Hannah S Heil
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Katrin G Heinze
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
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10
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Deep enzymology studies on DNA methyltransferases reveal novel connections between flanking sequences and enzyme activity. J Mol Biol 2021; 433:167186. [PMID: 34375615 DOI: 10.1016/j.jmb.2021.167186] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 11/22/2022]
Abstract
DNA interacting enzymes recognize their target sequences embedded in variable flanking sequence context. The influence of flanking sequences on enzymatic activities of DNA methyltransferases (DNMTs) can be systematically studied with "deep enzymology" approaches using pools of double-stranded DNA substrates, which contain target sites in random flanking sequence context. After incubation with DNMTs and bisulfite conversion, the methylation states and flanking sequences of individual DNA molecules are determined by NGS. Deep enzymology studies with different human and mouse DNMTs revealed strong influences of flanking sequences on the CpG and non-CpG methylation activity and structure of DNMT-DNA complexes. Differences in flanking sequence preferences of DNMT3A and DNMT3B were shown to be related to the prominent role of DNMT3B in the methylation of human SATII repeat elements. Mutational studies in DNMT3B discovered alternative interaction networks between the enzyme and the DNA leading to a partial equalization of the effects of different flanking sequences. Structural studies in DNMT1 revealed striking correlations between enzymatic activities and flanking sequence dependent conformational changes upon DNA binding. Correlation of the biochemical data with cellular methylation patterns demonstrated that flanking sequence preferences are an important parameter that influences genomic DNA methylation patterns together with other mechanisms targeting DNMTs to genomic sites.
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11
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Rodriguez-Casanova A, Costa-Fraga N, Bao-Caamano A, López-López R, Muinelo-Romay L, Diaz-Lagares A. Epigenetic Landscape of Liquid Biopsy in Colorectal Cancer. Front Cell Dev Biol 2021; 9:622459. [PMID: 33614651 PMCID: PMC7892964 DOI: 10.3389/fcell.2021.622459] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies and is a major cause of cancer-related deaths worldwide. Thus, there is a clinical need to improve early detection of CRC and personalize therapy for patients with this disease. In the era of precision oncology, liquid biopsy has emerged as a major approach to characterize the circulating tumor elements present in body fluids, including cell-free DNA and RNA, circulating tumor cells, and extracellular vesicles. This non-invasive tool has allowed the identification of relevant molecular alterations in CRC patients, including some indicating the disruption of epigenetic mechanisms. Epigenetic alterations found in solid and liquid biopsies have shown great utility as biomarkers for early detection, prognosis, monitoring, and evaluation of therapeutic response in CRC patients. Here, we summarize current knowledge of the most relevant epigenetic mechanisms associated with cancer development and progression, and the implications of their deregulation in cancer cells and liquid biopsy of CRC patients. In particular, we describe the methodologies used to analyze these epigenetic alterations in circulating tumor material, and we focus on the clinical utility of epigenetic marks in liquid biopsy as tumor biomarkers for CRC patients. We also discuss the great challenges and emerging opportunities of this field for the diagnosis and personalized management of CRC patients.
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Affiliation(s)
- Aitor Rodriguez-Casanova
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Nicolás Costa-Fraga
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aida Bao-Caamano
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Rafael López-López
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Laura Muinelo-Romay
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
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12
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Van MV, Fujimori T, Bintu L. Nanobody-mediated control of gene expression and epigenetic memory. Nat Commun 2021; 12:537. [PMID: 33483487 PMCID: PMC7822885 DOI: 10.1038/s41467-020-20757-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/15/2020] [Indexed: 01/10/2023] Open
Abstract
Targeting chromatin regulators to specific genomic locations for gene control is emerging as a powerful method in basic research and synthetic biology. However, many chromatin regulators are large, making them difficult to deliver and combine in mammalian cells. Here, we develop a strategy for gene control using small nanobodies that bind and recruit endogenous chromatin regulators to a gene. We show that an antiGFP nanobody can be used to simultaneously visualize GFP-tagged chromatin regulators and control gene expression, and that nanobodies against HP1 and DNMT1 can silence a reporter gene. Moreover, combining nanobodies together or with other regulators, such as DNMT3A or KRAB, can enhance silencing speed and epigenetic memory. Finally, we use the slow silencing speed and high memory of antiDNMT1 to build a signal duration timer and recorder. These results set the basis for using nanobodies against chromatin regulators for controlling gene expression and epigenetic memory.
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Affiliation(s)
- Mike V Van
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Taihei Fujimori
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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13
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Bai G, Ross H, Zhang Y, Lee K, Ro JY. The Role of DNA Methylation in Transcriptional Regulation of Pro-Nociceptive Genes in Rat Trigeminal Ganglia. Epigenet Insights 2020; 13:2516865720938677. [PMID: 32974606 PMCID: PMC7495519 DOI: 10.1177/2516865720938677] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/04/2020] [Indexed: 12/25/2022] Open
Abstract
Epigenetic modulation by DNA methylation is associated with aberrant gene
expression in sensory neurons, which consequently leads to pathological pain
responses. In this study, we sought to investigate whether peripheral
inflammation alters global DNA methylation in trigeminal ganglia (TG) and
results in abnormal expression of pro-nociceptive genes. Our results show that
peripheral inflammation remotely reduced the level of global DNA methylation in
rat TG with a concurrent reduction in DNMT1 and
DNMT3a expression. Using unbiased steps, we selected the
following pro-nociceptive candidate genes that are potentially regulated by DNA
methylation: TRPV1, TRPA1, P2X3, and PIEZO2.
Inhibition of DNMT with 5-Aza-dC in dissociated TG cells produced dose-dependent
upregulation of TRPV1, TRPA1, and P2X3.
Systemic treatment of animals with 5-Aza-dC significantly increased the
expression of TRPV1, TRPA1, and PIEZO2 in TG.
Furthermore, the overexpression of DNMT3a, as delivered by a lentiviral vector,
significantly downregulated TRPV1 and PIEZO2
expression and also reliably decreased TRPA1 and
P2X3 transcripts. MeDIP revealed that this overexpression
also significantly enhanced methylation of CGIs associated with
TRPV1 and TRPA1. In addition, bisulfite
sequencing data indicated that the CGI associated with TRPA1
was methylated in a pattern catalyzed by DNMT3a. Taken together, our results
show that all 4 pro-nociceptive genes are subject to epigenetic modulation via
DNA methylation, likely via DNMT3a under inflammatory conditions. These findings
provide the first evidence for the functional importance of DNA methylation as
an epigenetic factor in the transcription of pro-nociceptive genes in TG that
are implicated in pathological orofacial pain responses.
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Affiliation(s)
- Guang Bai
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD, USA
| | - Holly Ross
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD, USA
| | - Youping Zhang
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD, USA
| | - KiSeok Lee
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD, USA
| | - Jin Y Ro
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD, USA
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14
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Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S, Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H, Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang GG, Jeltsch A, Song J. Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. Nat Commun 2020; 11:3355. [PMID: 32620778 PMCID: PMC7335073 DOI: 10.1038/s41467-020-17109-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022] Open
Abstract
Mammalian DNA methylation patterns are established by two de novo DNA methyltransferases, DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substrate-recognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis.
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Affiliation(s)
- Linfeng Gao
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
| | - Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sara A Grimm
- Division of Intramural Research, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Wendan Ren
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Sabrina Adam
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Hidetaka Uryu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Zhi-Min Zhang
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Dongliang Chen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
| | - Michael Dukatz
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Hiwot Anteneh
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Pavel Bashtrykov
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Paul A Wade
- Division of Intramural Research, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
| | - Jikui Song
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA.
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA.
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15
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Bao-Caamano A, Rodriguez-Casanova A, Diaz-Lagares A. Epigenetics of Circulating Tumor Cells in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1220:117-134. [PMID: 32304083 DOI: 10.1007/978-3-030-35805-1_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid biopsy based on the analysis of circulating tumor cells (CTCs) has emerged as an important field of research. Molecular characterization of CTCs can provide insights into cancer biology and biomarkers for the clinic, representing a non-invasive powerful tool for monitoring breast cancer metastasis and predict the therapeutic response. Epigenetic mechanisms play a key role in the control of gene expression and their alteration contributes to cancer development and progression. These epigenetic modifications in CTCs have been described mainly related to modifications of the DNA methylation pattern and changes in the expression profile of noncoding RNAs. Here we summarize the recent findings on the epigenetic characterization of CTCs in breast cancer and their clinical value as tumor biomarkers, and discuss challenges and opportunities in this field.
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Affiliation(s)
- Aida Bao-Caamano
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain. .,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.
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16
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Norvil AB, AlAbdi L, Liu B, Tu YH, Forstoffer NE, Michie A, Chen T, Gowher H. The acute myeloid leukemia variant DNMT3A Arg882His is a DNMT3B-like enzyme. Nucleic Acids Res 2020; 48:3761-3775. [PMID: 32123902 PMCID: PMC7144950 DOI: 10.1093/nar/gkaa139] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 12/31/2022] Open
Abstract
We have previously shown that the highly prevalent acute myeloid leukemia (AML) mutation, Arg882His, in DNMT3A disrupts its cooperative mechanism and leads to reduced enzymatic activity, thus explaining the genomic hypomethylation in AML cells. However, the underlying cause of the oncogenic effect of Arg882His in DNMT3A is not fully understood. Here, we discovered that DNMT3A WT enzyme under conditions that favor non-cooperative kinetic mechanism as well as DNMT3A Arg882His variant acquire CpG flanking sequence preference akin to that of DNMT3B, which is non-cooperative. We tested if DNMT3A Arg882His could preferably methylate DNMT3B-specific target sites in vivo. Rescue experiments in Dnmt3a/3b double knockout mouse embryonic stem cells show that the corresponding Arg878His mutation in mouse DNMT3A severely impairs its ability to methylate major satellite DNA, a DNMT3A-preferred target, but has no overt effect on the ability to methylate minor satellite DNA, a DNMT3B-preferred target. We also observed a previously unappreciated CpG flanking sequence bias in major and minor satellite repeats that is consistent with DNMT3A and DNMT3B specificity suggesting that DNA methylation patterns are guided by the sequence preference of these enzymes. We speculate that aberrant methylation of DNMT3B target sites could contribute to the oncogenic potential of DNMT3A AML variant.
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Affiliation(s)
- Allison B Norvil
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Lama AlAbdi
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Bigang Liu
- Department of Epigenetics and Molecular Carcinogenesis, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yu Han Tu
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Nicole E Forstoffer
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Amie R Michie
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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17
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Lin CC, Chen YP, Yang WZ, Shen JCK, Yuan H. Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B. Nucleic Acids Res 2020; 48:3949-3961. [PMID: 32083663 PMCID: PMC7144912 DOI: 10.1093/nar/gkaa111] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/07/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
DNA methyltransferases are primary enzymes for cytosine methylation at CpG sites of epigenetic gene regulation in mammals. De novo methyltransferases DNMT3A and DNMT3B create DNA methylation patterns during development, but how they differentially implement genomic DNA methylation patterns is poorly understood. Here, we report crystal structures of the catalytic domain of human DNMT3B-3L complex, noncovalently bound with and without DNA of different sequences. Human DNMT3B uses two flexible loops to enclose DNA and employs its catalytic loop to flip out the cytosine base. As opposed to DNMT3A, DNMT3B specifically recognizes DNA with CpGpG sites via residues Asn779 and Lys777 in its more stable and well-ordered target recognition domain loop to facilitate processive methylation of tandemly repeated CpG sites. We also identify a proton wire water channel for the final deprotonation step, revealing the complete working mechanism for cytosine methylation by DNMT3B and providing the structural basis for DNMT3B mutation-induced hypomethylation in immunodeficiency, centromere instability and facial anomalies syndrome.
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Affiliation(s)
- Chien-Chu Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ping Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - James C K Shen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei 10048, Taiwan
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18
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Dynamic CpG methylation delineates subregions within super-enhancers selectively decommissioned at the exit from naive pluripotency. Nat Commun 2020; 11:1112. [PMID: 32111830 PMCID: PMC7048827 DOI: 10.1038/s41467-020-14916-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 02/08/2020] [Indexed: 12/29/2022] Open
Abstract
Clusters of enhancers, referred as to super-enhancers (SEs), control the expression of cell identity genes. The organisation of these clusters, and how they are remodelled upon developmental transitions remain poorly understood. Here, we report the existence of two types of enhancer units within SEs typified by distinctive CpG methylation dynamics in embryonic stem cells (ESCs). We find that these units are either prone for decommissioning or remain constitutively active in epiblast stem cells (EpiSCs), as further established in the peri-implantation epiblast in vivo. Mechanistically, we show a pivotal role for ESRRB in regulating the activity of ESC-specific enhancer units and propose that the developmentally regulated silencing of ESRRB triggers the selective inactivation of these units within SEs. Our study provides insights into the molecular events that follow the loss of ESRRB binding, and offers a mechanism by which the naive pluripotency transcriptional programme can be partially reset upon embryo implantation.
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19
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de la Calle-Fabregat C, Morante-Palacios O, Ballestar E. Understanding the Relevance of DNA Methylation Changes in Immune Differentiation and Disease. Genes (Basel) 2020; 11:E110. [PMID: 31963661 PMCID: PMC7017047 DOI: 10.3390/genes11010110] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Immune cells are one of the most complex and diverse systems in the human organism. Such diversity implies an intricate network of different cell types and interactions that are dependently interconnected. The processes by which different cell types differentiate from progenitors, mature, and finally exert their function requires an orchestrated succession of molecular processes that determine cell phenotype and function. The acquisition of these phenotypes is highly dependent on the establishment of unique epigenetic profiles that confer identity and function on the various types of effector cells. These epigenetic mechanisms integrate microenvironmental cues into the genome to establish specific transcriptional programs. Epigenetic modifications bridge environment and genome regulation and play a role in human diseases by their ability to modulate physiological programs through external stimuli. DNA methylation is one of the most ubiquitous, stable, and widely studied epigenetic modifications. Recent technological advances have facilitated the generation of a vast amount of genome-wide DNA methylation data, providing profound insights into the roles of DNA methylation in health and disease. This review considers the relevance of DNA methylation to immune system cellular development and function, as well as the participation of DNA methylation defects in immune-mediated pathologies, illustrated by selected paradigmatic diseases.
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Affiliation(s)
| | | | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain; (C.d.l.C.-F.); (O.M.-P.)
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20
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Luck A, Giehr P, Nordstrom K, Walter J, Wolf V. Hidden Markov Modelling Reveals Neighborhood Dependence of Dnmt3a and 3b Activity. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1598-1609. [PMID: 31027045 DOI: 10.1109/tcbb.2019.2910814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA methylation is an epigenetic mark whose important role in development has been widely recognized. This epigenetic modification results in heritable information not encoded by the DNA sequence. The underlying mechanisms controlling DNA methylation are only partly understood. Several mechanistic models of enzyme activities responsible for DNA methylation have been proposed. Here, we extend existing Hidden Markov Models (HMMs) for DNA methylation by describing the occurrence of spatial methylation patterns over time and propose several models with different neighborhood dependences. Furthermore, we investigate correlations between the neighborhood dependence and other genomic information. We perform numerical analysis of the HMMs applied to comprehensive hairpin and non-hairpin bisulfite sequencing measurements and accurately predict wild-type data. We find evidence that the activities of Dnmt3a and Dnmt3b responsible for de novo methylation depend on 5' (left) but not on 3' (right) neighboring CpGs in a sequencing string.
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21
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Emperle M, Rajavelu A, Kunert S, Arimondo PB, Reinhardt R, Jurkowska RZ, Jeltsch A. The DNMT3A R882H mutant displays altered flanking sequence preferences. Nucleic Acids Res 2019. [PMID: 29518238 PMCID: PMC5887309 DOI: 10.1093/nar/gky168] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The DNMT3A R882H mutation is frequently observed in acute myeloid leukemia (AML). It is located in the subunit and DNA binding interface of DNMT3A and has been reported to cause a reduction in activity and dominant negative effects. We investigated the mechanistic consequences of the R882H mutation on DNMT3A showing a roughly 40% reduction in overall DNA methylation activity. Biochemical assays demonstrated that R882H does not change DNA binding affinity, protein stability or subnuclear distribution of DNMT3A. Strikingly, DNA methylation experiments revealed pronounced changes in the flanking sequence preference of the DNMT3A-R882H mutant. Based on these results, different DNA substrates with selected flanking sequences were designed to be favored or disfavored by R882H. Kinetic analyses showed that the R882H favored substrate was methylated by R882H with 45% increased rate when compared with wildtype DNMT3A, while methylation of the disfavored substrate was reduced 7-fold. Our data expand the model of the potential carcinogenic effect of the R882H mutation by showing CpG site specific activity changes. This result suggests that R882 is involved in the indirect readout of flanking sequence preferences of DNMT3A and it may explain the particular enrichment of the R882H mutation in cancer patients by revealing mutation specific effects.
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Affiliation(s)
- Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Arumugam Rajavelu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Stefan Kunert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Paola B Arimondo
- CNRS ETaC FRE3600, Bât. IBCG. 118, Route de Narbonne, 31062 Toulouse cedex 9, France
| | - Richard Reinhardt
- Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
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22
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Dukatz M, Requena CE, Emperle M, Hajkova P, Sarkies P, Jeltsch A. Mechanistic Insights into Cytosine-N3 Methylation by DNA Methyltransferase DNMT3A. J Mol Biol 2019; 431:3139-3145. [PMID: 31229457 DOI: 10.1016/j.jmb.2019.06.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/03/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
Abstract
Recently, it has been discovered that different DNA-(cytosine C5)-methyltransferases including DNMT3A generate low levels of 3mC [Rosic et al. (2018), Nat. Genet., 50, 452-459]. This reaction resulted in the co-evolution of DNMTs and ALKB2 DNA repair enzymes, but its mechanism remained elusive. Here, we investigated the catalytic mechanism of DNMT3A for cytosine N3 methylation. We generated several DNMT3A variants with mutated catalytic residues and measured their activities in 5mC and 3mC generation by liquid chromatography linked to tandem mass spectrometry. Our data suggest that the methylation of N3 instead of C5 is caused by an inverted binding of the flipped cytosine target base into the active-site pocket of the DNA methyltransferase, which is partially compatible with the arrangement of catalytic amino acid residues. Given that all DNA-(cytosine C5)-methyltransferases have a common catalytic mechanism, it is likely that other enzymes of this class generate 3mC following the same mechanism.
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Affiliation(s)
- Michael Dukatz
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Cristina E Requena
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Petra Hajkova
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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23
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Sergeev AV, Tevyashova AN, Vorobyov AP, Gromova ES. The Effect of Antitumor Antibiotic Olivomycin A and Its New Semi-synthetic Derivative Olivamide on the Activity of Murine DNA Methyltransferase Dnmt3a. BIOCHEMISTRY (MOSCOW) 2019; 84:62-70. [PMID: 30927527 DOI: 10.1134/s0006297919010085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Olivomycin A is a highly active antitumor drug that belongs to the family of aureolic acid antibiotics. The antitumor effect of olivomycin A is related to its ability to bind to the DNA minor groove in GC-rich regions as Mg2+-coordinated complexes. Characterization of cellular targets of olivomycin A and its mechanism of action is crucial for the successful application of this antibiotic in clinical practice and development of semi-synthetic derivatives with improved pharmacological properties. Previously, we have shown that minor groove ligands are able to disrupt the key epigenetic process of DNA methylation. In this paper, we have studied the impact of olivomycin A and its improved semi-synthetic analogue N,N-dimethylaminoethylamide of 1'-des-(2,3-dihydroxy-n-butyroyl)-1'-carboxy-olivomycin A (olivamide) on the functioning of de novo DNA methyltransferase Dnmt3a (enzyme that carries out methylation of cytosine residues in the DNA CG-sites in eukaryotic cells) using an in vitro system consisting of the murine Dnmt3a catalytic domain and a 30-mer DNA duplex containing four consecutive GC pairs. We have shown that olivomycin A and olivamide inhibit Dnmt3a with IC50 of 6 ± 1 and 7.1 ± 0.7 μM, respectively. Neither olivomycin A nor olivamide interfered with the formation of the specific enzyme-substrate complex; however, olivomycin A prevented formation of the covalent DNA-Dnmt3a intermediate that is necessary for the methylation reaction to proceed. The inhibitory effects of olivomycin A and olivamide can be explained by the disruption of the enzyme catalytic loop movement through the DNA minor groove (the reaction stage that precedes the covalent bond formation between DNA and the enzyme). The results of this work indicate the epigenetic contribution to the antitumor effect of aureolic acid group antibiotics.
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Affiliation(s)
- A V Sergeev
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.
| | - A N Tevyashova
- Gause Institute of New Antibiotics, Moscow, 119021, Russia.,D. Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russia
| | - A P Vorobyov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia
| | - E S Gromova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia
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24
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Zhou X, Gan F, Hou L, Liu Z, Su J, Lin Z, Le G, Huang K. Aflatoxin B 1 Induces Immunotoxicity through the DNA Methyltransferase-Mediated JAK2/STAT3 Pathway in 3D4/21 Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3772-3780. [PMID: 30848898 DOI: 10.1021/acs.jafc.8b07309] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
As the most toxic mycotoxin of all of the fungal toxins, aflatoxin B1 (AFB1) has carcinogenesis, heptotoxicity, and immunotoxicity. DNA methylation plays a critical role in gene expression regulation of the pathological process. However, the relationship between DNA methylation and AFB1-induced immunotoxicity was not yet reported. Therefore, the objectives of this study were to verify AFB1-induced immunotoxicity and investigate the potential role of the DNA methyltransferase (DNMT) family in AFB1-induced immunotoxicity and the pathway mechanism in 3D4/21 cells. The results showed that AFB1 could induce cytotoxicity, apoptosis, pro-inflammatory cytokine expression, DNA damage, and oxidative stress and decrease phagocytotic capacity. Meanwhile, the levels of DNMT1 and DNMT3a were significantly increased in 0.04 and 0.08 μg/mL AFB1 compared to the control. Inhibition of DNMT1 and DNMT3a by 5-Aza-2dc could reverse changes of the above parameters. Further, the JAK2/STAT3 pathway was significantly activated in 0.04 μg/mL AFB1. Inhibition of p-JAK2 and p-STAT3 by AG490 could alleviate AFB1-induced immunotoxicity. Moreover, inhibition of DNMT1 and DNMT3a by 5-Aza-2dc could suppress the phosphorylation of JAK2 and STAT3. Taken together, AFB1-induced immunotoxicity is related to the JAK2/STAT3 pathway mediated by DNMTs in 3D4/21 cells.
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25
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Campos-Sanchez E, Martínez-Cano J, Del Pino Molina L, López-Granados E, Cobaleda C. Epigenetic Deregulation in Human Primary Immunodeficiencies. Trends Immunol 2018; 40:49-65. [PMID: 30509895 DOI: 10.1016/j.it.2018.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PIDs) are immune disorders resulting from defects in genes involved in immune regulation, and manifesting as an increased susceptibility to infections, autoimmunity, and cancer. However, the molecular basis of some prevalent entities remains poorly understood. Epigenetic control is essential for immune functions, and epigenetic alterations have been identified in different PIDs, including syndromes such as immunodeficiency-centromeric-instability-facial-anomalies, Kabuki, or Wolf-Hirschhorn, among others. Although the epigenetic changes may differ among these PIDs, the reversibility of epigenetic modifications suggests that they might become potential therapeutic targets. Here, we review recent mechanistic advances in our understanding of epigenetic alterations associated with certain PIDs, propose that a fully epigenetically driven mechanism might underlie some PIDs, and discuss the possible prophylactic and therapeutic implications.
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Affiliation(s)
- Elena Campos-Sanchez
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Jorge Martínez-Cano
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Lucía Del Pino Molina
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain.
| | - Cesar Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain.
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26
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Gowher H, Jeltsch A. Mammalian DNA methyltransferases: new discoveries and open questions. Biochem Soc Trans 2018; 46:1191-1202. [PMID: 30154093 PMCID: PMC6581191 DOI: 10.1042/bst20170574] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 11/17/2022]
Abstract
As part of the epigenetic network, DNA methylation is a major regulator of chromatin structure and function. In mammals, it mainly occurs at palindromic CpG sites, but asymmetric methylation at non-CpG sites is also observed. Three enzymes are involved in the generation and maintenance of DNA methylation patterns. DNMT1 has high preference for hemimethylated CpG sites, and DNMT3A and DNMT3B equally methylate unmethylated and hemimethylated DNA, and also introduce non-CpG methylation. Here, we review recent observations and novel insights into the structure and function of mammalian DNMTs (DNA methyltransferases), including new structures of DNMT1 and DNMT3A, data on their mechanism, regulation by post-translational modifications and on the function of DNMTs in cells. In addition, we present news findings regarding the allosteric regulation and targeting of DNMTs by chromatin modifications and chromatin proteins. In combination, the recent publications summarized here impressively illustrate the intensity of ongoing research in this field. They provide a deeper understanding of key mechanistic properties of DNMTs, but they also document still unsolved issues, which need to be addressed in future research.
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Affiliation(s)
- Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
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27
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Emperle M, Dukatz M, Kunert S, Holzer K, Rajavelu A, Jurkowska RZ, Jeltsch A. The DNMT3A R882H mutation does not cause dominant negative effects in purified mixed DNMT3A/R882H complexes. Sci Rep 2018; 8:13242. [PMID: 30185810 PMCID: PMC6125428 DOI: 10.1038/s41598-018-31635-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/23/2018] [Indexed: 12/17/2022] Open
Abstract
The DNA methyltransferase DNMT3A R882H mutation is observed in 25% of all AML patients. DNMT3A is active as tetramer and the R882H mutation is located in one of the subunit/subunit interfaces. Previous work has reported that formation of mixed wildtype/R882H complexes leads to a strong loss of catalytic activity observed in in vitro DNA methylation assays (Russler-Germain et al., 2014, Cancer Cell 25:442–454). To investigate this effect further, we have prepared mixed wildtype/R882H DNMT3A complexes by incubation of individually purified subunits of the DNMT3A catalytic domain and full-length DNMT3A2. In addition, we have used a double affinity tag approach and specifically purified mixed catalytic domain complexes formed after co-expression of R882H and wildtype subunits in E. coli cells. Afterwards, we determined the catalytic activity of the mixed complexes and compared it to that of purified complexes only consisting of one subunit type. In both settings, the expected catalytic activities of mixed R882H/wildtype complexes were observed demonstrating an absence of a dominant negative effect of the R882H mutation in purified DNMT3A enzymes. This result suggests that heterocomplex formation of DNMT3A and R882H is unlikely to cause dominant negative effects in human cells as well. The limitations of this conclusion and its implications are discussed.
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Affiliation(s)
- Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Michael Dukatz
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Stefan Kunert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Katharina Holzer
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Arumugam Rajavelu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.,Rajiv Gandhi Center for Biotechnology (RGCB), Trivandrum, 695014, Kerala, India
| | - Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.,BioMed X Innovation Center, Im Neuenheimer Feld 583, D-69120, Heidelberg, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.
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28
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Qu J, Zhu L, Zhou Z, Chen P, Liu S, Locy ML, Thannickal VJ, Zhou Y. Reversing Mechanoinductive DSP Expression by CRISPR/dCas9-mediated Epigenome Editing. Am J Respir Crit Care Med 2018; 198:599-609. [PMID: 29924937 PMCID: PMC6118013 DOI: 10.1164/rccm.201711-2242oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 06/20/2018] [Indexed: 12/29/2022] Open
Abstract
RATIONALE DSP (desmoplakin), the most abundant component of desmosomes, which maintain the mechanical integrity of epithelium, is a genome-wide association study-identified genetic risk locus in human idiopathic pulmonary fibrosis (IPF). Subjects with IPF express a significantly higher level of DSP than control subjects. OBJECTIVES Determine potential mechanisms by which DSP is regulated in lung fibrosis. METHODS Matrigel-coated soft and stiff polyacrylamide gels were made to simulate the stiffness of normal and fibrotic lungs. Quantitative chromatin immunoprecipitation and electrophoretic mobility shift assay were used to evaluate transcription factor binding to the DSP promoter. Targeted DNA methylation was achieved by CRISPR (clustered regularly interspaced short palindromic repeats)/dCas9 (deactivated CRISPR-associated protein-9 nuclease)-mediated Dnmt3A (DNA methyltransferase 3A) expression under the guidance of sequence-specific single guide RNAs. MEASUREMENTS AND MAIN RESULTS Stiff matrix promotes DSP gene expression in both human and rodent lung epithelial cells as compared with soft matrix. A conserved region in the proximal DSP promoter is hypermethylated under soft matrix conditions and becomes hypomethylated/demethylated under stiff matrix conditions. Demethylation of this conserved DSP promoter region is associated with transactivation of transcription factor EGR1 (early growth response protein 1), resulting in EGR1-dependent DSP overexpression. Targeted DNA methylation by CRISPR/dCas9/Dnmt3A-mediated epigenome editing blocks EGR1 binding to the DSP promoter and inhibits stiff matrix-induced DSP overexpression. CONCLUSIONS DSP is a matrix stiffness-regulated mechanosensitive gene. CRISPR/dCas9-Dnmt3A-mediated epigenome editing reverses DSP overexpression by reestablishment of the epigenetic control of DSP under the mechanically homeostatic environment. It provides a useful tool for investigations of the functional role of DSP in the pathogenesis of lung fibrosis.
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Affiliation(s)
- Jing Qu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lanyan Zhu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China; and
| | - Zijing Zhou
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China; and
| | - Ping Chen
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China; and
| | - Shuyan Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Morgan L. Locy
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Victor J. Thannickal
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Yong Zhou
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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29
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Norvil AB, Petell CJ, Alabdi L, Wu L, Rossie S, Gowher H. Dnmt3b Methylates DNA by a Noncooperative Mechanism, and Its Activity Is Unaffected by Manipulations at the Predicted Dimer Interface. Biochemistry 2018; 57:4312-4324. [PMID: 27768276 PMCID: PMC5992102 DOI: 10.1021/acs.biochem.6b00964] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The catalytic domains of the de novo DNA methyltransferases Dnmt3a-C and Dnmt3b-C are highly homologous. However, their unique biochemical properties could potentially contribute to differences in the substrate preferences or biological functions of these enzymes. Dnmt3a-C forms tetramers through interactions at the dimer interface, which also promote multimerization on DNA and cooperativity. Similar to the case for processive enzymes, cooperativity allows Dnmt3a-C to methylate multiple sites on the same DNA molecule; however, it is unclear whether Dnmt3b-C methylates DNA by a cooperative or processive mechanism. The importance of the tetramer structure and cooperative mechanism is emphasized by the observation that the R882H mutation in the dimer interface of DNMT3A is highly prevalent in acute myeloid leukemia and leads to a substantial loss of its activity. Under conditions that distinguish between cooperativity and processivity, we show that in contrast to that of Dnmt3a-C, the activity of Dnmt3b-C is not cooperative and confirm the processivity of Dnmt3b-C and the full length Dnmt3b enzyme. Whereas the R878H mutation (mouse homologue of R882H) led to the loss of cooperativity of Dnmt3a-C, the activity and processivity of the analogous Dnmt3b-C R829H variant were comparable to those of the wild-type enzyme. Additionally, buffer acidification that attenuates the dimer interface interactions of Dnmt3a-C had no effect on Dnmt3b-C activity. Taken together, these results demonstrate an important mechanistic difference between Dnmt3b and Dnmt3a and suggest that interactions at the dimer interface may play a limited role in regulating Dnmt3b-C activity. These new insights have potential implications for the distinct biological roles of Dnmt3a and Dnmt3b.
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Affiliation(s)
- Allison B. Norvil
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Christopher J. Petell
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lama Alabdi
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lanchen Wu
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sandra Rossie
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Humaira Gowher
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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30
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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] [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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31
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Hervouet E, Peixoto P, Delage-Mourroux R, Boyer-Guittaut M, Cartron PF. Specific or not specific recruitment of DNMTs for DNA methylation, an epigenetic dilemma. Clin Epigenetics 2018; 10:17. [PMID: 29449903 PMCID: PMC5807744 DOI: 10.1186/s13148-018-0450-y] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/30/2018] [Indexed: 11/28/2022] Open
Abstract
Our current view of DNA methylation processes is strongly moving: First, even if it was generally admitted that DNMT3A and DNMT3B are associated with de novo methylation and DNMT1 is associated with inheritance DNA methylation, these distinctions are now not so clear. Secondly, since one decade, many partners of DNMTs have been involved in both the regulation of DNA methylation activity and DNMT recruitment on DNA. The high diversity of interactions and the combination of these interactions let us to subclass the different DNMT-including complexes. For example, the DNMT3L/DNMT3A complex is mainly related to de novo DNA methylation in embryonic states, whereas the DNMT1/PCNA/UHRF1 complex is required for maintaining global DNA methylation following DNA replication. On the opposite to these unspecific DNA methylation machineries (no preferential DNA sequence), some recently identified DNMT-including complexes are recruited on specific DNA sequences. The coexistence of both types of DNA methylation (un/specific) suggests a close cooperation and an orchestration between these systems to maintain genome and epigenome integrities. Deregulation of these systems can lead to pathologic disorders.
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Affiliation(s)
- Eric Hervouet
- INSERM unit 1098, University of Bourgogne Franche-Comté, Besançon, France.,EPIGENExp (EPIgenetics and GENe EXPression Technical Platform), Besançon, France
| | - Paul Peixoto
- INSERM unit 1098, University of Bourgogne Franche-Comté, Besançon, France.,EPIGENExp (EPIgenetics and GENe EXPression Technical Platform), Besançon, France
| | | | | | - Pierre-François Cartron
- 3INSERM unit S1232, University of Nantes, Nantes, France.,4Institut de cancérologie de l'Ouest, Nantes, France.,REpiCGO (Cancéropole Grand-Ouest), Nantes, France.,EpiSAVMEN Networks, Nantes, Région Pays de la Loire France
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32
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Ravichandran M, Jurkowska RZ, Jurkowski TP. Target specificity of mammalian DNA methylation and demethylation machinery. Org Biomol Chem 2018; 16:1419-1435. [DOI: 10.1039/c7ob02574b] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.
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Affiliation(s)
| | | | - T. P. Jurkowski
- Universität Stuttgart
- Abteilung Biochemie
- Institute für Biochemie und Technische Biochemie
- Stuttgart D-70569
- Germany
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33
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Choi M, Genereux DP, Goodson J, Al-Azzawi H, Allain SQ, Simon N, Palasek S, Ware CB, Cavanaugh C, Miller DG, Johnson WC, Sinclair KD, Stöger R, Laird CD. Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells. PLoS Genet 2017; 13:e1007060. [PMID: 29107996 PMCID: PMC5690686 DOI: 10.1371/journal.pgen.1007060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/16/2017] [Accepted: 10/08/2017] [Indexed: 11/25/2022] Open
Abstract
In storing and transmitting epigenetic information, organisms must balance the need to maintain information about past conditions with the capacity to respond to information in their current and future environments. Some of this information is encoded by DNA methylation, which can be transmitted with variable fidelity from parent to daughter strand. High fidelity confers strong pattern matching between the strands of individual DNA molecules and thus pattern stability over rounds of DNA replication; lower fidelity confers reduced pattern matching, and thus greater flexibility. Here, we present a new conceptual framework, Ratio of Concordance Preference (RCP), that uses double-stranded methylation data to quantify the flexibility and stability of the system that gave rise to a given set of patterns. We find that differentiated mammalian cells operate with high DNA methylation stability, consistent with earlier reports. Stem cells in culture and in embryos, in contrast, operate with reduced, albeit significant, methylation stability. We conclude that preference for concordant DNA methylation is a consistent mode of information transfer, and thus provides epigenetic stability across cell divisions, even in stem cells and those undergoing developmental transitions. Broader application of our RCP framework will permit comparison of epigenetic-information systems across cells, developmental stages, and organisms whose methylation machineries differ substantially or are not yet well understood.
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Affiliation(s)
- Minseung Choi
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
| | - Diane P. Genereux
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
| | - Jamie Goodson
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Haneen Al-Azzawi
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Shannon Q. Allain
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Noah Simon
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Stan Palasek
- Department of Mathematics, Princeton University, Princeton, New Jersey, United States of America
| | - Carol B. Ware
- Department of Comparative Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Chris Cavanaugh
- Department of Comparative Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Daniel G. Miller
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Winslow C. Johnson
- Department of Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Kevin D. Sinclair
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Charles D. Laird
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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34
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van den Boogaard ML, Thijssen PE, Aytekin C, Licciardi F, Kıykım AA, Spossito L, Dalm VASH, Driessen GJ, Kersseboom R, de Vries F, van Ostaijen-Ten Dam MM, Ikinciogullari A, Dogu F, Oleastro M, Bailardo E, Daxinger L, Nain E, Baris S, van Tol MJD, Weemaes C, van der Maarel SM. Expanding the mutation spectrum in ICF syndrome: Evidence for a gender bias in ICF2. Clin Genet 2017; 92:380-387. [PMID: 28128455 DOI: 10.1111/cge.12979] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/13/2017] [Accepted: 01/23/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is a rare, genetically heterogeneous, autosomal recessive disorder. Patients suffer from recurrent infections caused by reduced levels or absence of serum immunoglobulins. Genetically, 4 subtypes of ICF syndrome have been identified to date: ICF1 (DNMT3B mutations), ICF2 (ZBTB24 mutations), ICF3 (CDCA7 mutations), and ICF4 (HELLS mutations). AIM To study the mutation spectrum in ICF syndrome. MATERIALS AND METHODS Genetic studies were performed in peripheral blood lymphocyte DNA from suspected ICF patients and family members. RESULTS We describe 7 ICF1 patients and 6 novel missense mutations in DNMT3B, affecting highly conserved residues in the catalytic domain. We also describe 5 new ICF2 patients, one of them carrying a homozygous deletion of the complete ZBTB24 locus. In a meta-analysis of all published ICF cases, we observed a gender bias in ICF2 with 79% male patients. DISCUSSION The biallelic deletion of ZBTB24 provides strong support for the hypothesis that most ICF2 patients suffer from a ZBTB24 loss of function mechanism and confirms that complete absence of ZBTB24 is compatible with human life. This is in contrast to the observed early embryonic lethality in mice lacking functional Zbtb24. The observed gender bias seems to be restricted to ICF2 as it is not observed in the ICF1 cohort. CONCLUSION Our study expands the mutation spectrum in ICF syndrome and supports that DNMT3B and ZBTB24 are the most common disease genes.
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Affiliation(s)
- M L van den Boogaard
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - P E Thijssen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - C Aytekin
- Department of Pediatric Immunology, Dr Sami Ulus Maternity and Children's Research and Educational Hospital, Ankara, Turkey
| | - F Licciardi
- Department of Paediatrics II, Regina Margherita Hospital Città della Salute e della Scienza di Torino, Torino, Italy
| | - A A Kıykım
- Pediatric Allergy and Immunology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey
| | - L Spossito
- Department of Immunology and Rheumatology, Hospital "J.P Garrahan", Buenos Aires, Argentina
| | - V A S H Dalm
- Department of Immunology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - G J Driessen
- Department of Paediatric Infectious Diseases, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
- Department of Pediatrics, Juliana Children's Hospital, Haga Teaching Hospital, The Hague, The Netherlands
| | - R Kersseboom
- Department of Clinical Genetics, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
- Medical service, Stichting Zuidwester, Middelharnis, The Netherlands
| | - F de Vries
- Department of Clinical Genetics, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - M M van Ostaijen-Ten Dam
- Department of Pediatrics, Laboratory Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - A Ikinciogullari
- Department of Pediatric Immunology and Allergy, Ankara University School of Medicine, Ankara, Turkey
| | - F Dogu
- Department of Pediatric Immunology and Allergy, Ankara University School of Medicine, Ankara, Turkey
| | - M Oleastro
- Department of Immunology and Rheumatology, Hospital "J.P Garrahan", Buenos Aires, Argentina
| | - E Bailardo
- Department of Genetics, Hospital "J.P. Garrahan", Buenos Aires, Argentina
| | - L Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - E Nain
- Pediatric Allergy and Immunology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey
| | - S Baris
- Pediatric Allergy and Immunology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey
| | - M J D van Tol
- Department of Pediatrics, Laboratory Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - C Weemaes
- Department of Pediatric Infectious Diseases and Immunology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - S M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Hassanzadeh M, Kasymov R, Mahernia S, Adib M, Emperle M, Dukatz M, Bashtrykov P, Jeltsch A, Amanlou M. Discovery of Novel and Selective DNA Methyltransferase 1 Inhibitors by Pharmacophore and Docking-Based Virtual Screening. ChemistrySelect 2017. [DOI: 10.1002/slct.201701734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Malihe Hassanzadeh
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
| | - Rustem Kasymov
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Shabnam Mahernia
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
| | - Mehdi Adib
- School of Chemistry; College of Science; University of Tehran; Tehran Iran
| | - Max Emperle
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Michael Dukatz
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Pavel Bashtrykov
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Albert Jeltsch
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Massoud Amanlou
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
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36
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Kirsanova OV, Sergeev AV, Yasko IS, Gromova ES. The impact of 6-thioguanine incorporation into DNA on the function of DNA methyltransferase Dnmt3a. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:392-405. [PMID: 28498075 DOI: 10.1080/15257770.2017.1287921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The incorporation of chemotherapeutic agent 6-thioguanine (SG) into DNA is a prerequisite for its cytotoxic action. This modification of DNA impedes the activity of enzymes involved in DNA repair and replication. Here, using hemimethylated DNA substrates we demonstrated that DNA methylation by Dnmt3a-CD is reduced if DNA is damaged by the incorporation of SG into one or two CpG sites separated by nine base pairs. An increase in the number of SG substitutions did not enhance the effect. Dnmt3a-CD binding to either of SG-containing DNA substrates was not distorted. Our results suggest that SG incorporation into DNA may influence epigenetic regulation via DNA methylation.
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Affiliation(s)
- Olga V Kirsanova
- a Department of Chemistry , M. V. Lomonosov Moscow State University , Moscow , Russia
| | - Alexander V Sergeev
- a Department of Chemistry , M. V. Lomonosov Moscow State University , Moscow , Russia
| | - Ivan S Yasko
- a Department of Chemistry , M. V. Lomonosov Moscow State University , Moscow , Russia
| | - Elizaveta S Gromova
- a Department of Chemistry , M. V. Lomonosov Moscow State University , Moscow , Russia
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37
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Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile G, Maldotti M, Anselmi F, Oliviero S. Intragenic DNA methylation prevents spurious transcription initiation. Nature 2017; 543:72-77. [PMID: 28225755 DOI: 10.1038/nature21373] [Citation(s) in RCA: 455] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/05/2017] [Indexed: 12/12/2022]
Abstract
In mammals, DNA methylation occurs mainly at CpG dinucleotides. Methylation of the promoter suppresses gene expression, but the functional role of gene-body DNA methylation in highly expressed genes has yet to be clarified. Here we show that, in mouse embryonic stem cells, Dnmt3b-dependent intragenic DNA methylation protects the gene body from spurious RNA polymerase II entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that this Dnmt3b function is dependent on its enzymatic activity and recruitment to the gene body by H3K36me3. Furthermore, the spurious transcripts can either be degraded by the RNA exosome complex or capped, polyadenylated, and delivered to the ribosome to produce aberrant proteins. Elongating RNA polymerase II therefore triggers an epigenetic crosstalk mechanism that involves SetD2, H3K36me3, Dnmt3b and DNA methylation to ensure the fidelity of gene transcription initiation, with implications for intragenic hypomethylation in cancer.
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Affiliation(s)
- Francesco Neri
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Stefania Rapelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Anna Krepelova
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Danny Incarnato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Caterina Parlato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Giulia Basile
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Mara Maldotti
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Anselmi
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Salvatore Oliviero
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
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38
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Engineering and Directed Evolution of DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 27826849 DOI: 10.1007/978-3-319-43624-1_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
DNA methyltransferases (MTases) constitute an attractive target for protein engineering, thus opening the road to new ways of manipulating DNA in a unique and selective manner. Here, we review various aspects of MTase engineering, both methodological and conceptual, and also discuss future directions and challenges. Bacterial MTases that are part of restriction/modification (R/M) systems offer a convenient way for the selection of large gene libraries, both in vivo and in vitro. We review these selection methods, their strengths and weaknesses, and also the prospects for new selection approaches that will enable the directed evolution of mammalian DNA methyltransferases (Dnmts). We explore various properties of MTases that may be subject to engineering. These include engineering for higher stability and soluble expression (MTases, including bacterial ones, are prone to misfolding), engineering of the DNA target specificity, and engineering for the usage of S-adenosyl-L-methionine (AdoMet) analogs. Directed evolution of bacterial MTases also offers insights into how these enzymes readily evolve in nature, thus yielding MTases with a huge spectrum of DNA target specificities. Engineering for alternative cofactors, on the other hand, enables modification of DNA with various groups other than methyl and thus can be employed to map and redirect DNA epigenetic modifications.
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39
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Plourde KV, Labrie Y, Ouellette G, Pouliot MC, Durocher F. Genome-wide methylation analysis of DNMT3B gene isoforms revealed specific methylation profiles in breast cell lines. Epigenomics 2016; 8:1209-26. [PMID: 27586997 DOI: 10.2217/epi-2016-0013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIM The goal of this study is to characterize the specific methylation profile triggered by DNMT3B protein isoforms expressed at different levels in breast cell lines. MATERIALS & METHODS Microarray DNA methylation data were analyzed and associated with functional genome annotation data. RESULTS A large spectrum of DNMT3B3/DNMT3B2 expression ratio values was observed in parental breast cell lines. According to their methylation profiles, hierarchical clustering of untransfected cell lines revealed clustering based on their ER/PR status. Overexpression of DNMT3B3 triggered methylation changes of thousands of CpG sites in breast cells. Based on the trend of methylation changes, the results suggest an antiproliferative action of the DNMT3B3 isoform through a dominant negative effect on its wild-type counterpart DNMT3B2. CONCLUSION This study revealed specific pathways modulated by DNMT3B isoforms, which could regulate cell proliferation and other biological mechanisms. This illustrates the importance of multiple interactions between isoforms in the complexity of methylation processes.
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Affiliation(s)
- Karine V Plourde
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Yvan Labrie
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Geneviève Ouellette
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Marie-Christine Pouliot
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Francine Durocher
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
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40
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Jeltsch A, Jurkowska RZ. Allosteric control of mammalian DNA methyltransferases - a new regulatory paradigm. Nucleic Acids Res 2016; 44:8556-8575. [PMID: 27521372 PMCID: PMC5062992 DOI: 10.1093/nar/gkw723] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/08/2016] [Indexed: 12/23/2022] Open
Abstract
In mammals, DNA methylation is introduced by the DNMT1, DNMT3A and DNMT3B methyltransferases, which are all large multi-domain proteins containing a catalytic C-terminal domain and an N-terminal part with regulatory functions. Recently, two novel regulatory principles of DNMTs were uncovered. It was shown that their catalytic activity is under allosteric control of N-terminal domains with autoinhibitory function, the RFT and CXXC domains in DNMT1 and the ADD domain in DNMT3. Moreover, targeting and activity of DNMTs were found to be regulated in a concerted manner by interactors and posttranslational modifications (PTMs). In this review, we describe the structures and domain composition of the DNMT1 and DNMT3 enzymes, their DNA binding, catalytic mechanism, multimerization and the processes controlling their stability in cells with a focus on their regulation and chromatin targeting by PTMs, interactors and chromatin modifications. We propose that the allosteric regulation of DNMTs by autoinhibitory domains acts as a general switch for the modulation of the function of DNMTs, providing numerous possibilities for interacting proteins, nucleic acids or PTMs to regulate DNMT activity and targeting. The combined regulation of DNMT targeting and catalytic activity contributes to the precise spatiotemporal control of DNMT function and genome methylation in cells.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry, Pfaffenwaldring 55, Faculty of Chemistry, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- BioMed X Innovation Center, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
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41
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Savell KE, Gallus NVN, Simon RC, Brown JA, Revanna JS, Osborn MK, Song EY, O'Malley JJ, Stackhouse CT, Norvil A, Gowher H, Sweatt JD, Day JJ. Extra-coding RNAs regulate neuronal DNA methylation dynamics. Nat Commun 2016; 7:12091. [PMID: 27384705 PMCID: PMC4941050 DOI: 10.1038/ncomms12091] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/28/2016] [Indexed: 02/06/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation are essential regulators of the function and information storage capacity of neurons. DNA methylation is highly dynamic in the developing and adult brain, and is actively regulated by neuronal activity and behavioural experiences. However, it is presently unclear how methylation status at individual genes is targeted for modification. Here, we report that extra-coding RNAs (ecRNAs) interact with DNA methyltransferases and regulate neuronal DNA methylation. Expression of ecRNA species is associated with gene promoter hypomethylation, is altered by neuronal activity, and is overrepresented at genes involved in neuronal function. Knockdown of the Fos ecRNA locus results in gene hypermethylation and mRNA silencing, and hippocampal expression of Fos ecRNA is required for long-term fear memory formation in rats. These results suggest that ecRNAs are fundamental regulators of DNA methylation patterns in neuronal systems, and reveal a promising avenue for therapeutic targeting in neuropsychiatric disease states. DNA methylation in the brain is a dynamic process, but gene-specific regulation of this process is poorly understood. Here, Day and colleagues show that extra-coding RNAs interact with DNA methyltransferases and regulate neuronal DNA methylation to control gene expression in locus-specific manner in neurons.
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Affiliation(s)
- Katherine E Savell
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Nancy V N Gallus
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Rhiana C Simon
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Jordan A Brown
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Jasmin S Revanna
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Mary Katherine Osborn
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Esther Y Song
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - John J O'Malley
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Christian T Stackhouse
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Allison Norvil
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - J David Sweatt
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Jeremy J Day
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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42
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Petell CJ, Alabdi L, He M, San Miguel P, Rose R, Gowher H. An epigenetic switch regulates de novo DNA methylation at a subset of pluripotency gene enhancers during embryonic stem cell differentiation. Nucleic Acids Res 2016; 44:7605-17. [PMID: 27179026 PMCID: PMC5027477 DOI: 10.1093/nar/gkw426] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/05/2016] [Indexed: 12/30/2022] Open
Abstract
Coordinated regulation of gene expression that involves activation of lineage specific genes and repression of pluripotency genes drives differentiation of embryonic stem cells (ESC). For complete repression of pluripotency genes during ESC differentiation, chromatin at their enhancers is silenced by the activity of the Lsd1-Mi2/NuRD complex. The mechanism/s that regulate DNA methylation at these enhancers are largely unknown. Here, we investigated the affect of the Lsd1-Mi2/NuRD complex on the dynamic regulatory switch that induces the local interaction of histone tails with the Dnmt3 ATRX-DNMT3-DNMT3L (ADD) domain, thus promoting DNA methylation at the enhancers of a subset of pluripotency genes. This is supported by previous structural studies showing a specific interaction between Dnmt3-ADD domain with H3K4 unmethylated histone tails that is disrupted by histone H3K4 methylation and histone acetylation. Our data suggest that Dnmt3a activity is triggered by Lsd1-Mi2/NuRD-mediated histone deacetylation and demethylation at these pluripotency gene enhancers when they are inactivated during mouse ESC differentiation. Using Dnmt3 knockout ESCs and the inhibitors of Lsd1 and p300 histone modifying enzymes during differentiation of E14Tg2A and ZHBTc4 ESCs, our study systematically reveals this mechanism and establishes that Dnmt3a is both reader and effector of the epigenetic state at these target sites.
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Affiliation(s)
| | - Lama Alabdi
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Phillip San Miguel
- DNA Sequencing Core Facility, Purdue University, West Lafayette, IN 47907, USA
| | - Richard Rose
- Department of Biochemistry, 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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43
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Lukashevich OV, Cherepanova NA, Jurkovska RZ, Jeltsch A, Gromova ES. Conserved motif VIII of murine DNA methyltransferase Dnmt3a is essential for methylation activity. BMC BIOCHEMISTRY 2016; 17:7. [PMID: 27001594 PMCID: PMC4802922 DOI: 10.1186/s12858-016-0064-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/02/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Dnmt3a is a DNA methyltransferase that establishes de novo DNA methylation in mammals. The structure of the Dnmt3a C-terminal domain is similar to the bacterial M. HhaI enzyme, a well-studied prokaryotic DNA methyltransferase. No X-ray structure is available for the complex of Dnmt3a with DNA and the mechanistic details of DNA recognition and catalysis by mammalian Dnmts are not completely understood. RESULTS Mutant variants of the catalytic domain of the murine Dnmt3a carrying substitutions of highly conserved N167, R200, and R202 have been generated by site directed mutagenesis and purified. Their methylation activity, DNA binding affinity, ability to flip the target cytosine out of the DNA double helix and covalent complex formation with DNA have been examined. Substitutions of N167 lead to reduced catalytic activity and reduced base flipping. Catalytic activity, base flipping, and covalent conjugate formation were almost completely abolished for the mutant enzymes with substitutions of R200 or R202. CONCLUSIONS We conclude that R202 plays a similar role in catalysis in Dnmt3a-CD as R232 in M.SssI and R165 in M.HhaI, which could be positioning of the cytosine for nucleophilic attack by a conserved Cys. R200 of Dnmt3a-CD is important in both catalysis and cytosine flipping. Both conserved R200 and R202 are involved in creating and stabilizing of the transient covalent intermediate of the methylation reaction. N167 might contribute to the positioning of the residues from the motif VI, but does not play a direct role in catalysis.
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Affiliation(s)
- Olga V Lukashevich
- Department of Chemistry, Moscow State University, 119991, Moscow, Russia
| | | | - Renata Z Jurkovska
- BioMedX Innovation Center, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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44
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Abstract
Genetic causes for human disorders are being discovered at an unprecedented pace. A growing subclass of disease-causing mutations involves changes in the epigenome or in the abundance and activity of proteins that regulate chromatin structure. This article focuses on research that has uncovered human diseases that stem from such epigenetic deregulation. Disease may be caused by direct changes in epigenetic marks, such as DNA methylation, commonly found to affect imprinted gene regulation. Also described are disease-causing genetic mutations in epigenetic modifiers that either affect chromatin in trans or have a cis effect in altering chromatin configuration.
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Affiliation(s)
- Huda Y Zoghbi
- Howard Hughes Medical Institute, Baylor College of Medicine, and Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
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45
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Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:87-122. [PMID: 27826836 DOI: 10.1007/978-3-319-43624-1_5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is currently one of the hottest topics in basic and biomedical research. Despite tremendous progress in understanding the structures and biochemical properties of the mammalian DNA nucleotide methyltransferases (DNMTs), principles of their regulation in cells have only begun to be uncovered. In mammals, DNA methylation is introduced by the DNMT1, DNMT3A, and DNMT3B enzymes, which are all large multi-domain proteins. These enzymes contain a catalytic C-terminal domain with a characteristic cytosine-C5 methyltransferase fold and an N-terminal part with different domains that interacts with other proteins and chromatin and is involved in targeting and regulation of the DNMTs. The subnuclear localization of the DNMT enzymes plays an important role in their biological function: DNMT1 is localized to replicating DNA via interaction with PCNA and UHRF1. DNMT3 enzymes bind to heterochromatin via protein multimerization and are targeted to chromatin by their ADD and PWWP domains. Recently, a novel regulatory mechanism has been discovered in DNMTs, as latest structural and functional data demonstrated that the catalytic activities of all three enzymes are under tight allosteric control of their N-terminal domains having autoinhibitory functions. This mechanism provides numerous possibilities for the precise regulation of the methyltransferases via controlling the binding and release of autoinhibitory domains by protein factors, noncoding RNAs, or by posttranslational modifications of the DNMTs. In this chapter, we summarize key enzymatic properties of DNMTs, including their specificity and processivity, and afterward we focus on the regulation of their activity and targeting via allosteric processes, protein interactors, and posttranslational modifications.
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Affiliation(s)
- Renata Z Jurkowska
- BioMed X Innovation Center, Im Neuenheimer Feld 583, Heidelberg, D-69120, Germany.
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, Stuttgart, D-70569, Germany.
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46
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Schrader A, Gross T, Thalhammer V, Längst G. Characterization of Dnmt1 Binding and DNA Methylation on Nucleosomes and Nucleosomal Arrays. PLoS One 2015; 10:e0140076. [PMID: 26496704 PMCID: PMC4619679 DOI: 10.1371/journal.pone.0140076] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/21/2015] [Indexed: 12/31/2022] Open
Abstract
The packaging of DNA into nucleosomes and the organisation into higher order structures of chromatin limits the access of sequence specific DNA binding factors to DNA. In cells, DNA methylation is preferentially occuring in the linker region of nucleosomes, suggesting a structural impact of chromatin on DNA methylation. These observations raise the question whether DNA methyltransferases are capable to recognize the nucleosomal substrates and to modify the packaged DNA. Here, we performed a detailed analysis of nucleosome binding and nucleosomal DNA methylation by the maintenance DNA methyltransferase Dnmt1. Our binding studies show that Dnmt1 has a DNA length sensing activity, binding cooperatively to DNA, and requiring a minimal DNA length of 20 bp. Dnmt1 needs linker DNA to bind to nucleosomes and most efficiently recognizes nucleosomes with symmetric DNA linkers. Footprinting experiments reveal that Dnmt1 binds to both DNA linkers exiting the nucleosome core. The binding pattern correlates with the efficient methylation of DNA linkers. However, the enzyme lacks the ability to methylate nucleosomal CpG sites on mononucleosomes and nucleosomal arrays, unless chromatin remodeling enzymes create a dynamic chromatin state. In addition, our results show that Dnmt1 functionally interacts with specific chromatin remodeling enzymes to enable complete methylation of hemi-methylated DNA in chromatin.
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Affiliation(s)
- Anna Schrader
- Institute of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Thomas Gross
- Institute of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Verena Thalhammer
- Institute of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Gernot Längst
- Institute of Biochemistry III, University of Regensburg, Regensburg, Germany
- * E-mail:
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47
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Hamidi T, Singh AK, Chen T. Genetic alterations of DNA methylation machinery in human diseases. Epigenomics 2015; 7:247-65. [PMID: 25942534 DOI: 10.2217/epi.14.80] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA methylation plays a critical role in the regulation of chromatin structure and gene expression and is involved in a variety of biological processes. The levels and patterns of DNA methylation are regulated by both DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) and 'demethylating' proteins, including the ten-eleven translocation (TET) family of dioxygenases (TET1, TET2 and TET3). The effects of DNA methylation on chromatin and gene expression are largely mediated by methylated DNA 'reader' proteins, including MeCP2. Numerous mutations in DNMTs, TETs and MeCP2 have been identified in cancer and developmental disorders, highlighting the importance of the DNA methylation machinery in human development and physiology. In this review, we describe these mutations and discuss how they may lead to disease phenotypes.
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Affiliation(s)
- Tewfik Hamidi
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park - Research Division, 1808 Park Road 1C, P. O. Box 389, Smithville, TX 78957, USA
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48
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Abstract
The life-threatening Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome is a genetically heterogeneous autosomal recessive disorder. Twenty percent of patients cannot be explained by mutations in the known ICF genes DNA methyltransferase 3B or zinc-finger and BTB domain containing 24. Here we report mutations in the cell division cycle associated 7 and the helicase, lymphoid-specific genes in 10 unexplained ICF cases. Our data highlight the genetic heterogeneity of ICF syndrome; however, they provide evidence that all genes act in common or converging pathways leading to the ICF phenotype.
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49
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Abstract
DNA methylation is a chemical modification that occurs predominantly on CG dinucleotides in mammalian genomes. However, recent studies have revealed that non-CG methylation (mCH) is abundant and nonrandomly distributed in the genomes of pluripotent cells and brain cells, and is present at lower levels in many other human cells and tissues. Surprisingly, mCH in pluripotent cells is distinct from that in brain cells in terms of sequence specificity and association with transcription, indicating the existence of different mCH pathways. In addition, several recent studies have begun to reveal the biological significance of mCH in diverse cellular processes. In reprogrammed somatic cells, mCH marks megabase-scale regions that have failed to revert to the pluripotent epigenetic state. In myocytes, promoter mCH accumulation is associated with the transcriptional response to environmental factors. In brain cells, mCH accumulates during the establishment of neural circuits and is associated with Rett syndrome. In this review, we summarize the current understanding of mCH and its possible functional consequences in different biological contexts.
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Affiliation(s)
- Yupeng He
- Bioinformatics Program, University of California, San Diego, La Jolla, California 92093
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50
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Holz-Schietinger C, Reich NO. De novo DNA methyltransferase DNMT3A: Regulation of oligomeric state and mechanism of action in response to pH changes. Biochim Biophys Acta Gen Subj 2015; 1850:1131-9. [PMID: 25681155 DOI: 10.1016/j.bbagen.2015.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/17/2015] [Accepted: 02/04/2015] [Indexed: 01/26/2023]
Abstract
BACKGROUND The oligomeric state of the human DNMT3A is functionally important and cancer cells are known to undergo changes in pH (intracellular). METHODS Light scattering, gel filtration, and fluorescence anisotropy. Also, methylation and processivity assays. CONCLUSIONS Physiologically relevant changes in pH result in changes in DNMT3A oligomer composition which have dramatic consequences on DNMT3A function. GENERAL SIGNIFICANCE The pH changes which occur within cancer cells alter the oligomeric state and function of DNMT3A which could contribute to changes in genomic DNA methylation observed in vivo.
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Affiliation(s)
- Celeste Holz-Schietinger
- Interdepartmental Program in Biomolecular Science & Engineering, University of California, Santa Barbara, CA 93106-9510, United States
| | - Norbert O Reich
- Interdepartmental Program in Biomolecular Science & Engineering, University of California, Santa Barbara, CA 93106-9510, United States; Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93106-9510, United States.
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