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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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Wanner N, Vornweg J, Combes A, Wilson S, Plappert J, Rafflenbeul G, Puelles VG, Rahman RU, Liwinski T, Lindner S, Grahammer F, Kretz O, Wlodek ME, Romano T, Moritz KM, Boerries M, Busch H, Bonn S, Little MH, Bechtel-Walz W, Huber TB. DNA Methyltransferase 1 Controls Nephron Progenitor Cell Renewal and Differentiation. J Am Soc Nephrol 2019; 30:63-78. [PMID: 30518531 PMCID: PMC6317605 DOI: 10.1681/asn.2018070736] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/22/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Nephron number is a major determinant of long-term renal function and cardiovascular risk. Observational studies suggest that maternal nutritional and metabolic factors during gestation contribute to the high variability of nephron endowment. However, the underlying molecular mechanisms have been unclear. METHODS We used mouse models, including DNA methyltransferase (Dnmt1, Dnmt3a, and Dnmt3b) knockout mice, optical projection tomography, three-dimensional reconstructions of the nephrogenic niche, and transcriptome and DNA methylation analysis to characterize the role of DNA methylation for kidney development. RESULTS We demonstrate that DNA hypomethylation is a key feature of nutritional kidney growth restriction in vitro and in vivo, and that DNA methyltransferases Dnmt1 and Dnmt3a are highly enriched in the nephrogenic zone of the developing kidneys. Deletion of Dnmt1 in nephron progenitor cells (in contrast to deletion of Dnmt3a or Dnm3b) mimics nutritional models of kidney growth restriction and results in a substantial reduction of nephron number as well as renal hypoplasia at birth. In Dnmt1-deficient mice, optical projection tomography and three-dimensional reconstructions uncovered a significant reduction of stem cell niches and progenitor cells. RNA sequencing analysis revealed that global DNA hypomethylation interferes in the progenitor cell regulatory network, leading to downregulation of genes crucial for initiation of nephrogenesis, Wt1 and its target Wnt4. Derepression of germline genes, protocadherins, Rhox genes, and endogenous retroviral elements resulted in the upregulation of IFN targets and inhibitors of cell cycle progression. CONCLUSIONS These findings establish DNA methylation as a key regulatory event of prenatal renal programming, which possibly represents a fundamental link between maternal nutritional factors during gestation and reduced nephron number.
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Affiliation(s)
| | - Julia Vornweg
- Faculty of Medicine, Department of Medicine IV, Medical Center-University of Freiburg, and
- Faculty of Biology
| | - Alexander Combes
- Anatomy and Neuroscience
- Cell Biology Theme, Murdoch Children's Research Institute, Melbourne, Australia
| | | | - Julia Plappert
- Faculty of Medicine, Department of Medicine IV, Medical Center-University of Freiburg, and
| | - Gesa Rafflenbeul
- Faculty of Medicine, Department of Medicine IV, Medical Center-University of Freiburg, and
| | | | - Raza-Ur Rahman
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, and
| | - Timur Liwinski
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, and
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Saskia Lindner
- Faculty of Medicine, Department of Medicine IV, Medical Center-University of Freiburg, and
| | | | - Oliver Kretz
- III. Department of Medicine
- Department of Neuroanatomy, University of Freiburg, Freiburg, Germany
| | | | - Tania Romano
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Karen M Moritz
- Child Health Research Centre and School of Biomedical Sciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Melanie Boerries
- German Cancer Consortium, Heidelberg, Germany
- German Cancer Research Center, Heidelberg, Germany
- Institute of Molecular Medicine and Cell Research
| | - Hauke Busch
- Institute of Molecular Medicine and Cell Research
- Lübeck Institute of Experimental Dermatology, Lübeck, Germany; and
| | - Stefan Bonn
- Institute of Molecular Medicine and Cell Research
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Melissa H Little
- Cell Biology Theme, Murdoch Children's Research Institute, Melbourne, Australia
- Pediatrics, University of Melbourne, Melbourne, Australia
| | - Wibke Bechtel-Walz
- Faculty of Medicine, Department of Medicine IV, Medical Center-University of Freiburg, and
| | - Tobias B Huber
- III. Department of Medicine,
- Faculty of Medicine, Department of Medicine IV, Medical Center-University of Freiburg, and
- Centre for Biological Signalling Studies (BIOSS) and Center for Biological Systems Analysis (ZBSA), and
- Freiburg Institute for Advanced Studies, Albert Ludwig University of Freiburg, Freiburg, Germany; Departments of
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Torroglosa A, Villalba-Benito L, Fernández RM, Moya-Jiménez MJ, Antiñolo G, Borrego S. Dnmt3b knock-down in enteric precursors reveals a possible mechanism by which this de novo methyltransferase is involved in the enteric nervous system development and the onset of Hirschsprung disease. Oncotarget 2017; 8:106443-106453. [PMID: 29290961 PMCID: PMC5739746 DOI: 10.18632/oncotarget.22473] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/27/2017] [Indexed: 12/30/2022] Open
Abstract
Hirschsprung disease (HSCR, OMIM 142623) is a pathology that shows a lack of enteric ganglia along of the distal gastrointestinal tract. This aganglionosis is attributed to an abnormal proliferation, migration, differentiation and/or survival of enteric precursor cells (EPCs) derived from neural crest cells (NCCs) during the enteric nervous system (ENS) embryogenesis. DNMT3b de novo methyltransferase is associated with NCCs development and has been shown to be implicated in ENS formation as well as in HSCR. In this study we have aimed to elucidate the specific mechanism underlying the DNMT3b role in such processes. We have performed the knockdown of Dnmt3b expression (Dnmt3b-KD) in enteric precursor cells (EPCs) to clarify its role on these cells in vitro. Moreover, we have analyzed several signaling pathways to determine the mechanisms responsible for the effect caused by Dnmt3b-KD in EPCs. Our results seem to support that Dnmt3b-KD promotes an increase EPCs proliferation that may be mediated by P53 and P21 activity, since both proteins were observed to be down-regulated in our Dnmt3b-KD cultures. Moreover, we observed a down-regulation of P53 and P21 in HSCR patients. These results lead us to propose that DNMT3b could be involved in HSCR through P53 and P21 activity.
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Affiliation(s)
- Ana Torroglosa
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío, CSIC, University of Seville, Seville 41013, Spain.,Center for Biomedical Network Research on Rare Diseases, Seville 41013, Spain
| | - Leticia Villalba-Benito
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío, CSIC, University of Seville, Seville 41013, Spain.,Center for Biomedical Network Research on Rare Diseases, Seville 41013, Spain
| | - Raquel María Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío, CSIC, University of Seville, Seville 41013, Spain.,Center for Biomedical Network Research on Rare Diseases, Seville 41013, Spain
| | | | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío, CSIC, University of Seville, Seville 41013, Spain.,Center for Biomedical Network Research on Rare Diseases, Seville 41013, Spain
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío, CSIC, University of Seville, Seville 41013, Spain.,Center for Biomedical Network Research on Rare Diseases, Seville 41013, Spain
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Elhamamsy AR. DNA methylation dynamics in plants and mammals: overview of regulation and dysregulation. Cell Biochem Funct 2016; 34:289-98. [PMID: 27003927 DOI: 10.1002/cbf.3183] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 02/18/2016] [Accepted: 02/29/2016] [Indexed: 12/22/2022]
Abstract
DNA methylation is a major epigenetic marking mechanism regulating various biological functions in mammals and plant. The crucial role of DNA methylation has been observed in cellular differentiation, embryogenesis, genomic imprinting and X-chromosome inactivation. Furthermore, DNA methylation takes part in disease susceptibility, responses to environmental stimuli and the biodiversity of natural populations. In plant, different types of environmental stress have demonstrated the ability to alter the archetype of DNA methylation through the genome, change gene expression and confer a mechanism of adaptation. DNA methylation dynamics are regulated by three processes de novo DNA methylation, methylation maintenance and DNA demethylation. These processes have their similarities and differences between mammals and plants. Furthermore, the dysregulation of DNA methylation dynamics represents one of the primary molecular mechanisms of developing diseases in mammals. This review discusses the regulation and dysregulation of DNA methylation in plants and mammals. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Amr Rafat Elhamamsy
- Clinical Pharmacy Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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Abstract
Epigenetic regulation is facilitated by a battery of proteins that act as 'writers' or 'erasers' to add or remove biochemical modifications to DNA and histone proteins. DNA modifications, histone modifications and long noncoding RNAs function interdependently through reciprocal crosstalk. This review will focus on DNA methylation and DNA methyltransferases with emphasis on how biological and biochemical factors such as histone modifications and noncoding RNAs might play a role in modulating DNA methylation. Other physiological and biochemical factors that can modify DNA methylation marks will also be discussed including chemical exposures and inflammation.
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Affiliation(s)
- Raymond Lo
- Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
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