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Meng WY, Wang ZX, Zhang Y, Hou Y, Xue JH. Epigenetic marks or not? The discovery of novel DNA modifications in eukaryotes. J Biol Chem 2024; 300:106791. [PMID: 38403247 PMCID: PMC11065753 DOI: 10.1016/j.jbc.2024.106791] [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: 10/29/2023] [Revised: 01/24/2024] [Accepted: 02/04/2024] [Indexed: 02/27/2024] Open
Abstract
DNA modifications add another layer of complexity to the eukaryotic genome to regulate gene expression, playing critical roles as epigenetic marks. In eukaryotes, the study of DNA epigenetic modifications has been confined to 5mC and its derivatives for decades. However, rapid developing approaches have witnessed the expansion of DNA modification reservoirs during the past several years, including the identification of 6mA, 5gmC, 4mC, and 4acC in diverse organisms. However, whether these DNA modifications function as epigenetic marks requires careful consideration. In this review, we try to present a panorama of all the DNA epigenetic modifications in eukaryotes, emphasizing recent breakthroughs in the identification of novel DNA modifications. The characterization of their roles in transcriptional regulation as potential epigenetic marks is summarized. More importantly, the pathways for generating or eliminating these DNA modifications, as well as the proteins involved are comprehensively dissected. Furthermore, we briefly discuss the potential challenges and perspectives, which should be taken into account while investigating novel DNA modifications.
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Affiliation(s)
- Wei-Ying Meng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zi-Xin Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yunfang Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yujun Hou
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Jian-Huang Xue
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
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2
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Li Q, Lu J, Yin X, Chang Y, Wang C, Yan M, Feng L, Cheng Y, Gao Y, Xu B, Zhang Y, Wang Y, Cui G, Xu L, Sun Y, Zeng R, Li Y, Jing N, Xu GL, Wu L, Tang F, Li J. Base editing-mediated one-step inactivation of the Dnmt gene family reveals critical roles of DNA methylation during mouse gastrulation. Nat Commun 2023; 14:2922. [PMID: 37217538 DOI: 10.1038/s41467-023-38528-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
During embryo development, DNA methylation is established by DNMT3A/3B and subsequently maintained by DNMT1. While much research has been done in this field, the functional significance of DNA methylation in embryogenesis remains unknown. Here, we establish a system of simultaneous inactivation of multiple endogenous genes in zygotes through screening for base editors that can efficiently introduce a stop codon. Embryos with mutations in Dnmts and/or Tets can be generated in one step with IMGZ. Dnmt-null embryos display gastrulation failure at E7.5. Interestingly, although DNA methylation is absent, gastrulation-related pathways are down-regulated in Dnmt-null embryos. Moreover, DNMT1, DNMT3A, and DNMT3B are critical for gastrulation, and their functions are independent of TET proteins. Hypermethylation can be sustained by either DNMT1 or DNMT3A/3B at some promoters, which are related to the suppression of miRNAs. The introduction of a single mutant allele of six miRNAs and paternal IG-DMR partially restores primitive streak elongation in Dnmt-null embryos. Thus, our results unveil an epigenetic correlation between promoter methylation and suppression of miRNA expression for gastrulation and demonstrate that IMGZ can accelerate deciphering the functions of multiple genes in vivo.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jiansen Lu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Xidi Yin
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yunjian Chang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Chao Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Meng Yan
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Li Feng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yanbo Cheng
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Yun Gao
- School of Life Sciences, Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Beiying Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yao Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yingyi Wang
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Guizhong Cui
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Luang Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Rong Zeng
- CAS Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yixue Li
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
| | - Ligang Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
| | - Fuchou Tang
- School of Life Sciences, Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China.
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China.
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3
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Xiang J, Zhang J, Liao L, Jiang B, Yuan R, Xiang Y. Label-free and sensitive fluorescent sensing of ten-eleven translocation enzyme via cascaded recycling signal amplifications. Anal Chim Acta 2023; 1251:341025. [PMID: 36925297 DOI: 10.1016/j.aca.2023.341025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/14/2023] [Accepted: 02/25/2023] [Indexed: 03/03/2023]
Abstract
The sensitive detection of ten-eleven translocation (TET) dioxygenase is of significance for understanding the demethylation mechanism of 5-methylocytosine (5mC), which is responsible for a wide range of biological functions that can affect gene expression in eukaryotic species. Here, a non-label and sensitive fluorescence biosensing method for TET assay using TET1 as the model target molecule is established on the basis of target-triggered Mg2+-dependent DNAzyme and catalytic hairpin assembly (CHA)-mediated multiple signal amplification cascades. 5mC sites in the hairpin DNA probe are first oxidized by TET1 into 5-carboxycytosine, which are further reduced by pyridine borane into dihydrouracil, followed by its recognition and cleavage by the USER enzyme to liberate active DNAzyme and G-quadruplex sequences from the probe. The DNAzyme further cyclically cleaves the substrate hairpins to trigger subsequent CHA reaction and DNAzyme cleavage cycles for yielding many G-quadruplex strands. Thioflavin T dye then intercalates into G-quadruplexes to cause a magnificent increase of fluorescence for high sensitivity assay of TET1 with 47 fM detection limit. And, application of this method for TET1 monitoring in diluted serum has also been confirmed.
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Affiliation(s)
- Jie Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Junyi Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Lei Liao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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4
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Ray S, Abugable AA, Parker J, Liversidge K, Palminha NM, Liao C, Acosta-Martin AE, Souza CDS, Jurga M, Sudbery I, El-Khamisy SF. A mechanism for oxidative damage repair at gene regulatory elements. Nature 2022; 609:1038-1047. [PMID: 36171374 DOI: 10.1038/s41586-022-05217-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/09/2022] [Indexed: 11/09/2022]
Abstract
Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate-early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.
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Affiliation(s)
- Swagat Ray
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK.,School of Life and Environmental Sciences, Department of Life Sciences, University of Lincoln, Lincoln, UK
| | - Arwa A Abugable
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Jacob Parker
- School of Biosciences, University of Sheffield, Sheffield, UK.,Center for Advanced Parkinson Research, Harvard Medical School, Boston, MA, USA
| | | | - Nelma M Palminha
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Chunyan Liao
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Adelina E Acosta-Martin
- biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield, UK
| | - Cleide D S Souza
- School of Biosciences, University of Sheffield, Sheffield, UK.,Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Mateusz Jurga
- Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
| | - Ian Sudbery
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Sherif F El-Khamisy
- School of Biosciences, University of Sheffield, Sheffield, UK. .,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK. .,Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK.
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5
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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6
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Yildiz CB, Zimmer-Bensch G. Role of DNMTs in the Brain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:363-394. [DOI: 10.1007/978-3-031-11454-0_15] [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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7
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Significance of base excision repair to human health. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:163-193. [PMID: 34507783 DOI: 10.1016/bs.ircmb.2021.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oxidative and alkylating DNA damage occurs under normal physiological conditions and exogenous exposure to DNA damaging agents. To counteract DNA base damage, cells have evolved several defense mechanisms that act at different levels to prevent or repair DNA base damage. Cells combat genomic lesions like these including base modifications, abasic sites, as well as single-strand breaks, via the base excision repair (BER) pathway. In general, the core BER process involves well-coordinated five-step reactions to correct DNA base damage. In this review, we will uncover the current understanding of BER mechanisms to maintain genomic stability and the biological consequences of its failure due to repair gene mutations. The malfunction of BER can often lead to BER intermediate accumulation, which is genotoxic and can lead to different types of human disease. Finally, we will address the use of BER intermediates for targeted cancer therapy.
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8
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Kreppel A, Ochsenfeld C. The Enzymatic Decarboxylation Mechanism of 5-Carboxy Uracil: A Comprehensive Quantum Chemical Study. J Chem Theory Comput 2021; 17:96-104. [PMID: 33356236 DOI: 10.1021/acs.jctc.0c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic regulation of DNA methylation is an important process for the control of gene expression in mammals. It is believed that in the demethylation pathway of 5-methyl cytosine, the intermediate 5-carboxy cytosine (5caC) can be actively decarboxylated alongside the substitution in the base excision repair. For the active decarboxylation of 5caC, a decarboxylase has not been identified so far. Due to the similar chemistry of the decarboxylation of 5-carboxy uracil (5caU) to uracil (U) in the pyrimidine salvage pathway catalyzed by the iso-orotate decarboxylase (IDCase), the study of this reaction might give valuable insights into the active 5caC decarboxylation process. In this work, we employ quantum chemical and molecular mechanic calculations and find that the catalytic mechanism of IDCase proceeds via a direct decarboxylation mechanism. Detailed investigations on the reaction coordinate reveal that it is a one-step mechanism with concerted proton transfer and C-C bond opening.
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Affiliation(s)
- Andrea Kreppel
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany.,Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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9
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Chen X, Cheng Y, Wang Y, Tang J, Wang F, Chen Z. Fluorescence assay based on the thioflavin T-induced conformation switch of G-quadruplexes for TET1 detection. Analyst 2021; 146:2126-2130. [DOI: 10.1039/d1an00109d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A simple and label-free fluorescence method is developed for the highly sensitive detection of TET1 based on ThT/G-quadruplexes in combination with the specific design of oligonucleotides.
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Affiliation(s)
- Xue Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Ying Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Yafen Wang
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biochemical Polymers of Ministry of Education. The Institute for Advanced Studies
- Hubei Province Key Laboratory of Allergy and Immunology
- Wuhan University
- Wuhan
| | - Jing Tang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Fang Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Zilin Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
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10
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Han M, Li J, Cao Y, Huang Y, Li W, Zhu H, Zhao Q, Han JDJ, Wu Q, Li J, Feng J, Wong J. A role for LSH in facilitating DNA methylation by DNMT1 through enhancing UHRF1 chromatin association. Nucleic Acids Res 2020; 48:12116-12134. [PMID: 33170271 PMCID: PMC7708066 DOI: 10.1093/nar/gkaa1003] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 12/25/2022] Open
Abstract
LSH, a SNF2 family DNA helicase, is a key regulator of DNA methylation in mammals. How LSH facilitates DNA methylation is not well defined. While previous studies with mouse embryonic stem cells (mESc) and fibroblasts (MEFs) derived from Lsh knockout mice have revealed a role of Lsh in de novo DNA methylation by Dnmt3a/3b, here we report that LSH contributes to DNA methylation in various cell lines primarily by promoting DNA methylation by DNMT1. We show that loss of LSH has a much bigger effect in DNA methylation than loss of DNMT3A and DNMT3B. Mechanistically, we demonstrate that LSH interacts with UHRF1 but not DNMT1 and facilitates UHRF1 chromatin association and UHRF1-catalyzed histone H3 ubiquitination in an ATPase activity-dependent manner, which in turn promotes DNMT1 recruitment to replication fork and DNA methylation. Notably, UHRF1 also enhances LSH association with the replication fork. Thus, our study identifies LSH as an essential factor for DNA methylation by DNMT1 and provides novel insight into how a feed-forward loop between LSH and UHRF1 facilitates DNMT1-mediated maintenance of DNA methylation in chromatin.
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Affiliation(s)
- Mengmeng Han
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jialun Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai 201499, China
| | - Yaqiang Cao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Room122, 320 Yue Yang Road, Shanghai 200031, China
| | - Yuanyong Huang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Haijun Zhu
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai 200032, China
| | - Qian Zhao
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jing-Dong Jackie Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Room122, 320 Yue Yang Road, Shanghai 200031, China
| | - Qihan Wu
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai 200032, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jing Feng
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai 201499, China
- Department of Laboratory Medicine & Central Laboratory, Southern Medical University Affiliated Fengxian Hospital, Shanghai 201499, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai 201499, China
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11
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Navarro-Martín L, Martyniuk CJ, Mennigen JA. Comparative epigenetics in animal physiology: An emerging frontier. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100745. [PMID: 33126028 DOI: 10.1016/j.cbd.2020.100745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 12/19/2022]
Abstract
The unprecedented access to annotated genomes now facilitates the investigation of the molecular basis of epigenetic phenomena in phenotypically diverse animals. In this critical review, we describe the roles of molecular epigenetic mechanisms in regulating mitotically and meiotically stable spatiotemporal gene expression, phenomena that provide the molecular foundation for the intra-, inter-, and trans-generational emergence of physiological phenotypes. By focusing principally on emerging comparative epigenetic roles of DNA-level and transcriptome-level epigenetic mark dynamics in the emergence of phenotypes, we highlight the relationship between evolutionary conservation and innovation of specific epigenetic pathways, and their interplay as a priority for future study. This comparative approach is expected to significantly advance our understanding of epigenetic phenomena, as animals show a diverse array of strategies to epigenetically modify physiological responses. Additionally, we review recent technological advances in the field of molecular epigenetics (single-cell epigenomics and transcriptomics and editing of epigenetic marks) in order to (1) investigate environmental and endogenous factor dependent epigenetic mark dynamics in an integrative manner; (2) functionally test the contribution of specific epigenetic marks for animal phenotypes via genome and transcript-editing tools. Finally, we describe advantages and limitations of emerging animal models, which under the Krogh principle, may be particularly useful in the advancement of comparative epigenomics and its potential translational applications in animal science, ecotoxicology, ecophysiology, climate change science and wild-life conservation, as well as organismal health.
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Affiliation(s)
- Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON K1N6N5, Canada
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12
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Li J, Wang R, Jin J, Han M, Chen Z, Gao Y, Hu X, Zhu H, Gao H, Lu K, Shao Y, Lyu C, Lai W, Li P, Hu G, Li J, Li D, Wang H, Wu Q, Wong J. USP7 negatively controls global DNA methylation by attenuating ubiquitinated histone-dependent DNMT1 recruitment. Cell Discov 2020; 6:58. [PMID: 32884836 PMCID: PMC7445300 DOI: 10.1038/s41421-020-00188-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/27/2020] [Indexed: 11/08/2022] Open
Abstract
Previous studies have implicated an essential role for UHRF1-mediated histone H3 ubiquitination in recruiting DNMT1 to replication sites for DNA maintenance methylation during S phase of the cell cycle. However, the regulatory mechanism on UHRF1-mediated histone ubiquitination is not clear. Here we present evidence that UHRF1 and USP7 oppositely control ubiquitination of histones H3 and H2B in S phase of the cell cycle and that DNMT1 binds both ubiquitinated H3 and H2B. USP7 knockout markedly increased the levels of ubiquitinated H3 and H2B in S phase, the association of DNMT1 with replication sites and importantly, led to a progressive increase of global DNA methylation shown with increased cell passages. Using DNMT3A/DNMT3B/USP7 triple knockout cells and various DNA methylation analyses, we demonstrated that USP7 knockout led to an overall elevation of DNA methylation levels. Mechanistic study demonstrated that USP7 suppresses DNMT1 recruitment and DNA methylation through its deubiquitinase activity and the interaction with DNMT1. Altogether our study provides evidence that USP7 is a negative regulator of global DNA methylation and that USP7 protects the genome from excessive DNA methylation by attenuating histone ubiquitination-dependent DNMT1 recruitment.
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Affiliation(s)
- Jialun Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai, 201499 China
| | - Ruiping Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Jianyu Jin
- College of Education, Wenzhou University, Wenzhou, Zhejiang 325035 China
| | - Mengmeng Han
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Zhaosu Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Yingying Gao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Xueli Hu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Haijun Zhu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Huifang Gao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Kongbin Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Yanjiao Shao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Cong Lyu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085 China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085 China
| | - Pishun Li
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, Durham, NC 27709 USA
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, Durham, NC 27709 USA
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085 China
| | - Qihan Wu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, 200032 China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai, 201499 China
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13
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Epigenomic Remodeling in Huntington's Disease-Master or Servant? EPIGENOMES 2020; 4:epigenomes4030015. [PMID: 34968288 PMCID: PMC8594700 DOI: 10.3390/epigenomes4030015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/03/2022] Open
Abstract
In light of our aging population, neurodegenerative disorders are becoming a tremendous challenge, that modern societies have to face. They represent incurable, progressive conditions with diverse and complex pathological features, followed by catastrophic occurrences of massive neuronal loss at the later stages of the diseases. Some of these disorders, like Huntington’s disease (HD), rely on defined genetic factors. HD, as an incurable, fatal hereditary neurodegenerative disorder characterized by its mid-life onset, is caused by the expansion of CAG trinucleotide repeats coding for glutamine (Q) in exon 1 of the huntingtin gene. Apart from the genetic defect, environmental factors are thought to influence the risk, onset and progression of HD. As epigenetic mechanisms are known to readily respond to environmental stimuli, they are proposed to play a key role in HD pathogenesis. Indeed, dynamic epigenomic remodeling is observed in HD patients and in brains of HD animal models. Epigenetic signatures, such as DNA methylation, histone variants and modifications, are known to influence gene expression and to orchestrate various aspects of neuronal physiology. Hence, deciphering their implication in HD pathogenesis might open up new paths for novel therapeutic concepts, which are discussed in this review.
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Zhang H, Gao Q, Tan S, You J, Lyu C, Zhang Y, Han M, Chen Z, Li J, Wang H, Liao L, Qin J, Li J, Wong J. SET8 prevents excessive DNA methylation by methylation-mediated degradation of UHRF1 and DNMT1. Nucleic Acids Res 2019; 47:9053-9068. [PMID: 31400111 PMCID: PMC6753495 DOI: 10.1093/nar/gkz626] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/08/2019] [Accepted: 08/09/2019] [Indexed: 11/14/2022] Open
Abstract
Faithful inheritance of DNA methylation across cell division requires DNMT1 and its accessory factor UHRF1. However, how this axis is regulated to ensure DNA methylation homeostasis remains poorly understood. Here we show that SET8, a cell-cycle-regulated protein methyltransferase, controls protein stability of both UHRF1 and DNMT1 through methylation-mediated, ubiquitin-dependent degradation and consequently prevents excessive DNA methylation. SET8 methylates UHRF1 at lysine 385 and this modification leads to ubiquitination and degradation of UHRF1. In contrast, LSD1 stabilizes both UHRF1 and DNMT1 by demethylation. Importantly, SET8 and LSD1 oppositely regulate global DNA methylation and do so most likely through regulating the level of UHRF1 than DNMT1. Finally, we show that UHRF1 downregulation in G2/M by SET8 has a role in suppressing DNMT1-mediated methylation on post-replicated DNA. Altogether, our study reveals a novel role of SET8 in promoting DNA methylation homeostasis and identifies UHRF1 as the hub for tuning DNA methylation through dynamic protein methylation.
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Affiliation(s)
- Huifang Zhang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Qinqin Gao
- Institute for Fetology, First Hospital of Soochow University, Suzhou, China
| | - Shuo Tan
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jia You
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Cong Lyu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yunpeng Zhang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Mengmeng Han
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Zhaosu Chen
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jialun Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing 102206, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
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15
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Chen B, Dai Q, Zhang Q, Yan P, Wang A, Qu L, Jin Y, Zhang D. The relationship among occupational irradiation, DNA methylation status, and oxidative damage in interventional physicians. Medicine (Baltimore) 2019; 98:e17373. [PMID: 31574886 PMCID: PMC6775365 DOI: 10.1097/md.0000000000017373] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Ionizing radiation can induce deoxyribonucleic acid (DNA) methylation pattern change, and ionizing radiation-induced oxidative damage may also affect DNA methylation status. However, the influence of low-dose ionizing radiation, such as occupational radiation exposure, on DNA methylation is still controversial.By investigating the relationship between occupational radiation exposure and DNA methylation changes, we evaluated whether radiation-induced oxidative damage was related to DNA methylation alterations and then determined the relationship among occupational radiation level, DNA methylation status, and oxidative damage in interventional physicians.The study population included 117 interventional physicians and 117 controls. We measured global methylation levels of peripheral blood leukocyte DNA and expression level of DNA methyltransferase (Dnmts) and homocysteine (Hcy) in serum to assess the DNA methylation status of the body. We measured 8-hydroxy-2'-deoxyguanosine (8-OHDG) and 4-hydroxynonenal (4-HNE) levels as indices of oxidative damage. Relevance analysis between multiple indices can reflect the relationship among occupational radiation exposure, DNA methylation changes, and oxidative damage in interventional physicians.The expression levels of Dnmts, 4-HNE, and 8-OHDG in interventional physicians were higher than those in controls, while there was no statistical difference in total DNA methylation rate and expression of Hcy between interventional physicians and controls. Total cumulative personal dose equivalent in interventional physicians was positively correlated with the expression levels of Dnmts, 8-OHDG, and 4-HNE. The expression levels of 8-OHDG in interventional physicians were negatively correlated with global DNA methylation levels and positively correlated with the expression levels of Hcy.Occupational radiation exposure of interventional physicians has a certain effect on the expression of related enzymes in the process of DNA methylation, while ionizing radiation-induced oxidative damage also has a certain effect on DNA methylation. However, there was no evidence that dose burden of occupational exposure was associated to changes of DNA methylation status of interventional physicians, since it is rather unclear which differences are observed among the effects produced by radiation exposure and oxidative damage.
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Affiliation(s)
- Bin Chen
- Department of Radiology, HwaMei Hospital, University of Chinese Academy of Sciences
| | - Qi Dai
- Department of Radiology, HwaMei Hospital, University of Chinese Academy of Sciences
| | - Qun Zhang
- Department of Environmental and Occupational Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, Zhejiang, China
| | - Peng Yan
- Department of Environmental and Occupational Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, Zhejiang, China
| | - Aihong Wang
- Department of Environmental and Occupational Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, Zhejiang, China
| | - Linyan Qu
- Department of Environmental and Occupational Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, Zhejiang, China
| | - Yinhua Jin
- Department of Radiology, HwaMei Hospital, University of Chinese Academy of Sciences
| | - Dandan Zhang
- Department of Environmental and Occupational Health, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, Zhejiang, China
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16
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Lei J, Nie Q, Chen DB. A single-cell epigenetic model for paternal psychological stress-induced transgenerational reprogramming in offspring. Biol Reprod 2019; 98:846-855. [PMID: 29506130 DOI: 10.1093/biolre/ioy050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/25/2018] [Indexed: 12/16/2022] Open
Abstract
Experimental evidence shows that parental psychological stress affects the long-term health of offspring in an inheritable fashion. Although epigenetic mechanisms, including DNA methylation, miRNA, and histone modifications, are involved in transgenerational programming, the underlining mechanisms of transgenerational inheritance remain unsolved. Here, we present a single-cell-based computational model for transgenerational inheritance for investigating the long-term dynamics of phenotype changes in response to parental stress. The model is based on a recent study that has identified the imprinted sperm gene Sfmbt2 as a key target, and incorporates crosstalks among drastically different time scales in mammalian development, including DNA methylation, transcription, cell division, and population dynamics. Computational analysis of the model suggests a positive feedback to DNA methylation in the promoter region of sperm Sfmbt2 gene that provides a possible mechanism to mediate the parental psychological stress reprogramming in offspring. This approach provides a modeling framework for the understanding of the roles that epigenetics play in transgenerational inheritance.
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Affiliation(s)
- Jinzhi Lei
- Zhou Pei-Yuan Center for Applied Mathematics, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Qing Nie
- Department of Mathematics, Department of Developmental and Cell Biology, Center for Mathematical and Computational Biology, University of California, Irvine, Irvine, California, USA
| | - Dong-Bao Chen
- Department of Obstetrics and Gynecology, University of California Irvine, Irvine, California, USA
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17
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Ishihara T, Hickford D, Shaw G, Pask AJ, Renfree MB. DNA methylation dynamics in the germline of the marsupial tammar wallaby, Macropus eugenii. DNA Res 2019; 26:85-94. [PMID: 30535324 PMCID: PMC6379045 DOI: 10.1093/dnares/dsy040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/29/2018] [Indexed: 01/25/2023] Open
Abstract
Parent specific-DNA methylation is the genomic imprint that induces mono-allelic gene expression dependent on parental origin. Resetting of DNA methylation in the germ line is mediated by a genome-wide re-methylation following demethylation known as epigenetic reprogramming. Most of our understanding of epigenetic reprogramming in germ cells is based on studies in mice, but little is known about this in marsupials. We examined genome-wide changes in DNA methylation levels by measuring 5-methylcytosine expression, and mRNA expression and protein localization of the key enzyme DNA methyltransferase 3 L (DNMT3L) during germ cell development of the marsupial tammar wallaby, Macropus eugenii. Our data clearly showed that the relative timing of genome-wide changes in DNA methylation was conserved between the tammar and mouse, but in the tammar it all occurred post-natally. In the female tammar, genome-wide demethylation occurred in two phases, I and II, suggesting that there is an unidentified demethylation mechanism in this species. Although the localization pattern of DNMT3L in male germ cells differed, the expression patterns of DNMT3L were broadly conserved between tammar, mouse and human. Thus, the basic mechanisms of DNA methylation-reprogramming must have been established before the marsupial-eutherian mammal divergence over 160 Mya.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Danielle Hickford
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Andrew J Pask
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
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Chatterjee B, Lin MH, Chen CC, Peng KL, Wu MS, Tseng MC, Chen YJ, Shen CKJ. DNA Demethylation by DNMT3A and DNMT3B in vitro and of Methylated Episomal DNA in Transiently Transfected Cells. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:1048-1061. [PMID: 30300721 DOI: 10.1016/j.bbagrm.2018.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/03/2018] [Accepted: 09/25/2018] [Indexed: 12/24/2022]
Abstract
The DNA methylation program in vertebrates is an essential part of the epigenetic regulatory cascade of development, cell differentiation, and progression of diseases including cancer. While the DNA methyltransferases (DNMTs) are responsible for the in vivo conversion of cytosine (C) to methylated cytosine (5mC), demethylation of 5mC on cellular DNA could be accomplished by the combined action of the ten-eleven translocation (TET) enzymes and DNA repair. Surprisingly, the mammalian DNMTs also possess active DNA demethylation activity in vitro in a Ca2+- and redox conditions-dependent manner, although little is known about its molecular mechanisms and occurrence in a cellular context. In this study, we have used LC-MS/MS to track down the fate of the methyl group removed from 5mC on DNA by mouse DNMT3B in vitro and found that it becomes covalently linked to the DNA methylation catalytic cysteine of the enzyme. We also show that Ca2+ homeostasis-dependent but TET1/TET2/TET3/TDG-independent demethylation of methylated episomal DNA by mouse DNMT3A or DNMT3B can occur in transfected human HEK 293 and mouse embryonic stem (ES) cells. Based on these results, we present a tentative working model of Ca2+ and redox conditions-dependent active DNA demethylation by DNMTs. Our study substantiates the potential roles of the vertebrate DNMTs as double-edged swords in DNA methylation-demethylation during Ca2+-dependent physiological processes.
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Affiliation(s)
| | - Miao-Hsia Lin
- Institute of Chemistry, Academia Sinica, Taipei City 115, Taiwan
| | - Chun-Chang Chen
- Institute of Molecular Biology, Academia Sinica, Taipei City 115, Taiwan
| | - Kai-Lin Peng
- Genomics Research Center, Academia Sinica, Taipei City 115, Taiwan
| | - Mu-Sheng Wu
- Genomics Research Center, Academia Sinica, Taipei City 115, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei City 112, Taiwan
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Taipei City 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei City 115, Taiwan.
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Taipei City 115, Taiwan.
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Ng GYQ, Yun-An L, Sobey CG, Dheen T, Fann DYW, Arumugam TV. Epigenetic regulation of inflammation in stroke. Ther Adv Neurol Disord 2018; 11:1756286418771815. [PMID: 29774056 PMCID: PMC5949939 DOI: 10.1177/1756286418771815] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 03/29/2018] [Indexed: 12/30/2022] Open
Abstract
Despite extensive research, treatments for clinical stroke are still limited only to the administration of tissue plasminogen activator and the recent introduction of mechanical thrombectomy, which can be used in only a limited proportion of patients due to time constraints. A plethora of inflammatory events occur during stroke, arising in part due to the body's immune response to brain injury. Neuroinflammation contributes significantly to neuronal cell death and the development of functional impairment and death in stroke patients. Therefore, elucidating the molecular and cellular mechanisms underlying inflammatory damage following stroke injury will be essential for the development of useful therapies. Research findings increasingly point to the likelihood that epigenetic mechanisms play a role in the pathophysiology of stroke. Epigenetics involves the differential regulation of gene expression, including those involved in brain inflammation and remodelling after stroke. Hence, it is conceivable that epigenetic mechanisms may contribute to differential interindividual vulnerability and injury responses to cerebral ischaemia. In this review, we summarize recent findings on the emerging role of epigenetics in the regulation of neuroinflammation in stroke. We also discuss potential epigenetic targets that may be assessed for the development of stroke therapies.
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Affiliation(s)
- Gavin Yong-Quan Ng
- Department of Physiology, Yong Loo Lin School Medicine, National University of Singapore, Singapore
| | - Lim Yun-An
- Department of Physiology, Yong Loo Lin School Medicine, National University of Singapore, Singapore
| | - Christopher G. Sobey
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, Australia
| | - Thameem Dheen
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David Yang-Wei Fann
- Department of Physiology, Yong Loo Lin School Medicine, National University of Singapore, Singapore
| | - Thiruma V. Arumugam
- Department of Physiology, Yong Loo Lin School Medicine, National University of Singapore, Medical Drive, MD9, Singapore School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, Singapore
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20
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Epigenetics in teleost fish: From molecular mechanisms to physiological phenotypes. Comp Biochem Physiol B Biochem Mol Biol 2018; 224:210-244. [PMID: 29369794 DOI: 10.1016/j.cbpb.2018.01.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 02/07/2023]
Abstract
While the field of epigenetics is increasingly recognized to contribute to the emergence of phenotypes in mammalian research models across different developmental and generational timescales, the comparative biology of epigenetics in the large and physiologically diverse vertebrate infraclass of teleost fish remains comparatively understudied. The cypriniform zebrafish and the salmoniform rainbow trout and Atlantic salmon represent two especially important teleost orders, because they offer the unique possibility to comparatively investigate the role of epigenetic regulation in 3R and 4R duplicated genomes. In addition to their sequenced genomes, these teleost species are well-characterized model species for development and physiology, and therefore allow for an investigation of the role of epigenetic modifications in the emergence of physiological phenotypes during an organism's lifespan and in subsequent generations. This review aims firstly to describe the evolution of the repertoire of genes involved in key molecular epigenetic pathways including histone modifications, DNA methylation and microRNAs in zebrafish, rainbow trout, and Atlantic salmon, and secondly, to discuss recent advances in research highlighting a role for molecular epigenetics in shaping physiological phenotypes in these and other teleost models. Finally, by discussing themes and current limitations of the emerging field of teleost epigenetics from both theoretical and technical points of view, we will highlight future research needs and discuss how epigenetics will not only help address basic research questions in comparative teleost physiology, but also inform translational research including aquaculture, aquatic toxicology, and human disease.
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21
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Wu M, Wei W, Chen J, Cong R, Shi T, Bouvet P, Li J, Wong J, Du JX. Acidic domains differentially read histone H3 lysine 4 methylation status and are widely present in chromatin-associated proteins. SCIENCE CHINA. LIFE SCIENCES 2017; 60:138-151. [PMID: 28194553 DOI: 10.1007/s11427-016-0413-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 01/09/2017] [Indexed: 02/03/2023]
Abstract
Histone methylation is believed to provide binding sites for specific reader proteins, which translate histone code into biological function. Here we show that a family of acidic domain-containing proteins including nucleophosmin (NPM1), pp32, SET/TAF1β, nucleolin (NCL) and upstream binding factor (UBF) are novel H3K4me2-binding proteins. These proteins exhibit a unique pattern of interaction with methylated H3K4, as their binding is stimulated by H3K4me2 and inhibited by H3K4me1 and H3K4me3. These proteins contain one or more acidic domains consisting mainly of aspartic and/or glutamic residues that are necessary for preferential binding of H3K4me2. Furthermore, we demonstrate that the acidic domain with sufficient length alone is capable of binding H3K4me2 in vitro and in vivo. NPM1, NCL and UBF require their acidic domains for association with and transcriptional activation of rDNA genes. Interestingly, by defining acidic domain as a sequence with at least 20 acidic residues in 50 continuous amino acids, we identified 655 acidic domain-containing protein coding genes in the human genome and Gene Ontology (GO) analysis showed that many of the acidic domain proteins have chromatin-related functions. Our data suggest that acidic domain is a novel histone binding motif that can differentially read the status of H3K4 methylation and is broadly present in chromatin-associated proteins.
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Affiliation(s)
- Meng Wu
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiwei Chen
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Rong Cong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, 69364, France
| | - Tieliu Shi
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, 69364, France
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - James X Du
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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22
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Epigenetics in Alzheimer's Disease: Perspective of DNA Methylation. Mol Neurobiol 2017; 55:1026-1044. [PMID: 28092081 DOI: 10.1007/s12035-016-0357-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/28/2016] [Indexed: 12/12/2022]
Abstract
Research over the years has shown that causes of Alzheimer's disease are not well understood, but over the past years, the involvement of epigenetic mechanisms in the developing memory formation either under pathological or physiological conditions has become clear. The term epigenetics represents the heredity of changes in phenotype that are independent of altered DNA sequences. Different studies validated that cytosine methylation of genomic DNA decreases with age in different tissues of mammals, and therefore, the role of epigenetic factors in developing neurological disorders in aging has been under focus. In this review, we summarized and reviewed the involvement of different epigenetic mechanisms especially the DNA methylation in Alzheimer's disease (AD), late-onset Alzheimer's disease (LOAD), familial Alzheimer's disease (FAD), and autosomal dominant Alzheimer's disease (ADAD). Down to the minutest of details, we tried to discuss the methylation patterns like mitochondrial DNA methylation and ribosomal DNA (rDNA) methylation. Additionally, we mentioned some therapeutic approaches related to epigenetics, which could provide a potential cure for AD. Moreover, we reviewed some recent studies that validate DNA methylation as a potential biomarker and its role in AD. We hope that this review will provide new insights into the understanding of AD pathogenesis from the epigenetic perspective especially from the perspective of DNA methylation.
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23
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Thomson JP, Meehan RR. The application of genome-wide 5-hydroxymethylcytosine studies in cancer research. Epigenomics 2016; 9:77-91. [PMID: 27936926 DOI: 10.2217/epi-2016-0122] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Early detection and characterization of molecular events associated with tumorgenesis remain high priorities. Genome-wide epigenetic assays are promising diagnostic tools, as aberrant epigenetic events are frequent and often cancer specific. The deposition and analysis of multiple patient-derived cancer epigenomic profiles contributes to our appreciation of the underlying biology; aiding the detection of novel identifiers for cancer subtypes. Modifying enzymes and co-factors regulating these epigenetic marks are frequently mutated in cancers, and as epigenetic modifications themselves are reversible, this makes their study very attractive with respect to pharmaceutical intervention. Here we focus on the novel modified base, 5-hydoxymethylcytosine, and discuss how genome-wide 5-hydoxymethylcytosine profiling expedites our molecular understanding of cancer, serves as a lineage tracer, classifies the mode of action of potentially carcinogenic agents and clarifies the roles of potential novel cancer drug targets; thus assisting the development of new diagnostic/prognostic tools.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
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24
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Bochtler M, Kolano A, Xu GL. DNA demethylation pathways: Additional players and regulators. Bioessays 2016; 39:1-13. [PMID: 27859411 DOI: 10.1002/bies.201600178] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA demethylation can occur passively by "dilution" of methylation marks by DNA replication, or actively and independently of DNA replication. Direct conversion of 5-methylcytosine (5mC) to cytosine (C), as originally proposed, does not occur. Instead, active DNA methylation involves oxidation of the methylated base by ten-eleven translocations (TETs), or deamination of the methylated or a nearby base by activation induced deaminase (AID). The modified nucleotide, possibly together with surrounding nucleotides, is then replaced by the BER pathway. Recent data clarify the roles and the regulation of well-known enzymes in this process. They identify base excision repair (BER) glycosylases that may cooperate with or replace thymine DNA glycosylase (TDG) in the base excision step, and suggest possible involvement of DNA damage repair pathways other than BER in active DNA demethylation. Here, we review these new developments.
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Affiliation(s)
- Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Kolano
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Guo-Liang Xu
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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25
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Hollwey E, Watson M, Meyer P. Expression of the C-Terminal Domain of Mammalian <i>TET</i>3 DNA Dioxygenase in <i>Arabidopsis thaliana</i> Induces Heritable Methylation Changes at <i>rDNA</i> Loci. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/abb.2016.75023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Xue JH, Xu GF, Gu TP, Chen GD, Han BB, Xu ZM, Bjørås M, Krokan HE, Xu GL, Du YR. Uracil-DNA Glycosylase UNG Promotes Tet-mediated DNA Demethylation. J Biol Chem 2015; 291:731-8. [PMID: 26620559 DOI: 10.1074/jbc.m115.693861] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Indexed: 01/10/2023] Open
Abstract
In mammals, active DNA demethylation involves oxidation of 5-methylcytosine (5mC) into 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) by Tet dioxygenases and excision of these two oxidized bases by thymine DNA glycosylase (TDG). Although TDG is essential for active demethylation in embryonic stem cells and induced pluripotent stem cells, it is hardly expressed in mouse zygotes and dispensable in pronuclear DNA demethylation. To search for other factors that might contribute to demethylation in mammalian cells, we performed a functional genomics screen based on a methylated luciferase reporter assay. UNG2, one of the glycosylases known to excise uracil residues from DNA, was found to reduce DNA methylation, thus activating transcription of a methylation-silenced reporter gene when co-transfected with Tet2 into HEK293T cells. Interestingly, UNG2 could decrease 5caC from the genomic DNA and a reporter plasmid in transfected cells, like TDG. Furthermore, deficiency in Ung partially impaired DNA demethylation in mouse zygotes. Our results suggest that UNG might be involved in Tet-mediated DNA demethylation.
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Affiliation(s)
- Jian-Huang Xue
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Gui-Fang Xu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China, the School of Life Science, Fudan University, Shanghai 200433, China
| | - Tian-Peng Gu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Dong Chen
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin-Bin Han
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhi-Mei Xu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Magnar Bjørås
- the Department of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, Rikshospitalet, P. O. Box 4950, Nydalen, N-0424 Oslo, Norway
| | - Hans E Krokan
- the Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway, and
| | - Guo-Liang Xu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China, the School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, Shanghai 200031, China
| | - Ya-Rui Du
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China,
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