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Kurasz K, Rzeszowska-Wolny J, Oliński R, Foksiński M, Fujarewicz K. The Role of Different TET Proteins in Cytosine Demethylation Revealed by Mathematical Modeling. EPIGENOMES 2024; 8:18. [PMID: 38804367 PMCID: PMC11130908 DOI: 10.3390/epigenomes8020018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/30/2024] [Accepted: 04/28/2024] [Indexed: 05/29/2024] Open
Abstract
In living cells, some reactions can be conducted by more than one enzyme and sometimes it is difficult to establish which enzyme is responsible. Such is the case with proteins from the TET family, capable of converting 5-methyl-2'-deoxycytidine (5-mdC) in DNA to 5-(hydroxymethyl)-2'-deoxycytidine (5-hmdC) and further to 5-formyl-2'-deoxycytidine (5-fdC) and 5-carboxy-2'-deoxycytidine (5-cadC). The estimation of the efficiency of particular TETs in particular oxidative reactions and different cell types is important but experimentally difficult. Here, we propose an approach with mathematical modeling in which methylation and known deoxycytidine modification pathways are presented by 343 possible model versions with assumed different combinations of TET1, 2, and 3 activities in different pathways. Model parameters were calculated on the basis of 5-mdC, 5-hmdC, 5-fdC, 5-cadC, and 5-hmdU levels experimentally assessed in five human cultured cell lines and previously published. Selection of the model versions that give in simulations the best average fit to experimental data suggested that not all TET proteins participate in all modification reactions and that TET3 activity may be especially important in the reaction of 5-fdC removal.
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Affiliation(s)
- Karolina Kurasz
- Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | | | - Ryszard Oliński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85-092 Bydgoszcz, Poland
| | - Marek Foksiński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85-092 Bydgoszcz, Poland
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Xia Y, Chen K, Yang Q, Chen Z, Jin L, Zhang L, Yu X, Wang L, Xie C, Zhao Y, Shen Y, Tong J. Methylation in cornea and corneal diseases: a systematic review. Cell Death Discov 2024; 10:169. [PMID: 38589350 PMCID: PMC11002037 DOI: 10.1038/s41420-024-01935-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024] Open
Abstract
Corneal diseases are among the primary causes of blindness and vision loss worldwide. However, the pathogenesis of corneal diseases remains elusive, and diagnostic and therapeutic tools are limited. Thus, identifying new targets for the diagnosis and treatment of corneal diseases has gained great interest. Methylation, a type of epigenetic modification, modulates various cellular processes at both nucleic acid and protein levels. Growing evidence shows that methylation is a key regulator in the pathogenesis of corneal diseases, including inflammation, fibrosis, and neovascularization, making it an attractive potential therapeutic target. In this review, we discuss the major alterations of methylation and demethylation at the DNA, RNA, and protein levels in corneal diseases and how these dynamics contribute to the pathogenesis of corneal diseases. Also, we provide insights into identifying potential biomarkers of methylation that may improve the diagnosis and treatment of corneal diseases.
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Affiliation(s)
- Yutong Xia
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Kuangqi Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Qianjie Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Zhitong Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Le Jin
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyue Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Xin Yu
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyin Wang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Chen Xie
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Yuan Zhao
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Ye Shen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
| | - Jianping Tong
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
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Deng JY, Wu XQ, He WJ, Liao X, Tang M, Nie XQ. Targeting DNA methylation and demethylation in diabetic foot ulcers. J Adv Res 2023; 54:119-131. [PMID: 36706989 DOI: 10.1016/j.jare.2023.01.009] [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: 12/05/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Poor wound healing is a significant complication of diabetes, which is commonly caused by neuropathy, trauma, deformities, plantar hypertension and peripheral arterial disease. Diabetic foot ulcers (DFU) are difficult to heal, which makes patients susceptible to infections and can ultimately conduce to limb amputation or even death in severe cases. An increasing number of studies have found that epigenetic alterations are strongly associated with poor wound healing in diabetes. AIM OF REVIEW This work provides significant insights into the development of therapeutics for improving chronic diabetic wound healing, particularly by targeting and regulating DNA methylation and demethylation in DFU. Key scientific concepts of review: DNA methylation and demethylation play an important part in diabetic wound healing, via regulating corresponding signaling pathways in different breeds of cells, including macrophages, vascular endothelial cells and keratinocytes. In this review, we describe the four main phases of wound healing and their abnormality in diabetic patients. Furthermore, we provided an in-depth summary and discussion on how DNA methylation and demethylation regulate diabetic wound healing in different types of cells; and gave a brief summary on recent advances in applying cellular reprogramming techniques for improving diabetic wound healing.
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Affiliation(s)
- Jun-Yu Deng
- Key Lab of the Basic Pharmacology of the Ministry of Education, Zunyi Medical University, Zunyi 563006, China; Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, China; College of Pharmacy, Zunyi Medical University, Zunyi 563006, China
| | - Xing-Qian Wu
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, China
| | - Wen-Jie He
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, China
| | - Xin Liao
- Affiliated Hospital of Zunyi Medical University, Zunyi 563006, China
| | - Ming Tang
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalized Health at the Translational Research Institute (TRI), Brisbane, QLD 4102, Australia.
| | - Xu-Qiang Nie
- Key Lab of the Basic Pharmacology of the Ministry of Education, Zunyi Medical University, Zunyi 563006, China; Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, China; College of Pharmacy, Zunyi Medical University, Zunyi 563006, China; Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalized Health at the Translational Research Institute (TRI), Brisbane, QLD 4102, Australia.
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Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Syst 2023; 14:953-967.e17. [PMID: 37944515 DOI: 10.1016/j.cels.2023.10.007] [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: 10/03/2022] [Revised: 07/18/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023]
Abstract
Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.
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Affiliation(s)
- Amy Briffa
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Elizabeth Hollwey
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK; Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Zaigham Shahzad
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK; Department of Life Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Jonathan D Moore
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - David B Lyons
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK.
| | - Daniel Zilberman
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK; Institute of Science and Technology, 3400 Klosterneuburg, Austria.
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Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Curr Opin Genet Dev 2023; 81:102087. [PMID: 37441873 DOI: 10.1016/j.gde.2023.102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023]
Abstract
Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations.
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Affiliation(s)
| | - Amy Briffa
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Daniel Zilberman
- Institute of Science and Technology, 3400 Klosterneuburg, Austria.
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De Riso G, Sarnataro A, Scala G, Cuomo M, Della Monica R, Amente S, Chiariotti L, Miele G, Cocozza S. MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data. NAR Genom Bioinform 2022; 4:lqac096. [PMID: 36601577 PMCID: PMC9803872 DOI: 10.1093/nargab/lqac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is an epigenetic mark implicated in crucial biological processes. Most of the knowledge about DNA methylation is based on bulk experiments, in which DNA methylation of genomic regions is reported as average methylation. However, average methylation does not inform on how methylated cytosines are distributed in each single DNA molecule. Here, we propose Methylation Class (MC) profiling as a genome-wide approach to the study of DNA methylation heterogeneity from bulk bisulfite sequencing experiments. The proposed approach is built on the concept of MCs, groups of DNA molecules sharing the same number of methylated cytosines. The relative abundances of MCs from sequencing reads incorporates the information on the average methylation, and directly informs on the methylation level of each molecule. By applying our approach to publicly available bisulfite-sequencing datasets, we individuated cell-to-cell differences as the prevalent contributor to methylation heterogeneity. Moreover, we individuated signatures of loci undergoing imprinting and X-inactivation, and highlighted differences between the two processes. When applying MC profiling to compare different conditions, we identified methylation changes occurring in regions with almost constant average methylation. Altogether, our results indicate that MC profiling can provide useful insights on the epigenetic status and its evolution at multiple genomic regions.
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Affiliation(s)
- Giulia De Riso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Antonella Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Giovanni Scala
- Department of Biology, University of Naples Federico II, Via Vicinale Cupa Cintia 21, 80126 Naples, Italy
| | - Mariella Cuomo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Rosa Della Monica
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Lorenzo Chiariotti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Gennaro Miele
- Department of Physics “E. Pancini”, University of Naples “Federico II”, Via Cinthia, 80126 Naples, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Napoli, 80126 Naples, Italy
| | - Sergio Cocozza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
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Turpin M, Salbert G. 5-methylcytosine turnover: Mechanisms and therapeutic implications in cancer. Front Mol Biosci 2022; 9:976862. [PMID: 36060265 PMCID: PMC9428128 DOI: 10.3389/fmolb.2022.976862] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
DNA methylation at the fifth position of cytosine (5mC) is one of the most studied epigenetic mechanisms essential for the control of gene expression and for many other biological processes including genomic imprinting, X chromosome inactivation and genome stability. Over the last years, accumulating evidence suggest that DNA methylation is a highly dynamic mechanism driven by a balance between methylation by DNMTs and TET-mediated demethylation processes. However, one of the main challenges is to understand the dynamics underlying steady state DNA methylation levels. In this review article, we give an overview of the latest advances highlighting DNA methylation as a dynamic cycling process with a continuous turnover of cytosine modifications. We describe the cooperative actions of DNMT and TET enzymes which combine with many additional parameters including chromatin environment and protein partners to govern 5mC turnover. We also discuss how mathematical models can be used to address variable methylation levels during development and explain cell-type epigenetic heterogeneity locally but also at the genome scale. Finally, we review the therapeutic implications of these discoveries with the use of both epigenetic clocks as predictors and the development of epidrugs that target the DNA methylation/demethylation machinery. Together, these discoveries unveil with unprecedented detail how dynamic is DNA methylation during development, underlying the establishment of heterogeneous DNA methylation landscapes which could be altered in aging, diseases and cancer.
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Affiliation(s)
- Marion Turpin
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
| | - Gilles Salbert
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
- *Correspondence: Gilles Salbert,
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Sun D, Yu H, Li Q. Genome-Wide Differential DNA Methylomes Provide Insights into the Infertility of Triploid Oysters. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:18-31. [PMID: 35041105 DOI: 10.1007/s10126-021-10083-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
Chromosomal incompatibility and gene expression changes would affect the development of polyploid gonad and gamete formation. The role of epigenetics like DNA methylation in reproductive development is fully demonstrated in diploid animals. The lack of polyploid species and the infertility of polyploid animals, especially the odd ploidy, limit the study of epigenetic regulation mechanism of polyploid reproduction. Fertile and infertile individuals exist in triploid Pacific oyster Crassostrea gigas, which provide an interesting model for studies on the effect of epigenetic regulation on gonadal development. The whole genome single base resolution DNA methylomes in gonads of triploid females α (F-3nα), triploid females β (F-3nβ), triploid males α (M-3nα), triploid hermaphrodite predominantly males (HPM-3n), diploid females (F-2n), and diploid males (M-2n) were generated by using bisulfite-sequencing. The overall DNA methylation profiles in gene regions and transposable regions of fertile and infertile triploid oysters were consistent with those of diploid oysters. The DNA methylation level of CG context decreased in infertile triploid oysters, with more hypomethylated than hypermethylated regions, and the opposite is true in fertile triploid oysters. Genes harbored with differentially methylated regions (DMRs) in infertile triploids were mainly related to the metabolism pathways and the signal pathways. Correlation analysis indicated that the expression of gene transcriptions was generally positively associated with DNA methylation in gene body regions, and DMRs in infertile triploid oysters played significant roles in gonadal development as a possible critical epigenetic regulator of gonadal development gene transcriptional activity. These findings indicate a potential relationship between DNA methylation variability and gene expression plasticity in newly formed polyploidy. As far as we know, this is the first study revealing the epigenetic regulation of gonadal development in invertebrates based on fertile and infertile models, meanwhile providing a new mentality to explore the regulatory mechanisms of infertility in triploids.
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Affiliation(s)
- Dongfang Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China), Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China), Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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