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Alex K, Winkler EC. Comparative ethical evaluation of epigenome editing and genome editing in medicine: first steps and future directions. JOURNAL OF MEDICAL ETHICS 2024; 50:398-406. [PMID: 37527926 PMCID: PMC11137457 DOI: 10.1136/jme-2022-108888] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
Targeted modifications of the human epigenome, epigenome editing (EE), are around the corner. For EE, techniques similar to genome editing (GE) techniques are used. While in GE the genetic information is changed by directly modifying DNA, intervening in the epigenome requires modifying the configuration of DNA, for example, how it is folded. This does not come with alterations in the base sequence ('genetic code'). To date, there is almost no ethical debate about EE, whereas the discussions about GE are voluminous. Our article introduces EE into bioethics by translating knowledge from science to ethics and by comparing the risks of EE with those of GE. We, first (I), make the case that a broader ethical debate on EE is due, provide scientific background on EE, compile potential use-cases and recap previous debates. We then (II) compare EE and GE and suggest that the severity of risks of novel gene technologies depends on three factors: (i) the choice of an ex vivo versus an in vivo editing approach, (ii) the time of intervention and intervention windows and (iii) the targeted diseases. Moreover, we show why germline EE is not effective and reject the position of strong epigenetic determinism. We conclude that EE is not always ethically preferable to GE in terms of risks, and end with suggestions for next steps in the current ethical debate on EE by briefly introducing ethical challenges of new areas of preventive applications of EE (III).
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Affiliation(s)
- Karla Alex
- Section Translational Medical Ethics, Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Eva C Winkler
- Section Translational Medical Ethics, Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
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2
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Knodel F, Pinter S, Kroll C, Rathert P. Fluorescent Reporter Systems to Investigate Chromatin Effector Proteins in Living Cells. Methods Mol Biol 2024; 2842:225-252. [PMID: 39012599 DOI: 10.1007/978-1-0716-4051-7_12] [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] [Indexed: 07/17/2024]
Abstract
Epigenetic research faces the challenge of the high complexity and tight regulation in chromatin modification networks. Although many isolated mechanisms of chromatin-mediated gene regulation have been described, solid approaches for the comprehensive analysis of specific processes as parts of the bigger epigenome network are missing. In order to expand the toolbox of methods by a system that will help to capture and describe the complexity of transcriptional regulation, we describe here a robust protocol for the generation of stable reporter systems for transcriptional activity and summarize their applications. The system allows for the induced recruitment of a chromatin regulator to a fluorescent reporter gene, followed by the detection of transcriptional changes using flow cytometry. The reporter gene is integrated into an endogenous chromatin environment, thus enabling the detection of regulatory dependencies of the investigated chromatin regulator on endogenous cofactors. The system allows for an easy and dynamic readout at the single-cell level and the ability to compensate for cell-to-cell variances of transcription. The modular design of the system enables the simple adjustment of the method for the investigation of different chromatin regulators in a broad panel of cell lines. We also summarize applications of this technology to characterize the silencing velocity of different chromatin effectors, removal of activating histone modifications, analysis of stability and reversibility of epigenome modifications, the investigation of the effects of small molecule on chromatin effectors and of functional effector-coregulator relationships. The presented method allows to investigate the complexity of transcriptional regulation by epigenetic effector proteins in living cells.
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Affiliation(s)
- Franziska Knodel
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Sabine Pinter
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Carolin Kroll
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Philipp Rathert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.
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3
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Fadul SM, Arshad A, Mehmood R. CRISPR-based epigenome editing: mechanisms and applications. Epigenomics 2023; 15:1137-1155. [PMID: 37990877 DOI: 10.2217/epi-2023-0281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Epigenomic anomalies contribute significantly to the development of numerous human disorders. The development of epigenetic research tools is essential for understanding how epigenetic marks contribute to gene expression. A gene-editing technique known as CRISPR (clustered regularly interspaced short palindromic repeats) typically targets a particular DNA sequence using a guide RNA (gRNA). CRISPR/Cas9 technology has been remodeled for epigenome editing by generating a 'dead' Cas9 protein (dCas9) that lacks nuclease activity and juxtaposing it with an epigenetic effector domain. Based on fusion partners of dCas9, a specific epigenetic state can be achieved. CRISPR-based epigenome editing has widespread application in drug screening, cancer treatment and regenerative medicine. This paper discusses the tools developed for CRISPR-based epigenome editing and their applications.
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Affiliation(s)
- Shaima M Fadul
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
| | - Aleeza Arshad
- Medical Teaching Insitute, Ayub Teaching Hospital, Abbottabad, 22020, Pakistan
| | - Rashid Mehmood
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
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4
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Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:1-19. [DOI: 10.1007/978-3-031-11454-0_1] [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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5
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Pacheco MB, Camilo V, Henrique R, Jerónimo C. Epigenetic Editing in Prostate Cancer: Challenges and Opportunities. Epigenetics 2021; 17:564-588. [PMID: 34130596 DOI: 10.1080/15592294.2021.1939477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Epigenome editing consists of fusing a predesigned DNA recognition unit to the catalytic domain of a chromatin modifying enzyme leading to the introduction or removal of an epigenetic mark at a specific locus. These platforms enabled the study of the mechanisms and roles of epigenetic changes in several research domains such as those addressing pathogenesis and progression of cancer. Despite the continued efforts required to overcome some limitations, which include specificity, off-target effects, efficacy, and longevity, these tools have been rapidly progressing and improving.Since prostate cancer is characterized by multiple genetic and epigenetic alterations that affect different signalling pathways, epigenetic editing constitutes a promising strategy to hamper cancer progression. Therefore, by modulating chromatin structure through epigenome editing, its conformation might be better understood and events that drive prostate carcinogenesis might be further unveiled.This review describes the different epigenome engineering tools, their mechanisms concerning gene's expression and regulation, highlighting the challenges and opportunities concerning prostate cancer research.
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Affiliation(s)
- Mariana Brütt Pacheco
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - Vânia Camilo
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. DR. António Bernardino De Almeida, Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, Portugal
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Brodie ED, Gregory B, Lisch D, Riddle NC. The epigenome and beyond: How does non-genetic inheritance change our view of evolution? Integr Comp Biol 2021; 61:2199-2207. [PMID: 34028538 DOI: 10.1093/icb/icab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evidence from across the tree of life suggests that epigenetic inheritance is more common than previously thought. If epigenetic inheritance is indeed as common as the data suggest, this finding has potentially important implications for evolutionary theory and our understanding of how evolution and adaptation progress. However, we currently lack an understanding of how common various epigenetic inheritance types are, and how they impact phenotypes. In this perspective, we review the open questions that need to be addressed to fully integrate epigenetic inheritance into evolutionary theory and to develop reliable predictive models for phenotypic evolution. We posit that addressing these challenges will require the collaboration of biologists from different disciplines and a focus on the exploration of data and phenomena without preconceived limits on potential mechanisms or outcomes.
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Affiliation(s)
- Edmund D Brodie
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Brian Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL
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7
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Policarpi C, Dabin J, Hackett JA. Epigenetic editing: Dissecting chromatin function in context. Bioessays 2021; 43:e2000316. [PMID: 33724509 DOI: 10.1002/bies.202000316] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/06/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
How epigenetic mechanisms regulate genome output and response to stimuli is a fundamental question in development and disease. Past decades have made tremendous progress in deciphering the regulatory relationships involved by correlating aggregated (epi)genomics profiles with global perturbations. However, the recent development of epigenetic editing technologies now enables researchers to move beyond inferred conclusions, towards explicit causal reasoning, through 'programing' precise chromatin perturbations in single cells. Here, we first discuss the major unresolved questions in the epigenetics field that can be addressed by programable epigenome editing, including the context-dependent function and memory of chromatin states. We then describe the epigenetic editing toolkit focusing on CRISPR-based technologies, and highlight its achievements, drawbacks and promise. Finally, we consider the potential future application of epigenetic editing to the study and treatment of specific disease conditions.
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Affiliation(s)
- Cristina Policarpi
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Juliette Dabin
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Jamie A Hackett
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
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8
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Novel strategies to cure imprinting disorders. MED GENET-BERLIN 2020. [DOI: 10.1515/medgen-2020-2043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In imprinting disorders, where the active copy of an imprinted gene is mutated or lost, there is a unique opportunity for causal treatment by unsilencing the other, dormant allele. Depending on the mechanism by which the allele is silenced, unsilencing can be achieved by epigenetic drugs, antisense-oligonucleotides (ASOs) or epigenome editing. While most of the research is still preclinical, first-in-humans studies with ASOs have started in 2020.
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Ling C. Epigenetic regulation of insulin action and secretion - role in the pathogenesis of type 2 diabetes. J Intern Med 2020; 288:158-167. [PMID: 32363639 DOI: 10.1111/joim.13049] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/17/2020] [Accepted: 01/30/2020] [Indexed: 12/21/2022]
Abstract
The prevalence of type 2 diabetes (T2D) is rapidly increasing worldwide. Obesity, physical inactivity and ageing increase the risk of T2D. Epigenetic modifications can change due to environmental exposures and may thereby predispose to disease. This review aims at summarizing recent advances in epigenetics related to T2D, with a special focus on impaired insulin action and secretion in humans. There will be an emphasis on analyses in human tissues; both from T2D case-control cohorts and intervention studies. Current data support an important role for epigenetics in the pathogenesis of T2D. Numerous studies have found differential DNA methylation and gene expression in skeletal muscle, adipose tissue, the liver and pancreatic islets from subjects with T2D compared with nondiabetic controls. For example, PDX1 has increased DNA methylation and decreased expression in pancreatic islets from patients with T2D compared with nondiabetic controls. Nongenetic risk factors for T2D such as ageing, unhealthy diets and physical activity do also impact the epigenome in human tissues. Interestingly, physical activity altered DNA methylation of candidate genes for T2D such as THADA in muscle and FTO, KCNQ1 and TCF7L2 in adipose tissue. There is also a strong interaction between genetic and epigenetic factors that together seem to affect T2D. mQTL studies in human adipose tissue and pancreatic islets showed that SNPs associated with DNA methylation levels in numerous sites. Several of these SNPs are also associated with T2D. Recent data also support that DNA methylation of some sites in blood may be developed into biomarkers that predict T2D since methylation of, for example TXNIP, ABCG1 and SREBF1 associated with future T2D. Future studies should use this information for development of new therapies and biomarkers and thereby improve prediction, prevention and treatment of T2D and its complications.
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Affiliation(s)
- C Ling
- From the, Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
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10
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Devesa-Guerra I, Morales-Ruiz T, Pérez-Roldán J, Parrilla-Doblas JT, Dorado-León M, García-Ortiz MV, Ariza RR, Roldán-Arjona T. DNA Methylation Editing by CRISPR-guided Excision of 5-Methylcytosine. J Mol Biol 2020; 432:2204-2216. [PMID: 32087201 DOI: 10.1016/j.jmb.2020.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 12/22/2022]
Abstract
Tools for actively targeted DNA demethylation are required to increase our knowledge about regulation and specific functions of this important epigenetic modification. DNA demethylation in mammals involves TET-mediated oxidation of 5-methylcytosine (5-meC), which may promote its replication-dependent dilution and/or active removal through base excision repair (BER). However, it is still unclear whether oxidized derivatives of 5-meC are simply DNA demethylation intermediates or rather epigenetic marks on their own. Unlike animals, plants have evolved enzymes that directly excise 5-meC without previous modification. In this work, we have fused the catalytic domain of Arabidopsis ROS1 5-meC DNA glycosylase to a CRISPR-associated null-nuclease (dCas9) and analyzed its capacity for targeted reactivation of methylation-silenced genes, in comparison to other dCas9-effectors. We found that dCas9-ROS1, but not dCas9-TET1, is able to reactivate methylation-silenced genes and induce partial demethylation in a replication-independent manner. We also found that reactivation induced by dCas9-ROS1, as well as that achieved by two different CRISPR-based chromatin effectors (dCas9-VP160 and dCas9-p300), generally decreases with methylation density. Our results suggest that plant 5-meC DNA glycosylases are a valuable addition to the CRISPR-based toolbox for epigenetic editing.
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Affiliation(s)
- Iván Devesa-Guerra
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Teresa Morales-Ruiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Juan Pérez-Roldán
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Jara Teresa Parrilla-Doblas
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Macarena Dorado-León
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - María Victoria García-Ortiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Rafael R Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain.
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11
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Zhao W, Wang Y, Liang FS. Chemical and Light Inducible Epigenome Editing. Int J Mol Sci 2020; 21:ijms21030998. [PMID: 32028669 PMCID: PMC7037166 DOI: 10.3390/ijms21030998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
The epigenome defines the unique gene expression patterns and resulting cellular behaviors in different cell types. Epigenome dysregulation has been directly linked to various human diseases. Epigenome editing enabling genome locus-specific targeting of epigenome modifiers to directly alter specific local epigenome modifications offers a revolutionary tool for mechanistic studies in epigenome regulation as well as the development of novel epigenome therapies. Inducible and reversible epigenome editing provides unique temporal control critical for understanding the dynamics and kinetics of epigenome regulation. This review summarizes the progress in the development of spatiotemporal-specific tools using small molecules or light as inducers to achieve the conditional control of epigenome editing and their applications in epigenetic research.
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12
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Perera BP, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC. The role of environmental exposures and the epigenome in health and disease. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:176-192. [PMID: 31177562 PMCID: PMC7252203 DOI: 10.1002/em.22311] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/02/2023]
Abstract
The genetic material of every organism exists within the context of regulatory networks that govern gene expression, collectively called the epigenome. Epigenetics has taken center stage in the study of diseases such as cancer and diabetes, but its integration into the field of environmental health is still emerging. As the Environmental Mutagenesis and Genomics Society (EMGS) celebrates its 50th Anniversary this year, we have come together to review and summarize the seminal advances in the field of environmental epigenomics. Specifically, we focus on the role epigenetics may play in multigenerational and transgenerational transmission of environmentally induced health effects. We also summarize state of the art techniques for evaluating the epigenome, environmental epigenetic analysis, and the emerging field of epigenome editing. Finally, we evaluate transposon epigenetics as they relate to environmental exposures and explore the role of noncoding RNA as biomarkers of environmental exposures. Although the field has advanced over the past several decades, including being recognized by EMGS with its own Special Interest Group, recently renamed Epigenomics, we are excited about the opportunities for environmental epigenetic science in the next 50 years. Environ. Mol. Mutagen. 61:176-192, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Bambarendage P.U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, St. Paul, Minnesota
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Correspondence to: Dana C. Dolinoy, Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan.
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Liu XS, Jaenisch R. Editing the Epigenome to Tackle Brain Disorders. Trends Neurosci 2019; 42:861-870. [PMID: 31706628 DOI: 10.1016/j.tins.2019.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/20/2019] [Accepted: 10/07/2019] [Indexed: 02/08/2023]
Abstract
Genetic studies of epigenetic modifiers such as DNA methyltransferases and histone acetyltransferases have revealed a critical role for epigenetic regulation during brain development and function. Alteration of epigenetic modifications have been documented in a variety of brain disorders, including neurodevelopmental, psychiatric, and neurodegenerative diseases. Development of epigenome editing tools enables a functional dissection of the link between altered epigenetic changes and disease outcomes. Here, we review the development of epigenome editing tools, summarize proof of concept applications focusing on brain disease-associated genes, and discuss the promising application and challenges of epigenome editing to tackle brain disorders.
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Affiliation(s)
- X Shawn Liu
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02142, USA.
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14
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Tiane A, Schepers M, Rombaut B, Hupperts R, Prickaerts J, Hellings N, van den Hove D, Vanmierlo T. From OPC to Oligodendrocyte: An Epigenetic Journey. Cells 2019; 8:E1236. [PMID: 31614602 PMCID: PMC6830107 DOI: 10.3390/cells8101236] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Oligodendrocytes provide metabolic and functional support to neuronal cells, rendering them key players in the functioning of the central nervous system. Oligodendrocytes need to be newly formed from a pool of oligodendrocyte precursor cells (OPCs). The differentiation of OPCs into mature and myelinating cells is a multistep process, tightly controlled by spatiotemporal activation and repression of specific growth and transcription factors. While oligodendrocyte turnover is rather slow under physiological conditions, a disruption in this balanced differentiation process, for example in case of a differentiation block, could have devastating consequences during ageing and in pathological conditions, such as multiple sclerosis. Over the recent years, increasing evidence has shown that epigenetic mechanisms, such as DNA methylation, histone modifications, and microRNAs, are major contributors to OPC differentiation. In this review, we discuss how these epigenetic mechanisms orchestrate and influence oligodendrocyte maturation. These insights are a crucial starting point for studies that aim to identify the contribution of epigenetics in demyelinating diseases and may thus provide new therapeutic targets to induce myelin repair in the long run.
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Affiliation(s)
- Assia Tiane
- Department of Immunology, Biomedical Research Institute, Hasselt University, Hasselt 3500, Belgium.
- Department Psychiatry and Neuropsychology, European Graduate School of Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht 6200 MD, The Netherlands.
| | - Melissa Schepers
- Department of Immunology, Biomedical Research Institute, Hasselt University, Hasselt 3500, Belgium.
- Department Psychiatry and Neuropsychology, European Graduate School of Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht 6200 MD, The Netherlands.
| | - Ben Rombaut
- Department of Immunology, Biomedical Research Institute, Hasselt University, Hasselt 3500, Belgium.
- Department Psychiatry and Neuropsychology, European Graduate School of Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht 6200 MD, The Netherlands.
| | - Raymond Hupperts
- Department of Neurology, Zuyderland Medical Center, Sittard-Geleen 6130 MB, The Netherlands.
- Department Psychiatry and Neuropsychology, European Graduate School of Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht 6200 MD, The Netherlands.
| | - Jos Prickaerts
- Department Psychiatry and Neuropsychology, European Graduate School of Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht 6200 MD, The Netherlands.
| | - Niels Hellings
- Department of Immunology, Biomedical Research Institute, Hasselt University, Hasselt 3500, Belgium.
| | - Daniel van den Hove
- Department Psychiatry and Neuropsychology, European Graduate School of Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht 6200 MD, The Netherlands.
- Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Wuerzburg 97080, Germany.
| | - Tim Vanmierlo
- Department of Immunology, Biomedical Research Institute, Hasselt University, Hasselt 3500, Belgium.
- Department Psychiatry and Neuropsychology, European Graduate School of Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht 6200 MD, The Netherlands.
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15
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Jeltsch A, Broche J, Bashtrykov P. Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes. Genes (Basel) 2018; 9:genes9110566. [PMID: 30469440 PMCID: PMC6266221 DOI: 10.3390/genes9110566] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is an essential part of the epigenome chromatin modification network, which also comprises several covalent histone protein post-translational modifications. All these modifications are highly interconnected, because the writers and erasers of one mark, DNA methyltransferases (DNMTs) and ten eleven translocation enzymes (TETs) in the case of DNA methylation, are directly or indirectly targeted and regulated by other marks. Here, we have collected information about the genomic distribution and variability of DNA methylation in human and mouse DNA in different genomic elements. After summarizing the impact of DNA methylation on genome evolution including CpG depletion, we describe the connection of DNA methylation with several important histone post-translational modifications, including methylation of H3K4, H3K9, H3K27, and H3K36, but also with nucleosome remodeling. Moreover, we present the mechanistic features of mammalian DNA methyltransferases and their associated factors that mediate the crosstalk between DNA methylation and chromatin modifications. Finally, we describe recent advances regarding the methylation of non-CpG sites, methylation of adenine residues in human cells and methylation of mitochondrial DNA. At several places, we highlight controversial findings or open questions demanding future experimental work.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Julian Broche
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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