51
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Swahari V, Nakamura A, Hollville E, Stroud H, Simon JM, Ptacek TS, Beck MV, Flowers C, Guo J, Plestant C, Liang J, Kurtz CL, Kanke M, Hammond SM, He YW, Anton ES, Sethupathy P, Moy SS, Greenberg ME, Deshmukh M. MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation. Cell Rep 2021; 35:108946. [PMID: 33826889 PMCID: PMC8103628 DOI: 10.1016/j.celrep.2021.108946] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/09/2020] [Accepted: 03/14/2021] [Indexed: 11/27/2022] Open
Abstract
Although embryonic brain development and neurodegeneration have received considerable attention, the events that govern postnatal brain maturation are less understood. Here, we identify the miR-29 family to be strikingly induced during the late stages of brain maturation. Brain maturation is associated with a transient, postnatal period of de novo non-CG (CH) DNA methylation mediated by DNMT3A. We examine whether an important function of miR-29 during brain maturation is to restrict the period of CH methylation via its targeting of Dnmt3a. Deletion of miR-29 in the brain, or knockin mutations preventing miR-29 to specifically target Dnmt3a, result in increased DNMT3A expression, higher CH methylation, and repression of genes associated with neuronal activity and neuropsychiatric disorders. These mouse models also develop neurological deficits and premature lethality. Our results identify an essential role for miR-29 in restricting CH methylation in the brain and illustrate the importance of CH methylation regulation for normal brain maturation.
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Affiliation(s)
- Vijay Swahari
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Ayumi Nakamura
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA
| | - Emilie Hollville
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Hume Stroud
- Department of Neurobiology, Harvard University, Boston, MA, USA
| | - Jeremy M Simon
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Travis S Ptacek
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew V Beck
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Cornelius Flowers
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jiami Guo
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jie Liang
- Department of Immunology, Duke University, Durham, NC, USA
| | - C Lisa Kurtz
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Matt Kanke
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Scott M Hammond
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - You-Wen He
- Department of Immunology, Duke University, Durham, NC, USA
| | - E S Anton
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | | | - Mohanish Deshmukh
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA.
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52
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Tillotson R, Cholewa-Waclaw J, Chhatbar K, Connelly JC, Kirschner SA, Webb S, Koerner MV, Selfridge J, Kelly DA, De Sousa D, Brown K, Lyst MJ, Kriaucionis S, Bird A. Neuronal non-CG methylation is an essential target for MeCP2 function. Mol Cell 2021; 81:1260-1275.e12. [PMID: 33561390 PMCID: PMC7980222 DOI: 10.1016/j.molcel.2021.01.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/17/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023]
Abstract
DNA methylation is implicated in neuronal biology via the protein MeCP2, the mutation of which causes Rett syndrome. MeCP2 recruits the NCOR1/2 co-repressor complexes to methylated cytosine in the CG dinucleotide, but also to sites of non-CG methylation, which are abundant in neurons. To test the biological significance of the dual-binding specificity of MeCP2, we replaced its DNA binding domain with an orthologous domain from MBD2, which can only bind mCG motifs. Knockin mice expressing the domain-swap protein displayed severe Rett-syndrome-like phenotypes, indicating that normal brain function requires the interaction of MeCP2 with sites of non-CG methylation, specifically mCAC. The results support the notion that the delayed onset of Rett syndrome is due to the simultaneous post-natal accumulation of mCAC and its reader MeCP2. Intriguingly, genes dysregulated in both Mecp2 null and domain-swap mice are implicated in other neurological disorders, potentially highlighting targets of relevance to the Rett syndrome phenotype.
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Affiliation(s)
- Rebekah Tillotson
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Justyna Cholewa-Waclaw
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Kashyap Chhatbar
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - John C Connelly
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Sophie A Kirschner
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Martha V Koerner
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Jim Selfridge
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - David A Kelly
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Dina De Sousa
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Kyla Brown
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Matthew J Lyst
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Skirmantas Kriaucionis
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Adrian Bird
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK.
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53
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Meireles ALF, Segabinazi E, Spindler C, Gasperini NF, Souza Dos Santos A, Pochmann D, Elsner VR, Marcuzzo S. Maternal resistance exercise promotes changes in neuroplastic and epigenetic marks of offspring's hippocampus during adult life. Physiol Behav 2020; 230:113306. [PMID: 33359430 DOI: 10.1016/j.physbeh.2020.113306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 12/01/2022]
Abstract
Studies indicate that gestational exercise practice positively impacts the offspring's cognition. Nevertheless, the influence of maternal resistance exercise, different periods of exercise practice, and the inter- and transgenerational effects involved in these responses are not known. This study sought to report the influence of the maternal practice of resistance exercise on offspring's cognitive function, exploring behavior, and neuroplastic and epigenetic marks in the hippocampus. Female Wistar rats were divided into four groups: sedentary (SS), exercised during pregnancy (SE), exercised before pregnancy (ES), and exercised before and during pregnancy (EE). Exercised rats were submitted to a resistance exercise protocol (vertical ladder climbing). Between postnatal days (P)81 and P85, male offspring were submitted to the Morris water maze test. At P85, the following analyses were performed in offspring's hippocampus: expression of IGF-1 and BrdU+ cells, global DNA methylation, H3/H4 acetylation, and HDAC2 amount. Only the offspring of SE mothers presented subtly better performance on learning and memory tasks, associated with lower HDAC2 amount. Offspring from ES mothers presented an overexpression of hippocampal neuroplastic marks (BrdU+ and IGF-1), as well as a decrease of DNA methylation and an increase in H4 acetylation. Offspring from EE mothers (continuously exercised) did not present modifications in plasticity or epigenetic parameters. This is the first study to observe the influence of maternal resistance exercise on offspring's brains. The findings provide evidence that offspring's hippocampus plasticity is influenced by exercise performed in isolated periods (pre- or gestationally) more than that performed continually.
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Affiliation(s)
- André Luís Ferreira Meireles
- Programa de Pós-Graduação em Neurociências, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Laboratório de Histofisiologia Comparada, Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Ethiane Segabinazi
- Programa de Pós-Graduação em Neurociências, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Laboratório de Histofisiologia Comparada, Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Christiano Spindler
- Programa de Pós-Graduação em Neurociências, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Laboratório de Histofisiologia Comparada, Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Natália Felix Gasperini
- Laboratório de Histofisiologia Comparada, Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Adriana Souza Dos Santos
- Programa de Pós-Graduação em Neurociências, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Laboratório de Histofisiologia Comparada, Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Daniela Pochmann
- Programa de Pós-Graduação em Biociências e Reabilitação, Centro Universitário Metodista-IPA, Porto Alegre, RS, Brazil
| | - Viviane Rostirola Elsner
- Programa de Pós-Graduação em Biociências e Reabilitação, Centro Universitário Metodista-IPA, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Simone Marcuzzo
- Programa de Pós-Graduação em Neurociências, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Laboratório de Histofisiologia Comparada, Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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54
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Cristancho AG, Marsh ED. Epigenetics modifiers: potential hub for understanding and treating neurodevelopmental disorders from hypoxic injury. J Neurodev Disord 2020; 12:37. [PMID: 33327934 PMCID: PMC7745506 DOI: 10.1186/s11689-020-09344-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 11/13/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The fetal brain is adapted to the hypoxic conditions present during normal in utero development. Relatively more hypoxic states, either chronic or acute, are pathologic and can lead to significant long-term neurodevelopmental sequelae. In utero hypoxic injury is associated with neonatal mortality and millions of lives lived with varying degrees of disability. MAIN BODY Genetic studies of children with neurodevelopmental disease indicate that epigenetic modifiers regulating DNA methylation and histone remodeling are critical for normal brain development. Epigenetic modifiers are also regulated by environmental stimuli, such as hypoxia. Indeed, epigenetic modifiers that are mutated in children with genetic neurodevelopmental diseases are regulated by hypoxia in a number of preclinical models and may be part of the mechanism for the long-term neurodevelopmental sequelae seem in children with hypoxic brain injury. Thus, a comprehensive understanding the role of DNA methylation and histone modifications in hypoxic injury is critical for developing novel strategies to treat children with hypoxic injury. CONCLUSIONS This review focuses on our current understanding of the intersection between epigenetics, brain development, and hypoxia. Opportunities for the use of epigenetics as biomarkers of neurodevelopmental disease after hypoxic injury and potential clinical epigenetics targets to improve outcomes after injury are also discussed. While there have been many published studies on the epigenetics of hypoxia, more are needed in the developing brain in order to determine which epigenetic pathways may be most important for mitigating the long-term consequences of hypoxic brain injury.
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Affiliation(s)
- Ana G Cristancho
- Departments of Neurology and Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
- Division of Child Neurology, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Eric D Marsh
- Departments of Neurology and Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA.
- Division of Child Neurology, Children's Hospital of Philadelphia, Philadelphia, USA.
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55
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Wei J, Cheng J, Waddell NJ, Wang ZJ, Pang X, Cao Q, Liu A, Chitaman JM, Abreu K, Jasrotia RS, Duffney LJ, Zhang J, Dietz DM, Feng J, Yan Z. DNA Methyltransferase 3A Is Involved in the Sustained Effects of Chronic Stress on Synaptic Functions and Behaviors. Cereb Cortex 2020; 31:1998-2012. [PMID: 33230530 DOI: 10.1093/cercor/bhaa337] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/29/2020] [Accepted: 10/18/2020] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence suggests that epigenetic mechanisms regulate aberrant gene transcription in stress-associated mental disorders. However, it remains to be elucidated about the role of DNA methylation and its catalyzing enzymes, DNA methyltransferases (DNMTs), in this process. Here, we found that male rats exposed to chronic (2-week) unpredictable stress exhibited a substantial reduction of Dnmt3a after stress cessation in the prefrontal cortex (PFC), a key target region of stress. Treatment of unstressed control rats with DNMT inhibitors recapitulated the effect of chronic unpredictable stress on decreased AMPAR expression and function in PFC. In contrast, overexpression of Dnmt3a in PFC of stressed animals prevented the loss of glutamatergic responses. Moreover, the stress-induced behavioral abnormalities, including the impaired recognition memory, heightened aggression, and hyperlocomotion, were partially attenuated by Dnmt3a expression in PFC of stressed animals. Finally, we found that there were genome-wide DNA methylation changes and transcriptome alterations in PFC of stressed rats, both of which were enriched at several neural pathways, including glutamatergic synapse and microtubule-associated protein kinase signaling. These results have therefore recognized the potential role of DNA epigenetic modification in stress-induced disturbance of synaptic functions and cognitive and emotional processes.
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Affiliation(s)
- Jing Wei
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jia Cheng
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Nicholas J Waddell
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Zi-Jun Wang
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Xiaodong Pang
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Qing Cao
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Aiyi Liu
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Javed M Chitaman
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.,Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Kristen Abreu
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Rahul Singh Jasrotia
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Lara J Duffney
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - David M Dietz
- Department of Pharmacology and Toxicology, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jian Feng
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.,Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Zhen Yan
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
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56
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Ait Boujmia OK, Nadifi S, Dehbi H, Lamchahab M, Quessar A. The influence of DNMT3A and DNMT3B gene polymorphisms on acute myeloid leukemia risk in a Moroccan population. Curr Res Transl Med 2020; 68:191-195. [PMID: 32912818 DOI: 10.1016/j.retram.2020.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/22/2020] [Accepted: 08/15/2020] [Indexed: 01/04/2023]
Abstract
Acute myeloid leukemia (AML) is a very complex disease that is linked to environmental, genetic and epigenetic factors. Several Studies have found that aberrations in DNA methylation process play a crucial role in leukemogenesis. The aim of this case control study was to evaluate the association between rs1569686, rs2424913 polymorphisms located in DNMT3B gene and rs7590760 polymorphism located in DNMT3A gene and AML risk in a Moroccan population. MATERIALS AND METHODS The present study was conducted in 142 cases of AML and 179 control subjects from the Moroccan population. Genomic DNA was isolated from whole blood samples by salting-out method and the genotype of the three polymorphisms was determined by the PCR-RFLP technique. RESULTS The study results indicated that rs1569686 polymorphism was significantly associated with the risk of AML in dominant model (OR=1.72, 95 % CI 1.01-2.95, P=0.04), but not in recessive model. In stratified analysis by gender, statistically significant association between the rs2424913 CT genotype and AML was found among males (OR=2.05, 95 % CI 1.00-4.19, P=0.04). Similarly, the rs1569686 TT genotype was associated with an increase risk of AML (OR=3.21, 95 % CI 1.15-8. 98, P=0.02), this association was also found under dominant genetic model (OR=2.47, 95 % CI 1.07-5. 67, P=0.03) among males. However, the rs2424913 polymorphism was not associated with AML. CONCLUSION Our findings have shown that rs1569686 polymorphism might be a risk factor of AML in males. While, the rs2424913 polymorphism was not associated with AML. Further studies with a large sample size are needed to validate our results.
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Affiliation(s)
- Oum Kaltoum Ait Boujmia
- Laboratory of Genetics and Molecular Pathology, Medical School, University Hassan II, Casablanca, Morocco; Department of Onco-Hematology, Ibn Rochd University Hospital, Casablanca, Morocco.
| | - Sellama Nadifi
- Laboratory of Genetics and Molecular Pathology, Medical School, University Hassan II, Casablanca, Morocco; Department of Onco-Hematology, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Hind Dehbi
- Laboratory of Genetics and Molecular Pathology, Medical School, University Hassan II, Casablanca, Morocco; Department of Onco-Hematology, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Mouna Lamchahab
- Laboratory of Genetics and Molecular Pathology, Medical School, University Hassan II, Casablanca, Morocco; Department of Onco-Hematology, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Asma Quessar
- Laboratory of Genetics and Molecular Pathology, Medical School, University Hassan II, Casablanca, Morocco; Department of Onco-Hematology, Ibn Rochd University Hospital, Casablanca, Morocco
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57
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Bayraktar G, Yuanxiang P, Confettura AD, Gomes GM, Raza SA, Stork O, Tajima S, Suetake I, Karpova A, Yildirim F, Kreutz MR. Synaptic control of DNA methylation involves activity-dependent degradation of DNMT3A1 in the nucleus. Neuropsychopharmacology 2020; 45:2120-2130. [PMID: 32726795 PMCID: PMC7547096 DOI: 10.1038/s41386-020-0780-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022]
Abstract
DNA methylation is a crucial epigenetic mark for activity-dependent gene expression in neurons. Very little is known about how synaptic signals impact promoter methylation in neuronal nuclei. In this study we show that protein levels of the principal de novo DNA-methyltransferase in neurons, DNMT3A1, are tightly controlled by activation of N-methyl-D-aspartate receptors (NMDAR) containing the GluN2A subunit. Interestingly, synaptic NMDARs drive degradation of the methyltransferase in a neddylation-dependent manner. Inhibition of neddylation, the conjugation of the small ubiquitin-like protein NEDD8 to lysine residues, interrupts degradation of DNMT3A1. This results in deficits in promoter methylation of activity-dependent genes, as well as synaptic plasticity and memory formation. In turn, the underlying molecular pathway is triggered by the induction of synaptic plasticity and in response to object location learning. Collectively, the data show that plasticity-relevant signals from GluN2A-containing NMDARs control activity-dependent DNA-methylation involved in memory formation.
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Affiliation(s)
- Gonca Bayraktar
- grid.418723.b0000 0001 2109 6265RG Neuroplasticity, Leibniz Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany ,grid.5335.00000000121885934Present Address: UK Dementia Research Institute at the University of Cambridge, Island Research Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH UK
| | - PingAn Yuanxiang
- grid.418723.b0000 0001 2109 6265RG Neuroplasticity, Leibniz Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany
| | - Alessandro D. Confettura
- grid.418723.b0000 0001 2109 6265RG Neuroplasticity, Leibniz Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany
| | - Guilherme M. Gomes
- grid.418723.b0000 0001 2109 6265RG Neuroplasticity, Leibniz Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany ,grid.5807.a0000 0001 1018 4307Center for Behavioral Brain Sciences, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Syed A. Raza
- grid.5807.a0000 0001 1018 4307Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke University, Leipziger Str. 44, Haus 91, 39120 Magdeburg, Germany
| | - Oliver Stork
- grid.5807.a0000 0001 1018 4307Center for Behavioral Brain Sciences, Otto von Guericke University, 39120 Magdeburg, Germany ,grid.5807.a0000 0001 1018 4307Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke University, Leipziger Str. 44, Haus 91, 39120 Magdeburg, Germany
| | - Shoji Tajima
- grid.136593.b0000 0004 0373 3971Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871 Osaka Japan
| | - Isao Suetake
- grid.412000.70000 0004 0640 6482Department of Nutritional Sciences, Faculty of Nutritional Sciences, Nakamura Gakuen University, Fukuoka, Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Organic Chemistry, Institute for Protein Research, Osaka University, Suita, Japan ,grid.136593.b0000 0004 0373 3971Center for Twin Research, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Anna Karpova
- grid.418723.b0000 0001 2109 6265RG Neuroplasticity, Leibniz Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany ,grid.5807.a0000 0001 1018 4307Center for Behavioral Brain Sciences, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Ferah Yildirim
- grid.6363.00000 0001 2218 4662NeuroCure Clinical Research Center & Department of Neuropsychiatry at Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Virchowweg 6, Charitéplatz 1, 10117 Berlin, Germany
| | - Michael R. Kreutz
- grid.418723.b0000 0001 2109 6265RG Neuroplasticity, Leibniz Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany ,grid.5807.a0000 0001 1018 4307Center for Behavioral Brain Sciences, Otto von Guericke University, 39120 Magdeburg, Germany ,Leibniz Group ‘Dendritic Organelles and Synaptic Function’, ZMNH, 20251 Hamburg, Germany ,grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
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Asada M, Hayashi H, Murakami K, Kikuiri K, Kaneko R, Yuan B, Takagi N. Investigating the Relationship Between Neuronal Cell Death and Early DNA Methylation After Ischemic Injury. Front Neurosci 2020; 14:581915. [PMID: 33177984 PMCID: PMC7591788 DOI: 10.3389/fnins.2020.581915] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/11/2020] [Indexed: 12/18/2022] Open
Abstract
Cerebral ischemia induces neuronal cell death and causes various kinds of brain dysfunction. Therefore, prevention of neuronal cell death is most essential for protection of the brain. On the other hand, it has been reported that epigenetics including DNA methylation plays a pivotal role in pathogenesis of some diseases such as cancer. Accumulating evidences indicate that aberrant DNA methylation is related to cell death. However, DNA methylation after cerebral ischemia has not been fully understood yet. The aim of this present study was to investigate the relationships between DNA methylation and neuronal cell death after cerebral ischemia. We examined DNA methylation under the ischemic condition by using transient middle cerebral artery occlusion and reperfusion (MCAO/R) model rats and N-methyl-D-aspartate (NMDA)–treated cortical neurons in primary culture. In this study, we demonstrated that DNA methylation increased in these neurons 24 h after MCAO/R and that DNA methylation, possibly through activation of DNA methyltransferases (DNMT) 3a, increased in such neurons immediately after NMDA treatment. Furthermore, NMDA-treated neurons were protected by treatment with a DNMT inhibitor that were accompanied by inhibition of DNA methylation. Our results showed that DNA methylation would be an initiation factor of neuronal cell death and that inhibition of such methylation could become an effective therapeutic strategy for stroke.
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Affiliation(s)
- Mayumi Asada
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Hideki Hayashi
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Kenjiro Murakami
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Kento Kikuiri
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Ryotaro Kaneko
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Bo Yuan
- Laboratory of Pharmacology, Faculty of Pharmacy and Pharmaceutical Sciences, School of Pharmacy, Josai University, Sakado, Japan
| | - Norio Takagi
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
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Alcohol as an early life stressor: Epigenetics, metabolic, neuroendocrine and neurobehavioral implications. Neurosci Biobehav Rev 2020; 118:654-668. [PMID: 32976915 DOI: 10.1016/j.neubiorev.2020.08.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/18/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
Abstract
Ethanol exposure during gestation is an early life stressor that profoundly dysregulates structure and functions of the embryonal nervous system, altering the cognitive and behavioral development. Such dysregulation is also achieved by epigenetic mechanisms, which, altering the chromatin structure, redraw the entire pattern of gene expression. In parallel, an oxidative stress response at the cellular level and a global upregulation of neuroendocrine stress response, regulated by the HPA axis, exist and persist in adulthood. This neurobehavioral framework matches those observed in other psychiatric diseases such as mood diseases, depression, autism; those early life stressing events, although probably triggered by specific and different epigenetic mechanisms, give rise to largely overlapping neurobehavioral phenotypes. An early diagnosis of prenatal alcohol exposure, using reliable markers of ethanol intake, together with a deeper understanding of the pathogenic mechanisms, some of them reversible by their nature, can offer a temporal "window" of intervention. Supplementing a mother's diet with protective and antioxidant substances in addition to supportive psychological therapies can protect newborns from being affected.
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60
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Santiago M, Antunes C, Guedes M, Iacovino M, Kyba M, Reik W, Sousa N, Pinto L, Branco MR, Marques CJ. Tet3 regulates cellular identity and DNA methylation in neural progenitor cells. Cell Mol Life Sci 2020; 77:2871-2883. [PMID: 31646359 PMCID: PMC7326798 DOI: 10.1007/s00018-019-03335-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/26/2019] [Accepted: 10/03/2019] [Indexed: 12/21/2022]
Abstract
TET enzymes oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), a process thought to be intermediary in an active DNA demethylation mechanism. Notably, 5hmC is highly abundant in the brain and in neuronal cells. Here, we interrogated the function of Tet3 in neural precursor cells (NPCs), using a stable and inducible knockdown system and an in vitro neural differentiation protocol. We show that Tet3 is upregulated during neural differentiation, whereas Tet1 is downregulated. Surprisingly, Tet3 knockdown led to a de-repression of pluripotency-associated genes such as Oct4, Nanog or Tcl1, with concomitant hypomethylation. Moreover, in Tet3 knockdown NPCs, we observed the appearance of OCT4-positive cells forming cellular aggregates, suggesting de-differentiation of the cells. Notably, Tet3 KD led to a genome-scale loss of DNA methylation and hypermethylation of a smaller number of CpGs that are located at neurogenesis-related genes and at imprinting control regions (ICRs) of Peg10, Zrsr1 and Mcts2 imprinted genes. Overall, our results suggest that TET3 is necessary to maintain silencing of pluripotency genes and consequently neural stem cell identity, possibly through regulation of DNA methylation levels in neural precursor cells.
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Affiliation(s)
- Mafalda Santiago
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal
| | - Claudia Antunes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal
| | - Marta Guedes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal
| | - Michelina Iacovino
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Medical Genetics, Department of Pediatrics, Harbor UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA, 90502, USA
| | - Michael Kyba
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- The Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal
| | - Luísa Pinto
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal
| | - Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
| | - C Joana Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal.
- Department of Genetics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.
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Kyono Y, Raj S, Sifuentes CJ, Buisine N, Sachs L, Denver RJ. DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain. Dev Biol 2020; 462:180-196. [PMID: 32240642 PMCID: PMC7251973 DOI: 10.1016/j.ydbio.2020.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/28/2020] [Accepted: 03/23/2020] [Indexed: 01/07/2023]
Abstract
Methylation of cytosine residues in DNA influences chromatin structure and gene transcription, and its regulation is crucial for brain development. There is mounting evidence that DNA methylation can be modulated by hormone signaling. We analyzed genome-wide changes in DNA methylation and their relationship to gene regulation in the brain of Xenopus tadpoles during metamorphosis, a thyroid hormone-dependent developmental process. We studied the region of the tadpole brain containing neurosecretory neurons that control pituitary hormone secretion, a region that is highly responsive to thyroid hormone action. Using Methylated DNA Capture sequencing (MethylCap-seq) we discovered a diverse landscape of DNA methylation across the tadpole neural cell genome, and pairwise stage comparisons identified several thousand differentially methylated regions (DMRs). During the pre-to pro-metamorphic period, the number of DMRs was lowest (1,163), with demethylation predominating. From pre-metamorphosis to metamorphic climax DMRs nearly doubled (2,204), with methylation predominating. The largest changes in DNA methylation were seen from metamorphic climax to the completion of metamorphosis (2960 DMRs), with 80% of the DMRs representing demethylation. Using RNA sequencing, we found negative correlations between differentially expressed genes and DMRs localized to gene bodies and regions upstream of transcription start sites. DNA demethylation at metamorphosis revealed by MethylCap-seq was corroborated by increased immunoreactivity for the DNA demethylation intermediates 5-hydroxymethylcytosine and 5-carboxymethylcytosine, and the methylcytosine dioxygenase ten eleven translocation 3 that catalyzes DNA demethylation. Our findings show that the genome of tadpole neural cells undergoes significant changes in DNA methylation during metamorphosis, and these changes likely influence chromatin architecture, and gene regulation programs occurring during this developmental period.
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Affiliation(s)
- Yasuhiro Kyono
- Neuroscience Graduate Program, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Samhitha Raj
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christopher J Sifuentes
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nicolas Buisine
- UMR-7221, Centre National de la recherche scientifique (CNRS), Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Laurent Sachs
- UMR-7221, Centre National de la recherche scientifique (CNRS), Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Robert J Denver
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, 48109, USA.
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Vaher K, Anier K, Jürgenson M, Harro J, Kalda A. Cocaine-induced changes in behaviour and DNA methylation in rats are influenced by inter-individual differences in spontaneous exploratory activity. J Psychopharmacol 2020; 34:680-692. [PMID: 32338111 DOI: 10.1177/0269881120916137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Individual differences in behavioural traits influence susceptibility to addictive disorders. Drug addiction involves changes in gene expression, proposed to occur via DNA methylation (DNAm). AIMS To investigate DNAm changes in reward-related brain structures (nucleus accumbens (NAc), lateral habenula (LHb)) in response to cocaine exposure in rats differing in spontaneous exploratory activity. METHODS Rats were observed in the exploration box and categorised as high- (HE) or low explorers (LE). Rats were administered vehicle or cocaine (12 mg/kg, i.p.) for 7 days, followed by a 14-day withdrawal period and cocaine challenge (7 mg/kg); horizontal locomotor activity was recorded. Brain tissue was dissected after 24 h; we analysed messenger RNA (mRNA) and activity levels of epigenetic DNA modifiers (DNMTs and TETs) as well as mRNA and promoter methylation levels at selected genes previously linked to addictive behaviours. RESULTS The cocaine challenge dose stimulated locomotor activity in both LE- and HE rats only when administered after a repeated cocaine schedule, suggesting development of behavioural sensitisation. Quantitative polymerase chain reaction analyses demonstrated higher basal expression of Dnmt3a, Tet2 and Tet3 in the LHb of HE- vs. LE rats, and we observed differential effects of cocaine exposure on the expression and activity of epigenetic DNA modifiers in the NAc and LHb of HE- and LE rats. Furthermore, cocaine exposure differentially altered promoter methylation levels of A2AR, Ppp1cc, and Taar7b in the NAc and LHb of HE- and LE rats. CONCLUSIONS DNAm might play a role in the HE- and LE phenotypes as well as mediate behavioural effects of LE- and HE rats in response to drugs of abuse.
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Affiliation(s)
- Kadi Vaher
- Department of Psychology, University of Tartu, Tartu, Estonia
| | - Kaili Anier
- Department of Pharmacology, University of Tartu, Tartu, Estonia
| | | | - Jaanus Harro
- Department of Psychology, University of Tartu, Tartu, Estonia
| | - Anti Kalda
- Department of Pharmacology, University of Tartu, Tartu, Estonia
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63
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Desai D, Pethe P. Polycomb repressive complex 1: Regulators of neurogenesis from embryonic to adult stage. J Cell Physiol 2020; 235:4031-4045. [PMID: 31608994 DOI: 10.1002/jcp.29299] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/27/2019] [Indexed: 02/05/2023]
Abstract
Development of vertebrate nervous system is a complex process which involves differential gene expression and disruptions in this process or in the mature brain, may lead to neurological disorders and diseases. Extensive work that spanned several decades using rodent models and recent work on stem cells have helped uncover the intricate process of neuronal differentiation and maturation. There are various morphological changes, genetic and epigenetic modifications which occur during normal mammalian neural development, one of the chromatin modifications that controls vital gene expression are the posttranslational modifications on histone proteins, that controls accessibility of translational machinery. Among the histone modifiers, polycomb group proteins (PcGs), such as Ezh2, Eed and Suz12 form large protein complexes-polycomb repressive complex 2 (PRC2); while Ring1b and Bmi1 proteins form core of PRC1 along with accessory proteins such as Cbx, Hph, Rybp and Pcgfs catalyse histone modifications such as H3K27me3 and H2AK119ub1. PRC1 proteins are known to play critical role in X chromosome inactivation in females but they also repress the expression of key developmental genes and tightly regulate the mammalian neuronal development. In this review we have discussed the signalling pathways, morphogens and nuclear factors that initiate, regulate and maintain cells of the nervous system. Further, we have extensively reviewed the recent literature on the role of Ring1b and Bmi1 in mammalian neuronal development and differentiation; as well as highlighted questions that are still unanswered.
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Affiliation(s)
- Divya Desai
- Department of Biological Sciences, Sunandan Divatia School of Science (SDSOS), Narsee Monjee Institute of Management Studies (NMIMS) deemed-to-be University, Mumbai, India
| | - Prasad Pethe
- Symbiosis Centre for Stem Cell Research (SCSCR), Symbiosis International University (SIU), Pune, India
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64
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Kovács T, Szabó-Meleg E, Ábrahám IM. Estradiol-Induced Epigenetically Mediated Mechanisms and Regulation of Gene Expression. Int J Mol Sci 2020; 21:ijms21093177. [PMID: 32365920 PMCID: PMC7246826 DOI: 10.3390/ijms21093177] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/22/2020] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
Gonadal hormone 17β-estradiol (E2) and its receptors are key regulators of gene transcription by binding to estrogen responsive elements in the genome. Besides the classical genomic action, E2 regulates gene transcription via the modification of epigenetic marks on DNA and histone proteins. Depending on the reaction partner, liganded estrogen receptor (ER) promotes DNA methylation at the promoter or enhancer regions. In addition, ERs are important regulators of passive and active DNA demethylation. Furthermore, ERs cooperating with different histone modifying enzymes and chromatin remodeling complexes alter gene transcription. In this review, we survey the basic mechanisms and interactions between estrogen receptors and DNA methylation, demethylation and histone modification processes as well as chromatin remodeling complexes. The particular relevance of these mechanisms to physiological processes in memory formation, embryonic development, spermatogenesis and aging as well as in pathophysiological changes in carcinogenesis is also discussed.
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Affiliation(s)
- Tamás Kovács
- Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Center, University of Pécs, H-7624 Pécs, Hungary;
| | - Edina Szabó-Meleg
- Department of Biophysics, Medical School, University of Pécs, H-7624 Pécs, Hungary;
| | - István M. Ábrahám
- Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Center, University of Pécs, H-7624 Pécs, Hungary;
- Correspondence:
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65
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He F, Wu H, Zhou L, Lin Q, Cheng Y, Sun YE. Tet2-mediated epigenetic drive for astrocyte differentiation from embryonic neural stem cells. Cell Death Discov 2020; 6:30. [PMID: 32377393 PMCID: PMC7190615 DOI: 10.1038/s41420-020-0264-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/04/2020] [Accepted: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
DNA methylation and demethylation at CpG di-nucleotide sites plays important roles in cell fate specification of neural stem cells (NSCs). We have previously reported that DNA methyltransferases, Dnmt1and Dnmt3a, serve to suppress precocious astrocyte differentiation from NSCs via methylation of astroglial lineage genes. However, whether active DNA demethylase also participates in astrogliogenesis remains undetermined. In this study, we discovered that a Ten-eleven translocation (Tet) protein, Tet2, which was critically involved in active DNA demethylation through oxidation of 5-Methylcytosine (5mC), drove astrocyte differentiation from NSCs by demethylation of astroglial lineage genes including Gfap. Moreover, we found that an NSC-specific bHLH transcription factor Olig2 was an upstream inhibitor for Tet2 expression through direct association with the Tet2 promoter, and indirectly inhibited astrocyte differentiation. Our research not only revealed a brand-new function of Tet2 to promote NSC differentiation into astrocytes, but also a novel mechanism for Olig2 to inhibit astrocyte formation.
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Affiliation(s)
- Fei He
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200092 China
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Liqiang Zhou
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200092 China
| | - Quan Lin
- Department of Psychiatry and Biobehavioral Sciences, Intellectual Development and Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Yin Cheng
- Department of Psychiatry and Biobehavioral Sciences, Intellectual Development and Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Yi E. Sun
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200092 China
- Department of Psychiatry and Biobehavioral Sciences, Intellectual Development and Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
- Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, 200092 China
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66
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Li Z, Ma Y, Wang G, Wang H, Dai Y, Zhu Y, Chen S, Zheng X, Sun F. Overexpression of human-derived DNMT3A induced intergenerational inheritance of DNA methylation and gene expression variations in rat brain and testis. Epigenetics 2020; 15:1107-1120. [PMID: 32338148 DOI: 10.1080/15592294.2020.1749962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
In mammals, DNA methylation patterns are established by various types of DNA methyltransferases and can be stably passed on during cell division, thus creating a paradigm for epigenetic regulation that can mediate long-lasting changes in gene expression even when the initial triggering signal has disappeared. Although functional deficiency of DNMT3A, one of the methyltransferases, leads to abnormal DNA methylation patterns that result in developmental deficits in mammals, the impacts of its overexpression on tissue gene expression and DNA methylation patterns remain unclear. Here, our previously established hDNMT3A transgenic rat model and mRNA sequencing and bisulphite sequencing PCR were used to analyse the impact of hDNMT3A overexpression on tissue transcriptome and methylome, and whether the impact could be inherited intergenerationally was subsequently investigated. Our results revealed that the overexpression of hDNMT3A could induce notable gene expression variations in rat testis and brain. More importantly, 36.02% and 38.89% of these variations could be intergenerationally inherited to offspring without the transmission of the initial endogenic trigger in the brain and testis, respectively. Furthermore, we found that intergenerationally inherited DNA methylation variations in their promoters and exons could be the underlying mechanism. Compared with inheritable variations that were passively induced by environmental factors, these variations were actively induced by endogenous epigenetic modifiers. This study provided evidence for the epigenetic inheritance of endogenous factors that actively induce gene expression and DNA methylation variations; however, more studies are needed to determine the number of generations that these variations can be stably inherited.
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Affiliation(s)
- Zhenhua Li
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease , Shanghai, China
| | - Yuanwu Ma
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medicine College, Chinese Academy of Medical Sciences , Beijing, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Diseases, Institute of Laboratory Animal Science, Peking Union Medicine College, Chinese Academy of Medical Sciences , Beijing, China
| | - Guishuan Wang
- Medical School, Institute of Reproductive Medicine, Nantong University , Nantong, Jiangsu, China
| | - Hanshu Wang
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease , Shanghai, China
| | - Yubing Dai
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease , Shanghai, China
| | - Yu Zhu
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease , Shanghai, China
| | - Shitao Chen
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease , Shanghai, China
| | - Xiaoguo Zheng
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease , Shanghai, China
| | - Fei Sun
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease , Shanghai, China.,Medical School, Institute of Reproductive Medicine, Nantong University , Nantong, Jiangsu, China
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67
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Blossom SJ, Melnyk SB, Simmen FA. Complex epigenetic patterns in cerebellum generated after developmental exposure to trichloroethylene and/or high fat diet in autoimmune-prone mice. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:583-594. [PMID: 31894794 PMCID: PMC7350281 DOI: 10.1039/c9em00514e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trichloroethylene (TCE) is an environmental contaminant associated with immune-mediated inflammatory disorders and neurotoxicity. Based on known negative effects of developmental overnutrition on neurodevelopment, we hypothesized that developmental exposure to high fat diet (HFD) consisting of 40% kcal fat would enhance neurotoxicity of low-level (6 μg per kg per day) TCE exposure in offspring over either stressor alone. Male offspring were evaluated at ∼6 weeks of age after exposure beginning 4 weeks preconception in the dams until weaning. TCE, whether used as a single exposure or together with HFD, appeared to be more robust than HFD alone in altering one-carbon metabolites involved in glutathione redox homeostasis and methylation capacity. In contrast, opposing effects of expression of key enzymes related to DNA methylation related to HFD and TCE exposure were observed. The mice generated unique patterns of anti-brain antibodies detected by western blotting attributable to both TCE and HFD. Taken together, developmental exposure to TCE and/or HFD appear to act in complex ways to alter brain biomarkers in offspring.
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Affiliation(s)
- Sarah J Blossom
- Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, AR 72202, USA.
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68
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Hossan T, Kundu S, Alam SS, Nagarajan S. Epigenetic Modifications Associated with the Pathogenesis of Type 2 Diabetes Mellitus. Endocr Metab Immune Disord Drug Targets 2020; 19:775-786. [PMID: 30827271 DOI: 10.2174/1871530319666190301145545] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/10/2018] [Accepted: 12/28/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND OBJECTIVE Type 2 diabetes mellitus (T2DM) is a multifactorial metabolic disorder. Pancreatic β-cell dysfunction and insulin resistance are the most common and crucial events of T2DM. Increasing evidence suggests the association of epigenetic modifications with the pathogenesis of T2DM through the changes in important biological processes including pancreatic β- cell differentiation, development and maintenance of normal β-cell function. Insulin sensitivity by the peripheral glucose uptake tissues is also changed by the altered epigenetic mechanisms. In this review, we discussed the major epigenetic alterations and their effects on β-cell function, insulin secretion and insulin resistance in context of T2DM. METHODS We investigated the presently available epigenetic modifications including DNA methylation, posttranslational histone modifications, ATP-dependent chromatin remodeling and non-coding RNAs related to the pathogenesis of T2DM. Published literatures on this topic were searched both on Google Scholar and Pubmed with related keywords and investigated for relevant information. RESULTS The epigenetic modifications introduce changes in gene expression which are essential for appropriate β-cell development and functions, insulin secretion and sensitivity resulting in the pathogenesis of T2DM. Interestingly, T2DM could also be a prominent reason for the mentioned epigenetic alterations. CONCLUSION This review article emphasized on the epigenetic modifications associated with T2DM and discussed the consequences in deterioration of the disease condition.
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Affiliation(s)
- Tareq Hossan
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Shoumik Kundu
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Sayeda Sadia Alam
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Sankari Nagarajan
- Cancer Research UK Cambridge Institute (CRUK-CI), University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, United Kingdom
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69
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Li Y, Lv Z, Zhang J, Ma Q, Li Q, Song L, Gong L, Zhu Y, Li X, Hao Y, Yang Y. Profiling of differentially expressed circular RNAs in peripheral blood mononuclear cells from Alzheimer's disease patients. Metab Brain Dis 2020; 35:201-213. [PMID: 31834549 DOI: 10.1007/s11011-019-00497-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/12/2019] [Indexed: 02/08/2023]
Abstract
Expression of circular RNA (circRNA), a class of noncoding RNAs that regulates gene expression, is altered in Alzheimer's disease. This study profiled differentially expressed circRNAs in peripheral blood mononuclear cells (PBMCs) from five patients with Alzheimer's disease compared to healthy controls using circRNA microarrays. We identified a total of 4060 differentially expressed circRNAs (1990 upregulated and 2070 downregulated) in Alzheimer's disease patients. Among these circRNAs, 10 randomly selected circRNAs were verified using qRT-PCR. The top 10 upregulated and downregulated circRNAs were used to predict their target miRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that these differentially expressed circRNAs were strongly associated with inflammation, metabolism, and immune responses, which are all risk factors for Alzheimer's disease. The circRNA-miRNA-mRNA network was most involved in the MAPK, mTOR, AMPK, and WNT signaling pathways in Alzheimer's disease. In conclusion, the current study demonstrated the importance of circRNAs in Alzheimer's disease development. Future studies will evaluate some of these circRNAs as biomarkers for early disease detection and to develop therapeutic strategies to clinically control Alzheimer's disease progression.
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Affiliation(s)
- Yanxin Li
- Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Zhanyun Lv
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Jing Zhang
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Qianqian Ma
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Qiuhua Li
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Li Song
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Li Gong
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Yunliang Zhu
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Xiangyuan Li
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Yanlei Hao
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China.
- Jining Medical University, Jining, 272067, China.
| | - Yan Yang
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China.
- Jining Medical University, Jining, 272067, China.
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70
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Urb M, Niinep K, Matsalu T, Kipper K, Herodes K, Zharkovsky A, Timmusk T, Anier K, Kalda A. The role of DNA methyltransferase activity in cocaine treatment and withdrawal in the nucleus accumbens of mice. Addict Biol 2020; 25:e12720. [PMID: 30730091 DOI: 10.1111/adb.12720] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/07/2018] [Accepted: 01/08/2019] [Indexed: 01/02/2023]
Abstract
An increasing number of reports have provided crucial evidence that epigenetic modifications, such as DNA methylation, may be involved in initiating and establishing psychostimulant-induced stable changes at the cellular level by coordinating the expression of gene networks, which then manifests as long-term behavioral changes. In this study, we evaluated the enzyme activity of DNA methyltransferases (DNMTs) after cocaine treatment and during withdrawal. Furthermore, we studied how genetic or pharmacological inhibition of DNMTs in mouse nucleus accumbens (NAc) affects the induction and expression of cocaine-induced behavioral sensitization. Our results showed that after silencing Dnmt3a in the NAc during the induction phase of cocaine-induced sensitization, overall DNMT activity decreases, correlating negatively with behavioral sensitization. Reduced Dnmt3a mRNA during this phase was the largest contributing factor for decreased DNMT activity. Cocaine withdrawal and a challenge dose increased DNMT activity in the NAc, which was associated with the expression of behavioral sensitization. Long-term selective Dnmt3a transcription silencing in the NAc did not alter DNMT activity or the expression of cocaine-induced behavioral sensitization. However, bilateral intra-NAc injection of a non-specific inhibitor of DNMT (RG108) during withdrawal from cocaine decreased DNMT activity in the NAc and had a small effect on the expression of cocaine-induced behavioral sensitization. Thus, cocaine treatment and withdrawal is associated with biphasic changes in DNMT activity in the NAc, and the expression of behavioral sensitization decreases with non-selective inhibition of DNMT but not with selective silencing of Dnmt3a.
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Affiliation(s)
- Mari Urb
- Department of PharmacologyInstitute of Biomedicine and Translational Medicine, University of Tartu Estonia
| | - Kerly Niinep
- Department of PharmacologyInstitute of Biomedicine and Translational Medicine, University of Tartu Estonia
| | - Terje Matsalu
- Department of PharmacologyInstitute of Biomedicine and Translational Medicine, University of Tartu Estonia
| | - Karin Kipper
- Institute of Chemistry, University of Tartu Estonia
| | - Koit Herodes
- Institute of Chemistry, University of Tartu Estonia
| | - Alexander Zharkovsky
- Department of PharmacologyInstitute of Biomedicine and Translational Medicine, University of Tartu Estonia
| | - Tõnis Timmusk
- Institute of Chemistry and Biotechnology, Tallinn University of Technology Estonia
| | - Kaili Anier
- Department of PharmacologyInstitute of Biomedicine and Translational Medicine, University of Tartu Estonia
| | - Anti Kalda
- Department of PharmacologyInstitute of Biomedicine and Translational Medicine, University of Tartu Estonia
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71
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Onuzulu CD, Rotimi OA, Rotimi SO. Epigenetic modifications associated with in utero exposure to endocrine disrupting chemicals BPA, DDT and Pb. REVIEWS ON ENVIRONMENTAL HEALTH 2019; 34:309-325. [PMID: 31271561 DOI: 10.1515/reveh-2018-0059] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are xenobiotics which adversely modify the hormone system. The endocrine system is most vulnerable to assaults by endocrine disruptors during the prenatal and early development window, and effects may persist into adulthood and across generations. The prenatal stage is a period of vulnerability to environmental chemicals because the epigenome is usually reprogrammed during this period. Bisphenol A (BPA), lead (Pb), and dichlorodiphenyltrichloroethane (DDT) were chosen for critical review because they have become serious public health concerns globally, especially in Africa where they are widely used without any regulation. In this review, we introduce EDCs and describe the various modes of action of EDCs and the importance of the prenatal and developmental windows to EDC exposure. We give a brief overview of epigenetics and describe the various epigenetic mechanisms: DNA methylation, histone modifications and non-coding RNAs, and how each of them affects gene expression. We then summarize findings from previous studies on the effects of prenatal exposure to the endocrine disruptors BPA, Pb and DDT on each of the previously described epigenetic mechanisms. We also discuss how the epigenetic alterations caused by these EDCs may be related to disease processes.
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Affiliation(s)
- Chinonye Doris Onuzulu
- Department of Biochemistry and Molecular Biology Research Laboratory, Covenant University, Ota, Ogun State, Nigeria
| | - Oluwakemi Anuoluwapo Rotimi
- Department of Biochemistry and Molecular Biology Research Laboratory, Covenant University, Ota, Ogun State, Nigeria
| | - Solomon Oladapo Rotimi
- Department of Biochemistry and Molecular Biology Research Laboratory, Covenant University, Ota, Ogun State, Nigeria
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72
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Abstract
The prevalence of autism spectrum disorder (ASD) has been increasing steadily over the last 20 years; however, the molecular basis for the majority of ASD cases remains unknown. Recent advances in next-generation sequencing and detection of DNA modifications have made methylation-dependent regulation of transcription an attractive hypothesis for being a causative factor in ASD etiology. Evidence for abnormal DNA methylation in ASD can be seen on multiple levels, from genetic mutations in epigenetic machinery to loci-specific and genome-wide changes in DNA methylation. Epimutations in DNA methylation can be acquired throughout life, as global DNA methylation reprogramming is dynamic during embryonic development and the early postnatal period that corresponds to the peak time of synaptogenesis. However, technical advances and causative evidence still need to be established before abnormal DNA methylation and ASD can be confidently associated.
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Affiliation(s)
- Martine W Tremblay
- Program in Genetics and Genomics, Duke University, Durham, North Carolina 27710, USA
| | - Yong-Hui Jiang
- Program in Genetics and Genomics, Duke University, Durham, North Carolina 27710, USA.,Departments of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA;
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73
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MacKay H, Scott CA, Duryea JD, Baker MS, Laritsky E, Elson AE, Garland T, Fiorotto ML, Chen R, Li Y, Coarfa C, Simerly RB, Waterland RA. DNA methylation in AgRP neurons regulates voluntary exercise behavior in mice. Nat Commun 2019; 10:5364. [PMID: 31792207 PMCID: PMC6889160 DOI: 10.1038/s41467-019-13339-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 10/16/2019] [Indexed: 12/16/2022] Open
Abstract
DNA methylation regulates cell type-specific gene expression. Here, in a transgenic mouse model, we show that deletion of the gene encoding DNA methyltransferase Dnmt3a in hypothalamic AgRP neurons causes a sedentary phenotype characterized by reduced voluntary exercise and increased adiposity. Whole-genome bisulfite sequencing (WGBS) and transcriptional profiling in neuronal nuclei from the arcuate nucleus of the hypothalamus (ARH) reveal differentially methylated genomic regions and reduced expression of AgRP neuron-associated genes in knockout mice. We use read-level analysis of WGBS data to infer putative ARH neural cell types affected by the knockout, and to localize promoter hypomethylation and increased expression of the growth factor Bmp7 to AgRP neurons, suggesting a role for aberrant TGF-β signaling in the development of this phenotype. Together, these data demonstrate that DNA methylation in AgRP neurons is required for their normal epigenetic development and neuron-specific gene expression profiles, and regulates voluntary exercise behavior. AgRP neurons in the hypothalamic arcuate nucleus (ARH) are involved in regulating hunger and energy balance. Here the authors show that knockout of the DNA methyltransferase Dnmt3a in AgRP neurons of the ARH leads to a reduction in voluntary exercise along with numerous epigenetic and gene expression changes in ARH neurons.
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Affiliation(s)
- Harry MacKay
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - C Anthony Scott
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - Jack D Duryea
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - Maria S Baker
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - Eleonora Laritsky
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - Amanda E Elson
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Marta L Fiorotto
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA.,Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rui Chen
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yumei Li
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Cristian Coarfa
- Department of Molecular & Cell Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard B Simerly
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Robert A Waterland
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA. .,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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74
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Lavery LA, Zoghbi HY. The distinct methylation landscape of maturing neurons and its role in Rett syndrome pathogenesis. Curr Opin Neurobiol 2019; 59:180-188. [PMID: 31542590 PMCID: PMC6892602 DOI: 10.1016/j.conb.2019.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
Rett syndrome (RTT) is one of the most common causes of intellectual and developmental disabilities in girls, and is caused by mutations in the gene encoding methyl-CpG binding protein 2 (MECP2). Here we will review our current understanding of RTT, the landscape of pathogenic mutations and function of MeCP2, and culminate with recent advances elucidating the distinct DNA methylation landscape in the brain that may explain why disease symptoms are delayed and selective to the nervous system.
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Affiliation(s)
- Laura A Lavery
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huda Y Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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75
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Radhakrishnan S, Trentz OA, Reddy MS, Rela M, Kandasamy M, Sellathamby S. In vitro transdifferentiation of human adipose tissue-derived stem cells to neural lineage cells - a stage-specific incidence. Adipocyte 2019; 8:164-177. [PMID: 31033391 PMCID: PMC6768268 DOI: 10.1080/21623945.2019.1607424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The present Study investigated the intrinsic ability of adipose tissue-derived stem cells (ADSCs) and their neural transdifferentiation in a stage-specific manner. Woodbury’s Chemical induction was implemented with modifications to achieve neural transdifferentiation. In Group I, ADSCs were preinduced with β-mercaptoethanol (β-ME) and later, with neural induction medium (NIM). In Group II, ADSCs were directly treated with NIM. In Group III, a DNA methyltransferase (DNMT) inhibitor 5-azacytidine was applied to understand whether transdifferentiation is controlled by epigenetic marks. Irrespective of the presence of (β-ME), the differentiation protocol resulted in glial-lineage cells. Group III produced poorly -differentiated neural cells with neuron-specific enolase positivity. A neuroprogenitor stage (NPC) was identified at d 11 after induction only in Group I. In other groups, this stage was not morphologically distinct. We explored the stage-specific incidence NPC, by alternatively treating them with basic fibroblast growth factor (bFGF), and antioxidants to validate if different signalling could cause varied outcomes (Group IV). They differentiated into neurons, as defined by cell polarity and expression of specific proteins. Meanwhile, neuroprogenitors exposed to NIM (Group I) produced glial-lineage cells. Further refinement and study of the occurrence and terminal differentiation of neuroprogenitors would identify a promising source for neural tissue replacement.
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Affiliation(s)
- Subathra Radhakrishnan
- National Foundation for Liver Research (NFLR), Gleneagles Global Health City, Chennai, India
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, India
| | - Omana Anna Trentz
- MIOT Institute of Research (MIR), MIOT International, Chennai, India
| | - Mettu Srinivas Reddy
- National Foundation for Liver Research (NFLR), Gleneagles Global Health City, Chennai, India
- Institute of Liver Disease and Transplantation, Gleneagles Global Health City, Chennai, India
| | - Mohamed Rela
- National Foundation for Liver Research (NFLR), Gleneagles Global Health City, Chennai, India
- Institute of Liver Disease and Transplantation, Gleneagles Global Health City, Chennai, India
| | - Mahesh Kandasamy
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, India
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76
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Green AL, Eid A, Zhan L, Zarbl H, Guo GL, Richardson JR. Epigenetic Regulation of the Ontogenic Expression of the Dopamine Transporter. Front Genet 2019; 10:1099. [PMID: 31749842 PMCID: PMC6844290 DOI: 10.3389/fgene.2019.01099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/11/2019] [Indexed: 01/19/2023] Open
Abstract
The dopamine transporter (DAT) is a plasma membrane transport protein responsible for regulating the duration and intensity of dopaminergic signaling. Altered expression of DAT is linked to neurodevelopmental disorders, including attention deficit hyperactivity disorder and autism spectrum disorder, and is shown to contribute to the response of psychotropic drugs and neurotoxicants. Although the postnatal levels of DAT have been characterized, there are few data regarding the mechanisms that regulate postnatal DAT expression. Here, we examine the ontogeny of DAT mRNA from postnatal days 0 to 182 in the rat brain and define a role for epigenetic mechanisms regulating DAT expression. DAT mRNA and protein significantly increased between PND 0 and 6 months in rat midbrain and striatum, respectively. The epigenetic modifiers Dnmt1, Dnmt3a, Dnmt3b, and Hdac2 demonstrated age associated decreases in mRNA expression whereas Hdac5 and Hdac8 showed increased mRNA expression with age. Chromatin immunoprecipitation studies revealed increased protein enrichment of acetylated histone 3 at lysines 9 and 14 and the dopaminergic transcription factors Nurr1 and Pitx3 within the DAT promoter in an age-related manner. Together these studies provide evidence for the role of epigenetic modifications in the regulation of DAT during development. The identification of these mechanisms may contribute to potential therapeutic interventions aimed at neurodevelopmental disorders of the dopaminergic system.
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Affiliation(s)
- Ashley L. Green
- Environmental and Occupational Health Sciences Institute and Department of Environmental and Occupational Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States
| | - Aseel Eid
- Department of Environmental Health Sciences, Robert Stempel School of Public Health and Social Work, Florida International University, Miami, FL, United States
| | - Le Zhan
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, United States
| | - Helmut Zarbl
- Environmental and Occupational Health Sciences Institute and Department of Environmental and Occupational Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States
| | - Grace L. Guo
- Environmental and Occupational Health Sciences Institute and Department of Environmental and Occupational Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States,Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, United States
| | - Jason R. Richardson
- Environmental and Occupational Health Sciences Institute and Department of Environmental and Occupational Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States,Department of Environmental Health Sciences, Robert Stempel School of Public Health and Social Work, Florida International University, Miami, FL, United States,*Correspondence: Jason R. Richardson,
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77
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Blanc M, Rüegg J, Scherbak N, Keiter SH. Environmental chemicals differentially affect epigenetic-related mechanisms in the zebrafish liver (ZF-L) cell line and in zebrafish embryos. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 215:105272. [PMID: 31442592 DOI: 10.1016/j.aquatox.2019.105272] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/07/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
A number of chemicals have been shown to affect epigenetic patterning and functions. Since epigenetic mechanisms regulate transcriptional networks, epigenetic changes induced by chemical exposure can represent early molecular events for long-term adverse physiological effects. Epigenetics has thus appeared as a research field of major interest within (eco)toxicological sciences. The present study aimed at measuring effects on epigenetic-related mechanisms of selected environmental chemicals (bisphenols, perfluorinated chemicals, methoxychlor, permethrin, vinclozolin and coumarin 47) in zebrafish embryos and liver cells (ZFL). Transcription of genes related to DNA methylation and histone modifications was measured and global DNA methylation was assessed in ZFL cells using the LUMA assay. The differences in results gathered from both models suggest that chemicals affect different mechanisms related to epigenetics in embryos and cells. In zebrafish embryos, exposure to bisphenol A, coumarin 47, methoxychlor and permethrin lead to significant transcriptional changes in epigenetic factors suggesting that they can impact early epigenome reprogramming related to embryonic development. In ZFL cells, significant transcriptional changes were observed upon exposure to all chemicals but coumarin 47; however, only perfluorooctane sulfonate induced significant effects on global DNA methylation. Notably, in contrast to the other tested chemicals, perfluorooctane sulfonate affected only the expression of the histone demethylase kdm5ba. In addition, kdm5ba appeared as a sensitive gene in zebrafish embryos as well. Taken together, the present results suggest a role for kdm5ba in regulating epigenetic patterns in response to chemical exposure, even though mechanisms remain unclear. To confirm these findings, further evidence is required regarding changes in site-specific histone marks and DNA methylation together with their long-term effects on physiological outcomes.
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Affiliation(s)
- Mélanie Blanc
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82, Örebro, Sweden.
| | - Joëlle Rüegg
- Institute for Environmental Medicine, Karolinska Institutet, Nobels väg 13, 171 65, Solna, Sweden
| | - Nikolai Scherbak
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82, Örebro, Sweden; Örebro Life Science Centre, School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82, Örebro, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82, Örebro, Sweden
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78
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Wang X. Stem cells in tissues, organoids, and cancers. Cell Mol Life Sci 2019; 76:4043-4070. [PMID: 31317205 PMCID: PMC6785598 DOI: 10.1007/s00018-019-03199-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/22/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022]
Abstract
Stem cells give rise to all cells and build the tissue structures in our body, and heterogeneity and plasticity are the hallmarks of stem cells. Epigenetic modification, which is associated with niche signals, determines stem cell differentiation and somatic cell reprogramming. Stem cells play a critical role in the development of tumors and are capable of generating 3D organoids. Understanding the properties of stem cells will improve our capacity to maintain tissue homeostasis. Dissecting epigenetic regulation could be helpful for achieving efficient cell reprograming and for developing new drugs for cancer treatment. Stem cell-derived organoids open up new avenues for modeling human diseases and for regenerative medicine. Nevertheless, in addition to the achievements in stem cell research, many challenges still need to be overcome for stem cells to have versatile application in clinics.
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Affiliation(s)
- Xusheng Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, 510275, China.
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79
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de Nijs L, Choe K, Steinbusch H, Schijns OEMG, Dings J, van den Hove DLA, Rutten BPF, Hoogland G. DNA methyltransferase isoforms expression in the temporal lobe of epilepsy patients with a history of febrile seizures. Clin Epigenetics 2019; 11:118. [PMID: 31426844 PMCID: PMC6701147 DOI: 10.1186/s13148-019-0721-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/02/2019] [Indexed: 11/10/2022] Open
Abstract
Background Temporal lobe epilepsy (TLE) with hippocampal sclerosis (HS) is a common pharmaco-resistant epilepsy referred for adult epilepsy surgery. Though associated with prolonged febrile seizures (FS) in childhood, the neurobiological basis for this relationship is not fully understood and currently no preventive or curative therapies are available. DNA methylation, an epigenetic mechanism catalyzed by DNA methyltransferases (DNMTs), potentially plays a pivotal role in epileptogenesis associated with FS. In an attempt to start exploring this notion, the present cross-sectional pilot study investigated whether global DNA methylation levels (5-mC and 5-hmC markers) and DNMT isoforms (DNMT1, DNMT3a1, and DNMT3a2) expression would be different in hippocampal and neocortical tissues between controls and TLE patients with or without a history of FS. Results We found that global DNA methylation levels and DNMT3a2 isoform expression were lower in the hippocampus for all TLE groups when compared to control patients, with a more significant decrease amongst the TLE groups with a history of FS. Interestingly, we showed that DNMT3a1 expression was severely diminished in the hippocampus of TLE patients with a history of FS in comparison with control and other TLE groups. In the neocortex, we found a higher expression of DNMT1 and DNMT3a1 as well as increased levels of global DNA methylation for all TLE patients compared to controls. Conclusion Together, the findings of this descriptive cross-sectional pilot study demonstrated brain region-specific changes in DNMT1 and DNMT3a isoform expression as well as global DNA methylation levels in human TLE with or without a history of FS. They highlighted a specific implication of DNMT3a isoforms in TLE after FS. Therefore, longitudinal studies that aim at targeting DNMT3a isoforms to evaluate the potential causal relationship between FS and TLE or treatment of FS-induced epileptogenesis seem warranted. Electronic supplementary material The online version of this article (10.1186/s13148-019-0721-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laurence de Nijs
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands. .,GIGA-Neurosciences, University of Liège, Liège, Belgium.
| | - Kyonghwan Choe
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands
| | - Hellen Steinbusch
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands
| | - Olaf E M G Schijns
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands.,Academic Center for Epileptology (ACE), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jim Dings
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands.,Academic Center for Epileptology (ACE), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Daniel L A van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Bart P F Rutten
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands
| | - Govert Hoogland
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands.,Academic Center for Epileptology (ACE), Maastricht University Medical Center, Maastricht, The Netherlands
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80
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Kong X, Gong Z, Zhang L, Sun X, Ou Z, Xu B, Huang J, Long D, He X, Lin X, Li Q, Xu L, Xuan A. JAK2/STAT3 signaling mediates IL-6-inhibited neurogenesis of neural stem cells through DNA demethylation/methylation. Brain Behav Immun 2019; 79:159-173. [PMID: 30763768 DOI: 10.1016/j.bbi.2019.01.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 01/10/2019] [Accepted: 01/30/2019] [Indexed: 10/27/2022] Open
Abstract
Neuroinflammation, considered as a pathological hallmark of Alzheimer's disease (AD), has been demonstrated to affect hippocampal neurogenesis and cognitive function. Interleukin-6 (IL-6) is a proinflammatory cytokine known to modulate neurogenesis. However, the mechanisms are still largely unknown. Here, we reported that IL-6 suppressed neurogenesis via a JAK2/STAT3 signaling in neural stem cells (NSCs). Importantly, we found that NeuroD1 (Neurogenic differentiation 1) gene expression, which drives NSCs neurodifferentiation, was regulated by TET3 and DNMT1 in a JAK2/STAT3-dependent manner. We further found that JAK2/STAT3 inhibition enhanced demethylation of NeuroD1 regulatory elements in IL-6-treated cells, which is related to the significant upregulation of TET3 expression as well as the decreased expression of DNMT1. Furthermore, Inhibiting JAK2/STAT3 significantly rescued the memory deficits and hippocampal neurogenesis dysfunction in APP/PS1 mice. Our data suggest that JAK2/STAT3 signaling plays a vital role in suppressing neurogenesis of NSCs exposed to IL-6 at the epigenetic level, by regulating DNA methylation/demethylation.
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Affiliation(s)
- Xuejian Kong
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China; Department of Neurology of the Sixth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511518, China
| | - Zhuo Gong
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Le Zhang
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Xiangdong Sun
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Zhenri Ou
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Biao Xu
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Jingyi Huang
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Dahong Long
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Xiaosong He
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Xiaohong Lin
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Qingqing Li
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Liping Xu
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Aiguo Xuan
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China.
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81
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Rajavelu A, Lungu C, Emperle M, Dukatz M, Bröhm A, Broche J, Hanelt I, Parsa E, Schiffers S, Karnik R, Meissner A, Carell T, Rathert P, Jurkowska RZ, Jeltsch A. Chromatin-dependent allosteric regulation of DNMT3A activity by MeCP2. Nucleic Acids Res 2019; 46:9044-9056. [PMID: 30102379 PMCID: PMC6158614 DOI: 10.1093/nar/gky715] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Despite their central importance in mammalian development, the mechanisms that regulate the DNA methylation machinery and thereby the generation of genomic methylation patterns are still poorly understood. Here, we identify the 5mC-binding protein MeCP2 as a direct and strong interactor of DNA methyltransferase 3 (DNMT3) proteins. We mapped the interaction interface to the transcriptional repression domain of MeCP2 and the ADD domain of DNMT3A and find that binding of MeCP2 strongly inhibits the activity of DNMT3A in vitro. This effect was reinforced by cellular studies where a global reduction of DNA methylation levels was observed after overexpression of MeCP2 in human cells. By engineering conformationally locked DNMT3A variants as novel tools to study the allosteric regulation of this enzyme, we show that MeCP2 stabilizes the closed, autoinhibitory conformation of DNMT3A. Interestingly, the interaction with MeCP2 and its resulting inhibition were relieved by the binding of K4 unmodified histone H3 N-terminal tail to the DNMT3A-ADD domain. Taken together, our data indicate that the localization and activity of DNMT3A are under the combined control of MeCP2 and H3 tail modifications where, depending on the modification status of the H3 tail at the binding sites, MeCP2 can act as either a repressor or activator of DNA methylation.
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Affiliation(s)
- Arumugam Rajavelu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Cristiana Lungu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Michael Dukatz
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Alexander Bröhm
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Julian Broche
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Ines Hanelt
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Sarah Schiffers
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Rahul Karnik
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas Carell
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Philipp Rathert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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82
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Amelioration of obsessive-compulsive disorder in three mouse models treated with one epigenetic drug: unraveling the underlying mechanism. Sci Rep 2019; 9:8741. [PMID: 31217515 PMCID: PMC6584622 DOI: 10.1038/s41598-019-45325-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 06/05/2019] [Indexed: 11/08/2022] Open
Abstract
Mental health disorders are manifested in families, yet cannot be fully explained by classical Mendelian genetics. Changes in gene expression via epigenetics present a plausible mechanism. Anxiety often leads to avoidant behaviors which upon repetition may become habitual, maladaptive and resistant to extinction as observed in obsessive compulsive disorders (OCD). Psychophysical models of OCD propose that anxiety (amygdala) and habits (dorsolateral striatum, DLS) may be causally linked. The amygdala activates spiny projection neurons in the DLS. Repetitive amygdala terminal stimulation in the DLS elicits long term OCD-like behavior in mice associated with circuitry changes and gene methylation-mediated decrease in the activity of protein phosphatase 1 (PP1). Treatment of OCD-like grooming behavior in Slitrk5, SAPAP3, and laser-stimulated mice with one dose of RG108 (DNA methyltransferase inhibitor), lead to marked symptom improvement lasting for at least one week as well as complete reversal of anomalous changes in circuitry and PP1 gene methylation.
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83
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Desai M, Han G, Li T, Ross MG. Programmed Epigenetic DNA Methylation-Mediated Reduced Neuroprogenitor Cell Proliferation and Differentiation in Small-for-Gestational-Age Offspring. Neuroscience 2019; 412:60-71. [PMID: 31153962 DOI: 10.1016/j.neuroscience.2019.05.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/01/2019] [Accepted: 05/22/2019] [Indexed: 12/28/2022]
Abstract
Small-for-gestational age (SGA) human newborns have an increased risk of hyperphagia and obesity, as well as a spectrum of neurologic and neurobehavioral abnormalities. We have shown that the SGA hypothalamic (appetite regulatory site) neuroprogenitor cells (NPCs) exhibit reduced proliferation and neuronal differentiation. DNA methylation (DNA methyltransferase; DNMT1) regulates neurogenesis by maintaining NPC proliferation and suppressing premature differentiation. Once differentiation ensues, DNMT1 preferentially promotes neuronal and inhibits astroglial fate. We hypothesized that the programmed dysfunction of NPC proliferation and differentiation in SGA offspring is epigenetically mediated via DNMT1. Pregnant rats received either ad libitum food (Control) or were 50% food-restricted to create SGA offspring. Primary hypothalamic NPCs from 1 day old SGA and Controls newborns were cultured and transfected with nonspecific or DNMT1-specific siRNA. NPC proliferation and protein expression of specific markers of NPC (nestin), neuroproliferative transcription factor (Hes1), neurons (Tuj1) and astrocytes (GFAP) were determined. Under basal conditions, SGA NPCs exhibited decreased DNMT1 and reduced proliferation and differentiation, as compared to Controls. In both SGA and Controls, DNMT1 siRNA in complete media inhibited NPC proliferation, consistent with reduced expression of nestin and Hes1. In differentiation media, DNMT1 siRNA decreased expression of Tuj1 but increased GFAP. In vivo data replicated these findings. In SGA offspring, impaired neurogenesis is epigenetically mediated, in part, via reduction in DNMT1 expression and suppression of Hes1 resulting in NPC differentiation. It is likely that the maturation of regions beyond the hypothalamus (e.g., cerebral cortex, hippocampus) may be impacted, contributing to poor cognitive and neurobehavioral competency in SGA offspring.
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Affiliation(s)
- Mina Desai
- Perinatal Research Laboratory, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Department of Obstetrics and Gynecology, Torrance, CA, USA; Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | - Guang Han
- Perinatal Research Laboratory, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Department of Obstetrics and Gynecology, Torrance, CA, USA
| | - Tie Li
- Perinatal Research Laboratory, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Department of Obstetrics and Gynecology, Torrance, CA, USA
| | - Michael G Ross
- Perinatal Research Laboratory, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Department of Obstetrics and Gynecology, Torrance, CA, USA; Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Obstetrics and Gynecology, Charles R. Drew University, Los Angeles, CA, USA
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84
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Sendžikaitė G, Hanna CW, Stewart-Morgan KR, Ivanova E, Kelsey G. A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice. Nat Commun 2019; 10:1884. [PMID: 31015495 PMCID: PMC6478690 DOI: 10.1038/s41467-019-09713-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/26/2019] [Indexed: 11/08/2022] Open
Abstract
DNA methyltransferases (DNMTs) deposit DNA methylation, which regulates gene expression and is essential for mammalian development. Histone post-translational modifications modulate the recruitment and activity of DNMTs. The PWWP domains of DNMT3A and DNMT3B are posited to interact with histone 3 lysine 36 trimethylation (H3K36me3); however, the functionality of this interaction for DNMT3A remains untested in vivo. Here we present a mouse model carrying a D329A point mutation in the DNMT3A PWWP domain. The mutation causes dominant postnatal growth retardation. At the molecular level, it results in progressive DNA hypermethylation across domains marked by H3K27me3 and bivalent chromatin, and de-repression of developmental regulatory genes in adult hypothalamus. Evaluation of non-CpG methylation, a marker of de novo methylation, further demonstrates the altered recruitment and activity of DNMT3AD329A at bivalent domains. This work provides key molecular insights into the function of the DNMT3A-PWWP domain and role of DNMT3A in regulating postnatal growth.
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Affiliation(s)
| | - Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Kathleen R Stewart-Morgan
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Biotech Research & Innovation Centre, 2200, Copenhagen, Denmark
| | - Elena Ivanova
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
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85
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Kuehner JN, Bruggeman EC, Wen Z, Yao B. Epigenetic Regulations in Neuropsychiatric Disorders. Front Genet 2019; 10:268. [PMID: 31019524 PMCID: PMC6458251 DOI: 10.3389/fgene.2019.00268] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/11/2019] [Indexed: 12/14/2022] Open
Abstract
Precise genetic and epigenetic spatiotemporal regulation of gene expression is critical for proper brain development, function and circuitry formation in the mammalian central nervous system. Neuronal differentiation processes are tightly regulated by epigenetic mechanisms including DNA methylation, histone modifications, chromatin remodelers and non-coding RNAs. Dysregulation of any of these pathways is detrimental to normal neuronal development and functions, which can result in devastating neuropsychiatric disorders, such as depression, schizophrenia and autism spectrum disorders. In this review, we focus on the current understanding of epigenetic regulations in brain development and functions, as well as their implications in neuropsychiatric disorders.
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Affiliation(s)
- Janise N Kuehner
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Emily C Bruggeman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States.,Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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86
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Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation of cell-type diversity in the cerebral cortex. J Neurochem 2019; 149:12-26. [PMID: 30276807 PMCID: PMC6587822 DOI: 10.1111/jnc.14601] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 09/13/2018] [Accepted: 09/26/2018] [Indexed: 12/29/2022]
Abstract
The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons, and glial cells which emerge from distinct neural stem cell lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that neural stem cell and radial glial progenitor lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development.
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Affiliation(s)
- Nicole Amberg
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Susanne Laukoter
- Institute of Science and Technology AustriaKlosterneuburgAustria
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87
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Migdalska-Richards A, Mill J. Epigenetic studies of schizophrenia: current status and future directions. Curr Opin Behav Sci 2019. [DOI: 10.1016/j.cobeha.2018.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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88
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Sakai A, Sugiyama S. Experience-dependent transcriptional regulation in juvenile brain development. Dev Growth Differ 2019; 60:473-482. [PMID: 30368782 DOI: 10.1111/dgd.12571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 12/26/2022]
Abstract
During brain development, once primary neural networks are formed, they are largely sculpted by environmental stimuli. The juvenile brain has a unique time window termed the critical period, in which neuronal circuits are remodeled by experience. Accumulating evidence indicates that abnormal rewiring of circuits in early life contributes to various neurodevelopmental disorders at later stages of life. Recent studies implicate two important aspects for activation of the critical period, both of which are experience-dependent: (a) proper excitatory/inhibitory (E/I) balance of neural circuit achieved during developmental trajectory of inhibitory interneurons, and (b) epigenetic regulation allowing flexible gene expression for neuronal plasticity. In this review, we discuss the molecular mechanisms of juvenile brain plasticity from the viewpoints of transcriptional and chromatin regulation, with a focus on Otx2 homeoprotein. Depending on experience, Otx2 is transported into cortical parvalbumin-positive interneurons (PV cells), where it induces PV cell maturation to activate the critical period. Understanding the unique behavior and function of Otx2 as a "messenger" of experience should therefore provide insights into mechanisms of juvenile brain development. Recently identified downstream targets of Otx2 suggest novel roles of Otx2 in homeostasis of PV cells, and, moreover, in regulation of chromatin state, which is important for neuronal plasticity. We further discuss epigenetic changes during postnatal brain development spanning the critical period. Different aspects of chromatin regulation may underlie experience-dependent neuronal development and plasticity.
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Affiliation(s)
- Akiko Sakai
- Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Sayaka Sugiyama
- Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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89
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Diverse facets of cortical interneuron migration regulation – Implications of neuronal activity and epigenetics. Brain Res 2018; 1700:160-169. [DOI: 10.1016/j.brainres.2018.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 01/21/2023]
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90
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Ciafrè S, Carito V, Ferraguti G, Greco A, Chaldakov GN, Fiore M, Ceccanti M. How alcohol drinking affects our genes: an epigenetic point of view. Biochem Cell Biol 2018; 97:345-356. [PMID: 30412425 DOI: 10.1139/bcb-2018-0248] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This work highlights recent studies in epigenetic mechanisms that play a role in alcoholism, which is a complex multifactorial disorder. There is a large body of evidence showing that alcohol can modify gene expression through epigenetic processes, namely DNA methylation and nucleosomal remodeling via histone modifications. In that regard, chronic exposure to ethanol modifies DNA and histone methylation, histone acetylation, and microRNA expression. The alcohol-mediated chromatin remodeling in the brain promotes the transition from use to abuse and addiction. Unravelling the multiplex pattern of molecular modifications induced by ethanol could support the development of new therapies for alcoholism and drug addiction targeting epigenetic processes.
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Affiliation(s)
- Stefania Ciafrè
- a Institute of Translational Pharmacology, IFT-CNR, 100 via del Fosso del Cavaliere, Rome 00133, Italy
| | - Valentina Carito
- b Institute of Cell Biology and Neurobiology, IBCN-CNR, c/o Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - Giampiero Ferraguti
- c Department of Experimental Medicine, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - Antonio Greco
- d Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - George N Chaldakov
- e Laboratory of Cell Biology, Department of Anatomy and Histology, Medical University, BG-9002 Varna, Bulgaria
| | - Marco Fiore
- b Institute of Cell Biology and Neurobiology, IBCN-CNR, c/o Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - Mauro Ceccanti
- f Centro Riferimento Alcologico Regione Lazio, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
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91
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Zeng P, Shi Y, Wang XM, Lin L, Du YJ, Tang N, Wang Q, Fang YY, Wang JZ, Zhou XW, Lu Y, Tian Q. Emodin Rescued Hyperhomocysteinemia-Induced Dementia and Alzheimer's Disease-Like Features in Rats. Int J Neuropsychopharmacol 2018; 22:57-70. [PMID: 30407508 PMCID: PMC6313134 DOI: 10.1093/ijnp/pyy090] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/04/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Hyperhomocysteinemia is an independent risk factor for dementia, including Alzheimer's disease. Lowering homocysteine levels with folic acid treatment with or without vitamin B12 has shown few clinical benefits on cognition. METHODS To verify the effect of emodin, a naturally active compound from Rheum officinale, on hyperhomocysteinemia-induced dementia, rats were treated with homocysteine injection (HCY, 400 μg/kg/d, 2 weeks) via vena caudalis. Afterwards, HCY rats with cognitive deficits were administered intragastric emodin at different concentrations for 2 weeks: 0 (HCY-E0), 20 (HCY-E20), 40 (HCY-E40), and 80 mg/kg/d (HCY-E80). RESULTS β-Amyloid overproduction, tau hyperphosphorylation, and losses of neuron and synaptic proteins were detected in the hippocampi of HCY-E0 rats with cognitive deficits. HCY-E40 and HCY-E80 rats had better behavioral performance. Although it did not reduce the plasma homocysteine level, emodin (especially 80 mg/kg/d) reduced the levels of β-amyloid and tau phosphorylation, decreased the levels of β-site amyloid precursor protein-cleaving enzyme 1, and improved the activity of protein phosphatase 2A. In the hippocampi of HCY-E40 and HCY-E80 rats, the neuron numbers, levels of synaptic proteins, and phosphorylation of the cAMP responsive element-binding protein at Ser133 were increased. In addition, depressed microglial activation and reduced levels of 5-lipoxygenase, interleukin-6, and tumor necrosis factor α were also observed. Lastly, hyperhomocysteinemia-induced microangiopathic alterations, oxidative stress, and elevated DNA methyltransferases 1 and 3β were rescued by emodin. CONCLUSIONS Emodin represents a novel potential candidate agent for hyperhomocysteinemia-induced dementia and Alzheimer's disease-like features.
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Affiliation(s)
- Peng Zeng
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Shi
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Ming Wang
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Li Lin
- Hubei University of Traditional Chinese Medicine, Wuhan, China
| | - Yan-Jun Du
- Hubei University of Traditional Chinese Medicine, Wuhan, China
| | - Na Tang
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Qun Wang
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Ying-Yan Fang
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Zhi Wang
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Xin-Wen Zhou
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Youming Lu
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China,Correspondence: Dr Youming Lu and Dr Qing Tian, Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China (, )
| | - Qing Tian
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China,Correspondence: Dr Youming Lu and Dr Qing Tian, Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China (, )
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Cui P, Ma T, Tamadon A, Han S, Li B, Chen Z, An X, Shao LR, Wang Y, Feng Y. Hypothalamic DNA methylation in rats with dihydrotestosterone-induced polycystic ovary syndrome: effects of low-frequency electro-acupuncture. Exp Physiol 2018; 103:1618-1632. [DOI: 10.1113/ep087163] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/10/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Peng Cui
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology; Fudan Institutes of Integrative Medicine; Fudan University; Shanghai 200032 China
| | - Tong Ma
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology; Fudan Institutes of Integrative Medicine; Fudan University; Shanghai 200032 China
| | - Amin Tamadon
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology; Fudan Institutes of Integrative Medicine; Fudan University; Shanghai 200032 China
| | - Sha Han
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology; Fudan Institutes of Integrative Medicine; Fudan University; Shanghai 200032 China
| | - Bing Li
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology; Fudan Institutes of Integrative Medicine; Fudan University; Shanghai 200032 China
| | - Zheyi Chen
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology; Fudan Institutes of Integrative Medicine; Fudan University; Shanghai 200032 China
| | - Xiaofei An
- Department of Endocrinology, Jiangsu Province Hospital of Chinese Medicine; Affiliated Hospital of Nanjing University of Chinese Medicine; Nanjing 210029 China
| | - Linus R. Shao
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy; University of Gothenburg; 40530 Gothenburg Sweden
| | - Yanqing Wang
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology; Fudan Institutes of Integrative Medicine; Fudan University; Shanghai 200032 China
- Shanghai Key Laboratory of Acupuncture Mechanism and Acupoint Function
| | - Yi Feng
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology; Fudan Institutes of Integrative Medicine; Fudan University; Shanghai 200032 China
- Shanghai Key Laboratory of Acupuncture Mechanism and Acupoint Function
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93
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DNA Methylation as a Biomarker of Treatment Response Variability in Serious Mental Illnesses: A Systematic Review Focused on Bipolar Disorder, Schizophrenia, and Major Depressive Disorder. Int J Mol Sci 2018; 19:ijms19103026. [PMID: 30287754 PMCID: PMC6213157 DOI: 10.3390/ijms19103026] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/28/2018] [Accepted: 09/29/2018] [Indexed: 12/11/2022] Open
Abstract
So far, genetic studies of treatment response in schizophrenia, bipolar disorder, and major depression have returned results with limited clinical utility. A gene × environment interplay has been proposed as a factor influencing not only pathophysiology but also the treatment response. Therefore, epigenetics has emerged as a major field of research to study the treatment of these three disorders. Among the epigenetic marks that can modify gene expression, DNA methylation is the best studied. We performed a systematic search (PubMed) following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA guidelines for preclinical and clinical studies focused on genome-wide and gene-specific DNA methylation in the context of schizophrenia, bipolar disorders, and major depressive disorder. Out of the 112 studies initially identified, we selected 31 studies among them, with an emphasis on responses to the gold standard treatments in each disorder. Modulations of DNA methylation levels at specific CpG sites have been documented for all classes of treatments (antipsychotics, mood stabilizers, and antidepressants). The heterogeneity of the models and methodologies used complicate the interpretation of results. Although few studies in each disorder have assessed the potential of DNA methylation as biomarkers of treatment response, data support this hypothesis for antipsychotics, mood stabilizers and antidepressants.
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94
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Saunders J, Hore Z, Gentry C, McMahon S, Denk F. Negative Evidence for a Functional Role of Neuronal DNMT3a in Persistent Pain. Front Mol Neurosci 2018; 11:332. [PMID: 30258352 PMCID: PMC6143791 DOI: 10.3389/fnmol.2018.00332] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/27/2018] [Indexed: 11/13/2022] Open
Abstract
Traditionally, neuroscience has had to rely on mixed tissue analysis to examine transcriptional and epigenetic changes in the context of nervous system function or pathology. However, particularly when studying chronic pain conditions, this approach can be flawed, since it neglects to take into account the shifting contribution of different cell types across experimental conditions. Here, we demonstrate this using the example of DNA methyltransferases (DNMTs) – a group of epigenetic modifiers consisting of Dnmt1, Dnmt3a, and Dnmt3b in mammalian cells. We used sensory neuron-specific knockout mice for Dnmt3a/3b as well as pharmacological blockade of Dnmt1 to study their role in nociception. In contrast to previous analyses on whole tissue, we find that Dnmt3a and 3b protein is not expressed in adult DRG neurons, that none of the DNA methyltransferases are regulated with injury and that interfering with their function has no effect on nociception. Our results therefore currently do not support a role for neuronal DNA methyltransferases in pain processing in adult animals.
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Affiliation(s)
- Jessica Saunders
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Zoe Hore
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Clive Gentry
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Stephen McMahon
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Franziska Denk
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
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95
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Ramírez Martínez L, Vargas Mejía M, Espadamala J, Gomez N, Lizcano JM, López-Bayghen E. Neuronal Growth Factor regulates Brain Specific Kinase 1 expression by inhibiting promoter methylation and promoting Sp1 recruitment. Neurochem Int 2018; 120:213-223. [PMID: 30196145 DOI: 10.1016/j.neuint.2018.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022]
Abstract
Brain specific kinases (BRSKs) are serine/threonine kinases, preferentially expressed in the brain after Embryonic Day 12. Although BRSKs are crucial neuronal development factors and regulation of their enzymatic activity has been widely explored, little is known of their transcriptional regulation. In this work, we show that Neuronal Growth Factor (NGF) increased the expression of Brsk1 in PC12 cells. Furthermore, during neuronal differentiation, Brsk1 mRNA increased through a MAPK-dependent Sp1 activation. To gain further insight into this regulation, we analyzed the transcriptional activity of the Brsk1 promoter in PC12 cells treated with NGF. Initially, we defined the minimal promoter region (-342 to +125 bp) responsive to NGF treatment. This region had multiple Sp1 binding sites, one of which was within a CpG island. In vitro binding assays showed that NGF-induced differentiation increased Sp1 binding to this site and that DNA methylation inhibited Sp1 binding. In vitro methylation of the Brsk1 promoter reduced its transcriptional activity and impaired the NGF effect. To evaluate the participation of DNA methyltransferases in Brsk1 gene regulation, the 5'Aza-dC inhibitor was used. 5'Aza-dC acted synergistically with NGF to promote Brsk1 promoter activity. Accordingly, DNMT3B overexpression abolished the response of the Brsk1 promoter to NGF. Surprisingly, we found Dnmt3b to be a direct target of NGF regulation, via the MAPK pathway. In conclusion, our results provide evidence of a novel mechanism of Brsk1 transcriptional regulation changing the promoter's methylation status, which was incited by the NGF-induced neuronal differentiation process.
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Affiliation(s)
- Leticia Ramírez Martínez
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México, 07360, Mexico; Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México, 07360, Mexico
| | - Miguel Vargas Mejía
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México, 07360, Mexico
| | - Josep Espadamala
- Institut de Neurociencies i Departament de Bioquímica i Biología Molecular, Facultat de Medicina, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Néstor Gomez
- Institut de Neurociencies i Departament de Bioquímica i Biología Molecular, Facultat de Medicina, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - José M Lizcano
- Institut de Neurociencies i Departament de Bioquímica i Biología Molecular, Facultat de Medicina, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Esther López-Bayghen
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México, 07360, Mexico.
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96
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Lintas C. Linking genetics to epigenetics: The role of folate and folate-related pathways in neurodevelopmental disorders. Clin Genet 2018; 95:241-252. [PMID: 30047142 DOI: 10.1111/cge.13421] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/09/2018] [Accepted: 07/21/2018] [Indexed: 12/12/2022]
Abstract
There is growing evidence that epigenetic dysregulation plays a role in neurodevelopmental disorders. In humans, folate is one of the main donors of the methyl group required for the synthesis of S-adenosylmethionine, which in turn is needed for DNA and histone methylation as key neurodevelopment processes. Folate deficiency during pregnancy has been correlated with neural tube defects and with a higher incidence of neurocognitive and/or neurobehavioral deficits. A similar outcome may be exerted by gene polymorphisms in folate or folate-related pathways. This has been documented by numerous case/control association studies performed on neurodevelopmental disorders such as autism spectrum disorder and attention deficit hyperactivity disorder. In this regard, the folate cycle represents a "perfect model" of how genetics influences epigenetics. Gene variants in folate and folate-related pathways can be considered risk factors for neurodevelopmental disorders and should therefore be assessed by genetic testing in pregnant women. High-risk women should be considered for folate supplementation during pregnancy. Here, we review all published case/control association studies on gene polymorphisms in folate and folate-related pathways performed on neurodevelopmental disorders, provide an overview of neurodevelopment and DNA methylation changes occurring at this time, and describe the biological basis of neurodevelopmental disorders and recent evidence of their epigenetic dysregulation.
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Affiliation(s)
- C Lintas
- Service for Neurodevelopmental Disorders, Laboratory of Molecular Psychiatry and Neurogenetics, Department of Medicine, University Campus Bio-Medico, Rome, Italy
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97
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Qu J, Zhu L, Zhou Z, Chen P, Liu S, Locy ML, Thannickal VJ, Zhou Y. Reversing Mechanoinductive DSP Expression by CRISPR/dCas9-mediated Epigenome Editing. Am J Respir Crit Care Med 2018; 198:599-609. [PMID: 29924937 PMCID: PMC6118013 DOI: 10.1164/rccm.201711-2242oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 06/20/2018] [Indexed: 12/29/2022] Open
Abstract
RATIONALE DSP (desmoplakin), the most abundant component of desmosomes, which maintain the mechanical integrity of epithelium, is a genome-wide association study-identified genetic risk locus in human idiopathic pulmonary fibrosis (IPF). Subjects with IPF express a significantly higher level of DSP than control subjects. OBJECTIVES Determine potential mechanisms by which DSP is regulated in lung fibrosis. METHODS Matrigel-coated soft and stiff polyacrylamide gels were made to simulate the stiffness of normal and fibrotic lungs. Quantitative chromatin immunoprecipitation and electrophoretic mobility shift assay were used to evaluate transcription factor binding to the DSP promoter. Targeted DNA methylation was achieved by CRISPR (clustered regularly interspaced short palindromic repeats)/dCas9 (deactivated CRISPR-associated protein-9 nuclease)-mediated Dnmt3A (DNA methyltransferase 3A) expression under the guidance of sequence-specific single guide RNAs. MEASUREMENTS AND MAIN RESULTS Stiff matrix promotes DSP gene expression in both human and rodent lung epithelial cells as compared with soft matrix. A conserved region in the proximal DSP promoter is hypermethylated under soft matrix conditions and becomes hypomethylated/demethylated under stiff matrix conditions. Demethylation of this conserved DSP promoter region is associated with transactivation of transcription factor EGR1 (early growth response protein 1), resulting in EGR1-dependent DSP overexpression. Targeted DNA methylation by CRISPR/dCas9/Dnmt3A-mediated epigenome editing blocks EGR1 binding to the DSP promoter and inhibits stiff matrix-induced DSP overexpression. CONCLUSIONS DSP is a matrix stiffness-regulated mechanosensitive gene. CRISPR/dCas9-Dnmt3A-mediated epigenome editing reverses DSP overexpression by reestablishment of the epigenetic control of DSP under the mechanically homeostatic environment. It provides a useful tool for investigations of the functional role of DSP in the pathogenesis of lung fibrosis.
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Affiliation(s)
- Jing Qu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lanyan Zhu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China; and
| | - Zijing Zhou
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China; and
| | - Ping Chen
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China; and
| | - Shuyan Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Morgan L. Locy
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Victor J. Thannickal
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Yong Zhou
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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98
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Lu YL, Yoo AS. Mechanistic Insights Into MicroRNA-Induced Neuronal Reprogramming of Human Adult Fibroblasts. Front Neurosci 2018; 12:522. [PMID: 30116172 PMCID: PMC6083049 DOI: 10.3389/fnins.2018.00522] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/12/2018] [Indexed: 12/16/2022] Open
Abstract
The use of transcriptional factors as cell fate regulators are often the primary focus in the direct reprogramming of somatic cells into neurons. However, in human adult fibroblasts, deriving functionally mature neurons with high efficiency requires additional neurogenic factors such as microRNAs (miRNAs) to evoke a neuronal state permissive to transcription factors to exert their reprogramming activities. As such, increasing evidence suggests brain-enriched miRNAs, miR-9/9∗ and miR-124, as potent neurogenic molecules through simultaneously targeting of anti-neurogenic effectors while allowing additional transcription factors to generate specific subtypes of human neurons. In this review, we will focus on methods that utilize neuronal miRNAs and provide mechanistic insights by which neuronal miRNAs, in synergism with brain-region specific transcription factors, drive the conversion of human fibroblasts into clinically relevant subtypes of neurons. Furthermore, we will provide insights into the age signature of directly converted neurons and how the converted human neurons can be utilized to model late-onset neurodegenerative disorders.
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Affiliation(s)
- Ya-Lin Lu
- Department of Developmental Biology, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States.,Program in Developmental, Regenerative and Stem Cell Biology, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Andrew S Yoo
- Department of Developmental Biology, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
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99
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Palmisano I, Di Giovanni S. Advances and Limitations of Current Epigenetic Studies Investigating Mammalian Axonal Regeneration. Neurotherapeutics 2018; 15:529-540. [PMID: 29948919 PMCID: PMC6095777 DOI: 10.1007/s13311-018-0636-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Axonal regeneration relies on the expression of regenerative associated genes within a coordinated transcriptional programme, which is finely tuned as a result of the activation of several regenerative signalling pathways. In mammals, this chain of events occurs in neurons following peripheral axonal injury, however it fails upon axonal injury in the central nervous system, such as in the spinal cord and the brain. Accumulating evidence has been suggesting that epigenetic control is a key factor to initiate and sustain the regenerative transcriptional response and that it might contribute to regenerative success versus failure. This review will discuss experimental evidence so far showing a role for epigenetic regulation in models of peripheral and central nervous system axonal injury. It will also propose future directions to fill key knowledge gaps and to test whether epigenetic control might indeed discriminate between regenerative success and failure.
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Affiliation(s)
- Ilaria Palmisano
- Laboratory for Neuroregeneration, Centre for Restorative Neuroscience, Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK.
| | - Simone Di Giovanni
- Laboratory for Neuroregeneration, Centre for Restorative Neuroscience, Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK.
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100
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Corso-Díaz X, Jaeger C, Chaitankar V, Swaroop A. Epigenetic control of gene regulation during development and disease: A view from the retina. Prog Retin Eye Res 2018; 65:1-27. [PMID: 29544768 PMCID: PMC6054546 DOI: 10.1016/j.preteyeres.2018.03.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/01/2018] [Accepted: 03/08/2018] [Indexed: 12/20/2022]
Abstract
Complex biological processes, such as organogenesis and homeostasis, are stringently regulated by genetic programs that are fine-tuned by epigenetic factors to establish cell fates and/or to respond to the microenvironment. Gene regulatory networks that guide cell differentiation and function are modulated and stabilized by modifications to DNA, RNA and proteins. In this review, we focus on two key epigenetic changes - DNA methylation and histone modifications - and discuss their contribution to retinal development, aging and disease, especially in the context of age-related macular degeneration (AMD) and diabetic retinopathy. We highlight less-studied roles of DNA methylation and provide the RNA expression profiles of epigenetic enzymes in human and mouse retina in comparison to other tissues. We also review computational tools and emergent technologies to profile, analyze and integrate epigenetic information. We suggest implementation of editing tools and single-cell technologies to trace and perturb the epigenome for delineating its role in transcriptional regulation. Finally, we present our thoughts on exciting avenues for exploring epigenome in retinal metabolism, disease modeling, and regeneration.
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Affiliation(s)
- Ximena Corso-Díaz
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Catherine Jaeger
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vijender Chaitankar
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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