1
|
Sun Z, Kou C, Gao Z, Guo X, Han B, Feng Y, Ding Q, Bai W. Association between the copy number variations of Methyl-CpG binding domain family and schizophrenia. Gene 2024; 930:148836. [PMID: 39127413 DOI: 10.1016/j.gene.2024.148836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/17/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Schizophrenia is recognized as one of the most severe psychiatric disorders, with its pathogenesis likely involving genetic, epigenetic, developmental, and environmental factors. Members of the Methyl-CpG Binding Domain (MBD) Family play a crucial role in the regulation of genomic DNA methylation, and studies have implicated the association between MBD family and neurodevelopmental disorders. Copy number variations (CNVs) are a significant genetic basis for human genomic variation, also playing a critical role in the genetic processes of schizophrenia. Therefore, we aimed to evaluate the susceptibility of MBD family CNVs to schizophrenia by exploring and validating them in two separate populations using CNVplex™ and qPCR methods, and to explore the relationship between MBD family CNVs and clinical phenotypes in the overall population using chi-square tests and Fisher's exact tests. Results suggest that an increase in MBD1 gene copy number and a deficiency in MBD2 gene copy number may be associated with the risk of schizophrenia. The deficiency in MBD2 gene copy number may increase the risk of delusion of reference and delusion of persecutory in the overall sample, as well as in males. This research provides preliminary evidence supporting the association between MBD family CNVs and schizophrenia, highlighting the potential role of the MBD family in the pathogenesis of schizophrenia.
Collapse
Affiliation(s)
- Zhouyang Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun, Jilin Province, 130021, China
| | - Changgui Kou
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun, Jilin Province, 130021, China
| | - Zibo Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun, Jilin Province, 130021, China
| | - Xinru Guo
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun, Jilin Province, 130021, China
| | - Beibei Han
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun, Jilin Province, 130021, China
| | - Yuan Feng
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun, Jilin Province, 130021, China
| | - Qianlu Ding
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun, Jilin Province, 130021, China
| | - Wei Bai
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun, Jilin Province, 130021, China.
| |
Collapse
|
2
|
Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Hoolehan W, Kulpa AM, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. Epigenetics Chromatin 2023; 16:45. [PMID: 37953264 PMCID: PMC10642035 DOI: 10.1186/s13072-023-00522-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation, DNA modifications in particular, of gene expression between neurons and glia. RESULTS After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT-whole genome oxidative bisulfite sequencing (WGoxBS) to assess the neuronal translatome and epigenome in the hippocampus of young mice (4 months old). WGoxBS findings were validated with enzymatic methyl-Seq (EM-Seq) and nanopore sequencing. Comparing neuronal data to microglial and astrocytic data from NuTRAP models, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, rather than proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of gene body mCG and a positive relationship between distal promoter and gene body hmCG with gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. CONCLUSIONS Neurons, astrocytes, and microglia demonstrate different genome-wide levels of mCG, hmCG, and mCH that are reproducible across analytical methods. However, modification-gene expression relationships are conserved across cell types. Enrichment of differential modifications across cell types in gene bodies and distal regulatory elements, but not proximal promoters, highlights epigenomic patterning in these regions as potentially greater determinants of cell identity. These findings also demonstrate the importance of differentiating between mC and hmC in neuroepigenomic analyses, as up to 30% of what is conventionally interpreted as mCG can be hmCG, which often has a different relationship to gene expression than mCG.
Collapse
Affiliation(s)
- Kyla B Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Ana J Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Sarah R Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adeline H Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Kevin D Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Walker Hoolehan
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adam M Kulpa
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - David R Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Willard M Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
| |
Collapse
|
3
|
Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543497. [PMID: 37333391 PMCID: PMC10274634 DOI: 10.1101/2023.06.05.543497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. This is especially true as for DNA modifications where most data are derived from bisulfite sequencing that cannot differentiate between DNA methylation and hydroxymethylation. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation of gene expression between neurons and glia. Results After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT whole genome oxidative bisulfite sequencing to assess the neuronal translatome and epigenome in the hippocampus of young mice (3 months old). These data were then compared to microglial and astrocytic data from NuTRAP models. When comparing the different cell types, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, with limited differences occurring within proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of mCG with gene expression within the gene body while a positive relationship between distal promoter and gene body hmCG and gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. Conclusions In this study, we identified differential usage of DNA modifications across CNS cell types, and assessed the relationship between DNA modifications and gene expression in neurons and glia. Despite having different global levels, the general modification-gene expression relationship was conserved across cell types. The enrichment of differential modifications in gene bodies and distal regulatory elements, but not proximal promoters, across cell types highlights epigenomic patterning in these regions as potentially greater determinants of cell identity.
Collapse
Affiliation(s)
- Kyla B. Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Ana J. Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Sarah R. Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Adeline H. Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Kevin D. Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - David R. Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Willard M. Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK USA
| |
Collapse
|
4
|
Jiang D, Li T, Guo C, Tang TS, Liu H. Small molecule modulators of chromatin remodeling: from neurodevelopment to neurodegeneration. Cell Biosci 2023; 13:10. [PMID: 36647159 PMCID: PMC9841685 DOI: 10.1186/s13578-023-00953-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
The dynamic changes in chromatin conformation alter the organization and structure of the genome and further regulate gene transcription. Basically, the chromatin structure is controlled by reversible, enzyme-catalyzed covalent modifications to chromatin components and by noncovalent ATP-dependent modifications via chromatin remodeling complexes, including switch/sucrose nonfermentable (SWI/SNF), inositol-requiring 80 (INO80), imitation switch (ISWI) and chromodomain-helicase DNA-binding protein (CHD) complexes. Recent studies have shown that chromatin remodeling is essential in different stages of postnatal and adult neurogenesis. Chromatin deregulation, which leads to defects in epigenetic gene regulation and further pathological gene expression programs, often causes a wide range of pathologies. This review first gives an overview of the regulatory mechanisms of chromatin remodeling. We then focus mainly on discussing the physiological functions of chromatin remodeling, particularly histone and DNA modifications and the four classes of ATP-dependent chromatin-remodeling enzymes, in the central and peripheral nervous systems under healthy and pathological conditions, that is, in neurodegenerative disorders. Finally, we provide an update on the development of potent and selective small molecule modulators targeting various chromatin-modifying proteins commonly associated with neurodegenerative diseases and their potential clinical applications.
Collapse
Affiliation(s)
- Dongfang Jiang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingting Li
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Caixia Guo
- grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tie-Shan Tang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongmei Liu
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| |
Collapse
|
5
|
Hyeon JW, Kim AH, Yano H. Epigenetic regulation in Huntington's disease. Neurochem Int 2021; 148:105074. [PMID: 34038804 DOI: 10.1016/j.neuint.2021.105074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/23/2021] [Accepted: 05/17/2021] [Indexed: 12/25/2022]
Abstract
Huntington's disease (HD) is a devastating and fatal monogenic neurodegenerative disorder characterized by progressive loss of selective neurons in the brain and is caused by an abnormal expansion of CAG trinucleotide repeats in a coding exon of the huntingtin (HTT) gene. Progressive gene expression changes that begin at premanifest stages are a prominent feature of HD and are thought to contribute to disease progression. Increasing evidence suggests the critical involvement of epigenetic mechanisms in abnormal transcription in HD. Genome-wide alterations of a number of epigenetic modifications, including DNA methylation and multiple histone modifications, are associated with HD, suggesting that mutant HTT causes complex epigenetic abnormalities and chromatin structural changes, which may represent an underlying pathogenic mechanism. The causal relationship of specific epigenetic changes to early transcriptional alterations and to disease pathogenesis require further investigation. In this article, we review recent studies on epigenetic regulation in HD with a focus on DNA and histone modifications. We also discuss the contribution of epigenetic modifications to HD pathogenesis as well as potential mechanisms linking mutant HTT and epigenetic alterations. Finally, we discuss the therapeutic potential of epigenetic-based treatments.
Collapse
Affiliation(s)
- Jae Wook Hyeon
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Boni JL, Kahanovitch U, Nwaobi SE, Floyd CL, Olsen ML. DNA methylation: A mechanism for sustained alteration of KIR4.1 expression following central nervous system insult. Glia 2020; 68:1495-1512. [PMID: 32068308 PMCID: PMC8665281 DOI: 10.1002/glia.23797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/22/2022]
Abstract
Kir4.1, a glial-specific inwardly rectifying potassium channel, is implicated in astrocytic maintenance of K+ homeostasis. Underscoring the role of Kir4.1 in central nervous system (CNS) functioning, genetic mutations in KCNJ10, the gene which encodes Kir4.1, causes seizures, ataxia and developmental disability in humans. Kir4.1 protein and mRNA loss are consistently observed in CNS injury and neurological diseases linked to hyperexcitability and neuronal dysfunction, leading to the notion that Kir4.1 represents an attractive therapeutic target. Despite this, little is understood regarding the mechanisms that underpin this downregulation. Previous work by our lab revealed that DNA hypomethylation of the Kcnj10 gene functions to regulate mRNA levels during astrocyte maturation whereas hypermethylation in vitro led to decreased promoter activity. In the present study, we utilized two vastly different injury models with known acute and chronic loss of Kir4.1 protein and mRNA to evaluate the methylation status of Kcnj10 as a candidate molecular mechanism for reduced transcription and subsequent protein loss. Examining whole hippocampal tissue and isolated astrocytes, in a lithium-pilocarpine model of epilepsy, we consistently identified hypermethylation of CpG island two, which resides in the large intronic region spanning the Kcnj10 gene. Strikingly similar results were observed using the second injury paradigm, a fifth cervical (C5) vertebral hemi-contusion model of spinal cord injury. Our previous work indicates the same gene region is significantly hypomethylated when transcription increases during astrocyte maturation. Our results suggest that DNA methylation can bidirectionally modulate Kcnj10 transcription and may represent a targetable molecular mechanism for the restoring astroglial Kir4.1 expression following CNS insult.
Collapse
Affiliation(s)
- Jessica L Boni
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- School of Neuroscience, Virginia Polytechnic and State University, Blacksburg, Virginia
| | - Uri Kahanovitch
- School of Neuroscience, Virginia Polytechnic and State University, Blacksburg, Virginia
| | - Sinifunanya E Nwaobi
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Division of Pediatric Neurology, UCLA Mattel Children's Hospital, University of California Los Angeles, Los Angeles, California
| | - Candace L Floyd
- Department of Physical Medicine and Rehabilitation, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Physical Medicine and Rehabilitation, University of Utah Health, Salt Lake City, Utah
| | - Michelle L Olsen
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- School of Neuroscience, Virginia Polytechnic and State University, Blacksburg, Virginia
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Antunes C, Sousa N, Pinto L, Marques CJ. TET enzymes in neurophysiology and brain function. Neurosci Biobehav Rev 2019; 102:337-344. [DOI: 10.1016/j.neubiorev.2019.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 02/07/2023]
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Egervari G, Kozlenkov A, Dracheva S, Hurd YL. Molecular windows into the human brain for psychiatric disorders. Mol Psychiatry 2019; 24:653-673. [PMID: 29955163 PMCID: PMC6310674 DOI: 10.1038/s41380-018-0125-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 12/20/2022]
Abstract
Delineating the pathophysiology of psychiatric disorders has been extremely challenging but technological advances in recent decades have facilitated a deeper interrogation of molecular processes in the human brain. Initial candidate gene expression studies of the postmortem brain have evolved into genome wide profiling of the transcriptome and the epigenome, a critical regulator of gene expression. Here, we review the potential and challenges of direct molecular characterization of the postmortem human brain, and provide a brief overview of recent transcriptional and epigenetic studies with respect to neuropsychiatric disorders. Such information can now be leveraged and integrated with the growing number of genome-wide association databases to provide a functional context of trait-associated genetic variants linked to psychiatric illnesses and related phenotypes. While it is clear that the field is still developing and challenges remain to be surmounted, these recent advances nevertheless hold tremendous promise for delineating the neurobiological underpinnings of mental diseases and accelerating the development of novel medication strategies.
Collapse
Affiliation(s)
- Gabor Egervari
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Yasmin L Hurd
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
12
|
Isles AR. Epigenetics, chromatin and brain development and function. Brain Neurosci Adv 2018; 2:2398212818812011. [PMID: 32166158 PMCID: PMC7058192 DOI: 10.1177/2398212818812011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Indexed: 11/30/2022] Open
Abstract
Research investigating epigenetics and chromatin function in brain and behaviour has mushroomed over the last two decades. And yet epigenetics as a biological concept predates the discovery in the 1950s of DNA as the principle mode of inheritance by over a decade. This review explores the past, present and future research into epigenetics as it relates to understanding brain development and function
Collapse
Affiliation(s)
- Anthony R Isles
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| |
Collapse
|
13
|
Stricker SH, Götz M. DNA-Methylation: Master or Slave of Neural Fate Decisions? Front Neurosci 2018; 12:5. [PMID: 29449798 PMCID: PMC5799221 DOI: 10.3389/fnins.2018.00005] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/04/2018] [Indexed: 01/05/2023] Open
Abstract
The pristine formation of complex organs depends on sharp temporal and spatial control of gene expression. Therefore, epigenetic mechanisms have been frequently attributed a central role in controlling cell fate determination. A prime example for this is the first discovered and still most studied epigenetic mark, DNA methylation, and the development of the most complex mammalian organ, the brain. Recently, the field of epigenetics has advanced significantly: new DNA modifications were discovered, epigenomic profiling became widely accessible, and methods for targeted epigenomic manipulation have been developed. Thus, it is time to challenge established models of epigenetic gene regulation. Here, we review the current state of knowledge about DNA modifications, their epigenomic distribution, and their regulatory role. We will summarize the evidence suggesting they possess crucial roles in neurogenesis and discuss whether this likely includes lineage choice regulation or rather effects on differentiation. Finally, we will attempt an outlook on how questions, which remain unresolved, could be answered soon.
Collapse
Affiliation(s)
- Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, Munich, Germany.,Physiological Genomics, BioMedical Center, Munich, Germany.,German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Germany and Biomedical Center, Institute of Stem Cell Research, Helmholtz Zentrum, Ludwig-Maximilian-Universität, Munich, Germany
| | - Magdalena Götz
- Physiological Genomics, BioMedical Center, Munich, Germany.,German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Germany and Biomedical Center, Institute of Stem Cell Research, Helmholtz Zentrum, Ludwig-Maximilian-Universität, Munich, Germany.,German Excellence Cluster of Systems Neurology, Munich, Germany
| |
Collapse
|
14
|
Methyl-CpG-Binding Protein MBD1 Regulates Neuronal Lineage Commitment through Maintaining Adult Neural Stem Cell Identity. J Neurosci 2017; 37:523-536. [PMID: 28100736 DOI: 10.1523/jneurosci.1075-16.2016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 10/31/2016] [Accepted: 11/22/2016] [Indexed: 01/09/2023] Open
Abstract
Methyl-CpG-binding domain 1 (MBD1) belongs to a family of methyl-CpG-binding proteins that are epigenetic "readers" linking DNA methylation to transcriptional regulation. MBD1 is expressed in neural stem cells residing in the dentate gyrus of the adult hippocampus (aNSCs) and MBD1 deficiency leads to reduced neuronal differentiation, impaired neurogenesis, learning deficits, and autism-like behaviors in mice; however, the precise function of MBD1 in aNSCs remains unexplored. Here, we show that MBD1 is important for maintaining the integrity and stemness of NSCs, which is critical for their ability to generate neurons. MBD1 deficiency leads to the accumulation of undifferentiated NSCs and impaired transition into the neuronal lineage. Transcriptome analysis of neural stem and progenitor cells isolated directly from the dentate gyrus of MBD1 mutant (KO) and WT mice showed that gene sets related to cell differentiation, particularly astrocyte lineage genes, were upregulated in KO cells. We further demonstrated that, in NSCs, MBD1 binds and represses directly specific genes associated with differentiation. Our results suggest that MBD1 maintains the multipotency of NSCs by restraining the onset of differentiation genes and that untimely expression of these genes in MBD1-deficient stem cells may interfere with normal cell lineage commitment and cause the accumulation of undifferentiated cells. Our data reveal a novel role for MBD1 in stem cell maintenance and provide insight into how epigenetic regulation contributes to adult neurogenesis and the potential impact of its dysregulation. SIGNIFICANCE STATEMENT Adult neural stem cells (aNSCs) in the hippocampus self-renew and generate neurons throughout life. We show that methyl-CpG-binding domain 1 (MBD1), a DNA methylation "reader," is important for maintaining the integrity of NSCs, which is critical for their neurogenic potency. Our data reveal a novel role for MBD1 in stem cell maintenance and provide insight into how epigenetic regulation preserves the multipotency of stem cells for subsequent differentiation.
Collapse
|
15
|
Weng YL, An R, Cassin J, Joseph J, Mi R, Wang C, Zhong C, Jin SG, Pfeifer GP, Bellacosa A, Dong X, Hoke A, He Z, Song H, Ming GL. An Intrinsic Epigenetic Barrier for Functional Axon Regeneration. Neuron 2017; 94:337-346.e6. [PMID: 28426967 PMCID: PMC6007997 DOI: 10.1016/j.neuron.2017.03.034] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 02/05/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022]
Abstract
Mature neurons in the adult peripheral nervous system can effectively switch from a dormant state with little axonal growth to robust axon regeneration upon injury. The mechanisms by which injury unlocks mature neurons' intrinsic axonal growth competence are not well understood. Here, we show that peripheral sciatic nerve lesion in adult mice leads to elevated levels of Tet3 and 5-hydroxylmethylcytosine in dorsal root ganglion (DRG) neurons. Functionally, Tet3 is required for robust axon regeneration of DRG neurons and behavioral recovery. Mechanistically, peripheral nerve injury induces DNA demethylation and upregulation of multiple regeneration-associated genes in a Tet3- and thymine DNA glycosylase-dependent fashion in DRG neurons. In addition, Pten deletion-induced axon regeneration of retinal ganglion neurons in the adult CNS is attenuated upon Tet1 knockdown. Together, our study suggests an epigenetic barrier that can be removed by active DNA demethylation to permit axon regeneration in the adult mammalian nervous system.
Collapse
Affiliation(s)
- Yi-Lan Weng
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ran An
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200040, China
| | - Jessica Cassin
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Pre-doctoral Human Genetics Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jessica Joseph
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ruifa Mi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chen Wang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Chun Zhong
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Seung-Gi Jin
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gerd P. Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ahmet Hoke
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Pre-doctoral Human Genetics Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
16
|
Genome-wide DNA Methylation Changes in a Mouse Model of Infection-Mediated Neurodevelopmental Disorders. Biol Psychiatry 2017; 81:265-276. [PMID: 27769567 DOI: 10.1016/j.biopsych.2016.08.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 07/12/2016] [Accepted: 08/01/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Prenatal exposure to infectious or inflammatory insults increases the risk of neurodevelopmental disorders. Using a well-established mouse model of prenatal viral-like immune activation, we examined whether this pathological association involves genome-wide DNA methylation differences at single nucleotide resolution. METHODS Prenatal immune activation was induced by maternal treatment with the viral mimetic polyriboinosinic-polyribocytidylic acid in middle or late gestation. Following behavioral and cognitive characterization of the adult offspring (n = 12 per group), unbiased capture array bisulfite sequencing was combined with subsequent matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and quantitative real-time polymerase chain reaction analyses to quantify DNA methylation changes and transcriptional abnormalities in the medial prefrontal cortex of immune-challenged and control offspring. Gene ontology term enrichment analysis was used to explore shared functional pathways of genes with differential DNA methylation. RESULTS Adult offspring of immune-challenged mothers displayed hyper- and hypomethylated CpGs at numerous loci and at distinct genomic regions, including genes relevant for gamma-aminobutyric acidergic differentiation and signaling (e.g., Dlx1, Lhx5, Lhx8), Wnt signaling (Wnt3, Wnt8a, Wnt7b), and neural development (e.g., Efnb3, Mid1, Nlgn1, Nrxn2). Altered DNA methylation was associated with transcriptional changes of the corresponding genes. The epigenetic and transcriptional effects were dependent on the offspring's age and were markedly influenced by the precise timing of prenatal immune activation. CONCLUSIONS Prenatal viral-like immune activation is capable of inducing stable DNA methylation changes in the medial prefrontal cortex. These long-term epigenetic modifications are a plausible mechanism underlying the disruption of prefrontal gene transcription and behavioral functions in subjects with prenatal infectious histories.
Collapse
|
17
|
Kyono Y, Sachs LM, Bilesimo P, Wen L, Denver RJ. Developmental and Thyroid Hormone Regulation of the DNA Methyltransferase 3a Gene in Xenopus Tadpoles. Endocrinology 2016; 157:4961-4972. [PMID: 27779916 PMCID: PMC5133355 DOI: 10.1210/en.2016-1465] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/21/2016] [Indexed: 11/19/2022]
Abstract
Thyroid hormone is essential for normal development in vertebrates. In amphibians, T3 controls metamorphosis by inducing tissue-specific gene regulation programs. A hallmark of T3 action is the modification of chromatin structure, which underlies changes in gene transcription. We found that mRNA for the de novo DNA methyltransferase (DNMT) dnmt3a, but not dnmt1, increased in the brain of Xenopus tadpoles during metamorphosis in parallel with plasma [T3]. Addition of T3 to the rearing water caused a time-dependent increase in dnmt3a mRNA in tadpole brain, tail, and hind limb. By analyzing data from a genome-wide analysis of T3 receptor (TR) binding in tadpole tail, we identified several putative T3 response elements (TREs) within the dnmt3a locus. Using in vitro DNA binding, transient transfection-reporter, and chromatin immunoprecipitation assays for TRs, we identified two functional TREs at -7.1 kb and +5.1 kb relative to the dnmt3a transcription start site. Sequence alignment showed that these TREs are conserved between two related frog species, X. laevis and X. tropicalis, but not with amniotes. Our previous findings showed that this gene is directly regulated by liganded TRs in mouse brain, and whereas the two mouse TREs are conserved among Eutherian mammals, they are not conserved in Xenopus species. Thus, although T3 regulation of dnmt3a may be an ancient pathway in vertebrates, the genomic sites responsible for hormone regulation may have diverged or arisen by convergent evolution. We hypothesize that direct T3 regulation of dnmt3a may be an important mechanism for modulating global changes in DNA methylation.
Collapse
Affiliation(s)
- Yasuhiro Kyono
- Neuroscience Graduate Program (Y.K.), The University of Michigan, Ann Arbor, Michigan 48109-1048; UMR-7221, Centre National de la Recherche Scientifique (L.M.S., P.B.), Muséum National d'Histoire Naturelle, 75005 Paris, France; and Department of Molecular, Cellular, and Developmental Biology (L.W., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109-1048
| | - Laurent M Sachs
- Neuroscience Graduate Program (Y.K.), The University of Michigan, Ann Arbor, Michigan 48109-1048; UMR-7221, Centre National de la Recherche Scientifique (L.M.S., P.B.), Muséum National d'Histoire Naturelle, 75005 Paris, France; and Department of Molecular, Cellular, and Developmental Biology (L.W., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109-1048
| | - Patrice Bilesimo
- Neuroscience Graduate Program (Y.K.), The University of Michigan, Ann Arbor, Michigan 48109-1048; UMR-7221, Centre National de la Recherche Scientifique (L.M.S., P.B.), Muséum National d'Histoire Naturelle, 75005 Paris, France; and Department of Molecular, Cellular, and Developmental Biology (L.W., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109-1048
| | - Luan Wen
- Neuroscience Graduate Program (Y.K.), The University of Michigan, Ann Arbor, Michigan 48109-1048; UMR-7221, Centre National de la Recherche Scientifique (L.M.S., P.B.), Muséum National d'Histoire Naturelle, 75005 Paris, France; and Department of Molecular, Cellular, and Developmental Biology (L.W., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109-1048
| | - Robert J Denver
- Neuroscience Graduate Program (Y.K.), The University of Michigan, Ann Arbor, Michigan 48109-1048; UMR-7221, Centre National de la Recherche Scientifique (L.M.S., P.B.), Muséum National d'Histoire Naturelle, 75005 Paris, France; and Department of Molecular, Cellular, and Developmental Biology (L.W., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109-1048
| |
Collapse
|
18
|
Kennedy AJ, Rahn EJ, Paulukaitis BS, Savell KE, Kordasiewicz HB, Wang J, Lewis JW, Posey J, Strange SK, Guzman-Karlsson MC, Phillips SE, Decker K, Motley ST, Swayze EE, Ecker DJ, Michael TP, Day JJ, Sweatt JD. Tcf4 Regulates Synaptic Plasticity, DNA Methylation, and Memory Function. Cell Rep 2016; 16:2666-2685. [PMID: 27568567 PMCID: PMC5710002 DOI: 10.1016/j.celrep.2016.08.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 05/31/2016] [Accepted: 07/27/2016] [Indexed: 12/26/2022] Open
Abstract
Human haploinsufficiency of the transcription factor Tcf4 leads to a rare autism spectrum disorder called Pitt-Hopkins syndrome (PTHS), which is associated with severe language impairment and development delay. Here, we demonstrate that Tcf4 haploinsufficient mice have deficits in social interaction, ultrasonic vocalization, prepulse inhibition, and spatial and associative learning and memory. Despite learning deficits, Tcf4(+/-) mice have enhanced long-term potentiation in the CA1 area of the hippocampus. In translationally oriented studies, we found that small-molecule HDAC inhibitors normalized hippocampal LTP and memory recall. A comprehensive set of next-generation sequencing experiments of hippocampal mRNA and methylated DNA isolated from Tcf4-deficient and WT mice before or shortly after experiential learning, with or without administration of vorinostat, identified "memory-associated" genes modulated by HDAC inhibition and dysregulated by Tcf4 haploinsufficiency. Finally, we observed that Hdac2 isoform-selective knockdown was sufficient to rescue memory deficits in Tcf4(+/-) mice.
Collapse
Affiliation(s)
- Andrew J Kennedy
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Department of Chemistry, Bates College, Lewiston, ME 04240, USA
| | - Elizabeth J Rahn
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Brynna S Paulukaitis
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Katherine E Savell
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Jing Wang
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - John W Lewis
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jessica Posey
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sarah K Strange
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Mikael C Guzman-Karlsson
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Scott E Phillips
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kyle Decker
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | | | | | | | - Jeremy J Day
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - J David Sweatt
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA.
| |
Collapse
|
19
|
Kyono Y, Subramani A, Ramadoss P, Hollenberg AN, Bonett RM, Denver RJ. Liganded Thyroid Hormone Receptors Transactivate the DNA Methyltransferase 3a Gene in Mouse Neuronal Cells. Endocrinology 2016; 157:3647-57. [PMID: 27387481 PMCID: PMC5007891 DOI: 10.1210/en.2015-1529] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/01/2016] [Indexed: 12/11/2022]
Abstract
Thyroid hormone (T3) is essential for proper neurological development. The hormone, bound to its receptors, regulates gene transcription in part by modulating posttranslational modifications of histones. Methylation of DNA, which is established by the de novo DNA methyltransferase (DNMT)3a and DNMT3b, and maintained by DNMT1 is another epigenetic modification influencing gene transcription. The expression of Dnmt3a, but not other Dnmt genes, increases in mouse brain in parallel with the postnatal rise in plasma [T3]. We found that treatment of the mouse neuroblastoma cell line Neuro2a[TRβ1] with T3 caused rapid induction of Dnmt3a mRNA, which was resistant to protein synthesis inhibition, supporting that it is a direct T3-response gene. Injection of T3 into postnatal day 6 mice increased Dnmt3a mRNA in the brain by 1 hour. Analysis of two chromatin immunoprecipitation-sequencing datasets, and targeted analyses using chromatin immunoprecipitation, transfection-reporter assays, and in vitro DNA binding identified 2 functional T3-response elements (TREs) at the mouse Dnmt3a locus located +30.3 and +49.3 kb from the transcription start site. Thyroid hormone receptors associated with both of these regions in mouse brain chromatin, but with only 1 (+30.3 kb) in Neuro2a[TRβ1] cells. Deletion of the +30.3-kb TRE using CRISPR/Cas9 genome editing eliminated or strongly reduced the Dnmt3a mRNA response to T3. Bioinformatics analysis showed that both TREs are highly conserved among eutherian mammals. Thyroid regulation of Dnmt3a may be an evolutionarily conserved mechanism for modulating global changes in DNA methylation during postnatal neurological development.
Collapse
Affiliation(s)
- Yasuhiro Kyono
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| | - Arasakumar Subramani
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| | - Preeti Ramadoss
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| | - Anthony N Hollenberg
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| | - Ronald M Bonett
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| | - Robert J Denver
- Neuroscience Graduate Program (Y.K., R.J.D.) and Department of Molecular, Cellular and Developmental Biology (A.S., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Division of Endocrinology, Diabetes and Metabolism (P.R., A.N.H.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02115; and Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104
| |
Collapse
|
20
|
Marshall P, Bredy TW. Cognitive neuroepigenetics: the next evolution in our understanding of the molecular mechanisms underlying learning and memory? NPJ SCIENCE OF LEARNING 2016; 1:16014. [PMID: 27512601 PMCID: PMC4977095 DOI: 10.1038/npjscilearn.2016.14] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/02/2016] [Accepted: 06/21/2016] [Indexed: 05/02/2023]
Abstract
A complete understanding of the fundamental mechanisms of learning and memory continues to elude neuroscientists. Although many important discoveries have been made, the question of how memories are encoded and maintained at the molecular level remains. To date, this issue has been framed within the context of one of the most dominant concepts in molecular biology, the central dogma, and the result has been a protein-centric view of memory. Here we discuss the evidence supporting a role for neuroepigenetic mechanisms, which constitute dynamic and reversible, state-dependent modifications at all levels of control over cellular function, and their role in learning and memory. This neuroepigenetic view suggests that DNA, RNA and protein each influence one another to produce a holistic cellular state that contributes to the formation and maintenance of memory, and predicts a parallel and distributed system for the consolidation, storage and retrieval of the engram.
Collapse
Affiliation(s)
- Paul Marshall
- Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, USA
| | - Timothy W Bredy
- Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, USA
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
21
|
Bailey J. Monkey-based research on human disease: the implications of genetic differences. Altern Lab Anim 2016; 42:287-317. [PMID: 25413291 DOI: 10.1177/026119291404200504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Assertions that the use of monkeys to investigate human diseases is valid scientifically are frequently based on a reported 90-93% genetic similarity between the species. Critical analyses of the relevance of monkey studies to human biology, however, indicate that this genetic similarity does not result in sufficient physiological similarity for monkeys to constitute good models for research, and that monkey data do not translate well to progress in clinical practice for humans. Salient examples include the failure of new drugs in clinical trials, the highly different infectivity and pathology of SIV/HIV, and poor extrapolation of research on Alzheimer's disease, Parkinson's disease and stroke. The major molecular differences underlying these inter-species phenotypic disparities have been revealed by comparative genomics and molecular biology - there are key differences in all aspects of gene expression and protein function, from chromosome and chromatin structure to post-translational modification. The collective effects of these differences are striking, extensive and widespread, and they show that the superficial similarity between human and monkey genetic sequences is of little benefit for biomedical research. The extrapolation of biomedical data from monkeys to humans is therefore highly unreliable, and the use of monkeys must be considered of questionable value, particularly given the breadth and potential of alternative methods of enquiry that are currently available to scientists.
Collapse
Affiliation(s)
- Jarrod Bailey
- New England Anti-Vivisection Society (NEAVS), Boston, MA, USA
| |
Collapse
|
22
|
Lee HB, Sundberg BN, Sigafoos AN, Clark KJ. Genome Engineering with TALE and CRISPR Systems in Neuroscience. Front Genet 2016; 7:47. [PMID: 27092173 PMCID: PMC4821859 DOI: 10.3389/fgene.2016.00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/16/2016] [Indexed: 12/26/2022] Open
Abstract
Recent advancement in genome engineering technology is changing the landscape of biological research and providing neuroscientists with an opportunity to develop new methodologies to ask critical research questions. This advancement is highlighted by the increased use of programmable DNA-binding agents (PDBAs) such as transcription activator-like effector (TALE) and RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems. These PDBAs fused or co-expressed with various effector domains allow precise modification of genomic sequences and gene expression levels. These technologies mirror and extend beyond classic gene targeting methods contributing to the development of novel tools for basic and clinical neuroscience. In this Review, we discuss the recent development in genome engineering and potential applications of this technology in the field of neuroscience.
Collapse
Affiliation(s)
- Han B Lee
- Neurobiology of Disease Graduate Program, Mayo Graduate School Rochester, MN, USA
| | - Brynn N Sundberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, MN, USA
| | - Ashley N Sigafoos
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, MN, USA
| | - Karl J Clark
- Neurobiology of Disease Graduate Program, Mayo Graduate SchoolRochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo ClinicRochester, MN, USA
| |
Collapse
|
23
|
Barr CL, Misener VL. Decoding the non-coding genome: elucidating genetic risk outside the coding genome. GENES, BRAIN, AND BEHAVIOR 2016; 15:187-204. [PMID: 26515765 PMCID: PMC4833497 DOI: 10.1111/gbb.12269] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/19/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
Current evidence emerging from genome-wide association studies indicates that the genetic underpinnings of complex traits are likely attributable to genetic variation that changes gene expression, rather than (or in combination with) variation that changes protein-coding sequences. This is particularly compelling with respect to psychiatric disorders, as genetic changes in regulatory regions may result in differential transcriptional responses to developmental cues and environmental/psychosocial stressors. Until recently, however, the link between transcriptional regulation and psychiatric genetic risk has been understudied. Multiple obstacles have contributed to the paucity of research in this area, including challenges in identifying the positions of remote (distal from the promoter) regulatory elements (e.g. enhancers) and their target genes and the underrepresentation of neural cell types and brain tissues in epigenome projects - the availability of high-quality brain tissues for epigenetic and transcriptome profiling, particularly for the adolescent and developing brain, has been limited. Further challenges have arisen in the prediction and testing of the functional impact of DNA variation with respect to multiple aspects of transcriptional control, including regulatory-element interaction (e.g. between enhancers and promoters), transcription factor binding and DNA methylation. Further, the brain has uncommon DNA-methylation marks with unique genomic distributions not found in other tissues - current evidence suggests the involvement of non-CG methylation and 5-hydroxymethylation in neurodevelopmental processes but much remains unknown. We review here knowledge gaps as well as both technological and resource obstacles that will need to be overcome in order to elucidate the involvement of brain-relevant gene-regulatory variants in genetic risk for psychiatric disorders.
Collapse
Affiliation(s)
- C. L. Barr
- Toronto Western Research Institute, University Health Network, Toronto, ON, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - V. L. Misener
- Toronto Western Research Institute, University Health Network, Toronto, ON, Canada
| |
Collapse
|
24
|
Isles AR. Neural and behavioral epigenetics; what it is, and what is hype. GENES BRAIN AND BEHAVIOR 2015; 14:64-72. [PMID: 25346298 DOI: 10.1111/gbb.12184] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/24/2014] [Accepted: 10/24/2014] [Indexed: 12/13/2022]
Abstract
The ability to examine epigenetic mechanisms in the brain has become readily available over the last 20 years. This has led to an explosion of research and interest in neural and behavioral epigenetics. Of particular interest to researchers, and indeed the lay public, is the possibility that epigenetic processes, such as changes in DNA-methylation and histone modification, may provide a biochemical record of environmental effects. This has led to some fascinating insights into how molecular changes in the brain can control behavior. However, some of this research has also attracted controversy and, as is dealt with here, some overblown claims. This latter problem is partly linked to the shifting sands of what is defined as 'epigenetics'. In this review, I provide an overview of what exactly epigenetics is, and what is hype, with the aim of opening up a debate as to how this exciting field moves forward.
Collapse
Affiliation(s)
- A R Isles
- Behavioural Genetics Group, MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Cardiff University, UK
| |
Collapse
|
25
|
Abstract
DNA methylation is a chemical modification that occurs predominantly on CG dinucleotides in mammalian genomes. However, recent studies have revealed that non-CG methylation (mCH) is abundant and nonrandomly distributed in the genomes of pluripotent cells and brain cells, and is present at lower levels in many other human cells and tissues. Surprisingly, mCH in pluripotent cells is distinct from that in brain cells in terms of sequence specificity and association with transcription, indicating the existence of different mCH pathways. In addition, several recent studies have begun to reveal the biological significance of mCH in diverse cellular processes. In reprogrammed somatic cells, mCH marks megabase-scale regions that have failed to revert to the pluripotent epigenetic state. In myocytes, promoter mCH accumulation is associated with the transcriptional response to environmental factors. In brain cells, mCH accumulates during the establishment of neural circuits and is associated with Rett syndrome. In this review, we summarize the current understanding of mCH and its possible functional consequences in different biological contexts.
Collapse
Affiliation(s)
- Yupeng He
- Bioinformatics Program, University of California, San Diego, La Jolla, California 92093
| | | |
Collapse
|
26
|
Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair. Nat Neurosci 2015; 18:836-43. [PMID: 25915473 PMCID: PMC4446239 DOI: 10.1038/nn.4008] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 03/25/2015] [Indexed: 02/08/2023]
Abstract
Contrary to the long-held belief that DNA methylation of terminally differentiated cells is permanent and essentially immutable, post-mitotic neurons exhibit extensive DNA demethylation. The cellular function of active DNA demethylation in neurons, however, remains largely unknown. Tet family proteins oxidize 5-methylcytosine to initiate active DNA demethylation through the base-excision repair (BER) pathway. We found that synaptic activity bi-directionally regulates neuronal Tet3 expression. Functionally, knockdown of Tet or inhibition of BER in hippocampal neurons elevated excitatory glutamatergic synaptic transmission, whereas overexpressing Tet3 or Tet1 catalytic domain decreased it. Furthermore, dysregulation of Tet3 signaling prevented homeostatic synaptic plasticity. Mechanistically, Tet3 dictated neuronal surface GluR1 levels. RNA-seq analyses further revealed a pivotal role of Tet3 in regulating gene expression in response to global synaptic activity changes. Thus, Tet3 serves as a synaptic activity sensor to epigenetically regulate fundamental properties and meta-plasticity of neurons via active DNA demethylation.
Collapse
|
27
|
Edelstein L, Smythies J, Noble D. Introduction. Philos Trans R Soc Lond B Biol Sci 2014; 369:rstb.2013.0501. [PMID: 25135962 DOI: 10.1098/rstb.2013.0501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - John Smythies
- Integrative Neuroscience Program, Center for Brain and Cognition, Department of Psychology, University of California San Diego, La Jolla, CA 92093, USA Department of Psychiatry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Denis Noble
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
| |
Collapse
|