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Ketchum HC, Suzuki M, Dawlaty MM. Catalytic-dependent and -independent roles of TET3 in the regulation of specific genetic programs during neuroectoderm specification. Commun Biol 2024; 7:415. [PMID: 38580843 PMCID: PMC10997653 DOI: 10.1038/s42003-024-06120-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/28/2024] [Indexed: 04/07/2024] Open
Abstract
The ten-eleven-translocation family of proteins (TET1/2/3) are epigenetic regulators of gene expression. They regulate genes by promoting DNA demethylation (i.e., catalytic activity) and by partnering with regulatory proteins (i.e., non-catalytic functions). Unlike Tet1 and Tet2, Tet3 is not expressed in mouse embryonic stem cells (ESCs) but is induced upon ESC differentiation. However, the significance of its dual roles in lineage specification is less defined. By generating TET3 catalytic-mutant (Tet3m/m) and knockout (Tet3-/-) mouse ESCs and differentiating them to neuroectoderm (NE), we identify distinct catalytic-dependent and independent roles of TET3 in NE specification. We find that the catalytic activity of TET3 is important for activation of neural genes while its non-catalytic functions are involved in suppressing mesodermal programs. Interestingly, the vast majority of differentially methylated regions (DMRs) in Tet3m/m and Tet3-/- NE cells are hypomethylated. The hypo-DMRs are associated to aberrantly upregulated genes while the hyper-DMRs are linked to downregulated neural genes. We find the maintenance methyltransferase Dnmt1 as a direct target of TET3, which is downregulated in TET3-deficient NE cells and may contribute to the increased DNA hypomethylation. Our findings establish that the catalytic-dependent and -independent roles of TET3 have distinct contributions to NE specification with potential implications in development.
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Affiliation(s)
- Harmony C Ketchum
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Masako Suzuki
- Department of Nutrition, Texas A&M University, College Station, Texas, USA
| | - Meelad M Dawlaty
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA.
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2
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Liu B, Xie D, Huang X, Jin S, Dai Y, Sun X, Li D, Bennett AM, Diano S, Huang Y. Skeletal muscle TET3 promotes insulin resistance through destabilisation of PGC-1α. Diabetologia 2024; 67:724-737. [PMID: 38216792 PMCID: PMC10904493 DOI: 10.1007/s00125-023-06073-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/17/2023] [Indexed: 01/14/2024]
Abstract
AIM/HYPOTHESIS The peroxisome proliferator-activated receptor-γ coactivator α (PGC-1α) plays a critical role in the maintenance of glucose, lipid and energy homeostasis by orchestrating metabolic programs in multiple tissues in response to environmental cues. In skeletal muscles, PGC-1α dysregulation has been associated with insulin resistance and type 2 diabetes but the underlying mechanisms have remained elusive. This research aims to understand the role of TET3, a member of the ten-eleven translocation (TET) family dioxygenases, in PGC-1α dysregulation in skeletal muscles in obesity and diabetes. METHODS TET expression levels in skeletal muscles were analysed in humans with or without type 2 diabetes, as well as in mouse models of high-fat diet (HFD)-induced or genetically induced (ob/ob) obesity/diabetes. Muscle-specific Tet3 knockout (mKD) mice were generated to study TET3's role in muscle insulin sensitivity. Genome-wide expression profiling (RNA-seq) of muscle tissues from wild-type (WT) and mKD mice was performed to mine deeper insights into TET3-mediated regulation of muscle insulin sensitivity. The correlation between PGC-1α and TET3 expression levels was investigated using muscle tissues and in vitro-derived myotubes. PGC-1α phosphorylation and degradation were analysed using in vitro assays. RESULTS TET3 expression was elevated in skeletal muscles of humans with type 2 diabetes and in HFD-fed and ob/ob mice compared with healthy controls. mKD mice exhibited enhanced glucose tolerance, insulin sensitivity and resilience to HFD-induced insulin resistance. Pathway analysis of RNA-seq identified 'Mitochondrial Function' and 'PPARα Pathway' to be among the top biological processes regulated by TET3. We observed higher PGC-1α levels (~25%) in muscles of mKD mice vs WT mice, and lower PGC-1α protein levels (~25-60%) in HFD-fed or ob/ob mice compared with their control counterparts. In human and murine myotubes, increased PGC-1α levels following TET3 knockdown contributed to improved mitochondrial respiration and insulin sensitivity. TET3 formed a complex with PGC-1α and interfered with its phosphorylation, leading to its destabilisation. CONCLUSIONS/INTERPRETATION Our results demonstrate an essential role for TET3 in the regulation of skeletal muscle insulin sensitivity and suggest that TET3 may be used as a potential therapeutic target for the metabolic syndrome. DATA AVAILABILITY Sequences are available from the Gene Expression Omnibus ( https://www.ncbi.nlm.nih.gov/geo/ ) with accession number of GSE224042.
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Affiliation(s)
- Beibei Liu
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Center of Reproductive Medicine, National Health Commission Key Laboratory of Advanced Reproductive Medicine and Fertility, Shengjing Hospital of China Medical University, Shenyang, China
| | - Di Xie
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Department of Reproductive Medicine, General Hospital of Central Theater Command, Wuhan, Hubei, China
| | - Xinmei Huang
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Department of Endocrinology, Fifth People's Hospital of Shanghai, Fudan University School of Medicine, Shanghai, China
| | - Sungho Jin
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, USA
| | - Yangyang Dai
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoli Sun
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Jiangsu, China
| | - Da Li
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Center of Reproductive Medicine, National Health Commission Key Laboratory of Advanced Reproductive Medicine and Fertility, Shengjing Hospital of China Medical University, Shenyang, China
| | - Anton M Bennett
- Departments of Pharmacology and of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, USA
| | - Sabrina Diano
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, USA
| | - Yingqun Huang
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, USA.
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3
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Shi J, Wang Z, Wang Z, Shao G, Li X. Epigenetic regulation in adult neural stem cells. Front Cell Dev Biol 2024; 12:1331074. [PMID: 38357000 PMCID: PMC10864612 DOI: 10.3389/fcell.2024.1331074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024] Open
Abstract
Neural stem cells (NSCs) exhibit self-renewing and multipotential properties. Adult NSCs are located in two neurogenic regions of adult brain: the ventricular-subventricular zone (V-SVZ) of the lateral ventricle and the subgranular zone of the dentate gyrus in the hippocampus. Maintenance and differentiation of adult NSCs are regulated by both intrinsic and extrinsic signals that may be integrated through expression of some key factors in the adult NSCs. A number of transcription factors have been shown to play essential roles in transcriptional regulation of NSC cell fate transitions in the adult brain. Epigenetic regulators have also emerged as key players in regulation of NSCs, neural progenitor cells and their differentiated progeny via epigenetic modifications including DNA methylation, histone modifications, chromatin remodeling and RNA-mediated transcriptional regulation. This minireview is primarily focused on epigenetic regulations of adult NSCs during adult neurogenesis, in conjunction with transcriptional regulation in these processes.
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Affiliation(s)
- Jiajia Shi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zilin Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhijun Wang
- Zhenhai Lianhua Hospital, Ningbo City, Zhejiang, China
| | - Guofeng Shao
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo City, Zhejiang, China
| | - Xiajun Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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4
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Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
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Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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5
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Murtaj V, Butti E, Martino G, Panina-Bordignon P. Endogenous neural stem cells characterization using omics approaches: Current knowledge in health and disease. Front Cell Neurosci 2023; 17:1125785. [PMID: 37091923 PMCID: PMC10113633 DOI: 10.3389/fncel.2023.1125785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Neural stem cells (NSCs), an invaluable source of neuronal and glial progeny, have been widely interrogated in the last twenty years, mainly to understand their therapeutic potential. Most of the studies were performed with cells derived from pluripotent stem cells of either rodents or humans, and have mainly focused on their potential in regenerative medicine. High-throughput omics technologies, such as transcriptomics, epigenetics, proteomics, and metabolomics, which exploded in the past decade, represent a powerful tool to investigate the molecular mechanisms characterizing the heterogeneity of endogenous NSCs. The transition from bulk studies to single cell approaches brought significant insights by revealing complex system phenotypes, from the molecular to the organism level. Here, we will discuss the current literature that has been greatly enriched in the “omics era”, successfully exploring the nature and function of endogenous NSCs and the process of neurogenesis. Overall, the information obtained from omics studies of endogenous NSCs provides a sharper picture of NSCs function during neurodevelopment in healthy and in perturbed environments.
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Affiliation(s)
- Valentina Murtaj
- Division of Neuroscience, San Raffaele Vita-Salute University, Milan, Italy
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Erica Butti
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Gianvito Martino
- Division of Neuroscience, San Raffaele Vita-Salute University, Milan, Italy
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Paola Panina-Bordignon
- Division of Neuroscience, San Raffaele Vita-Salute University, Milan, Italy
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
- *Correspondence: Paola Panina-Bordignon
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6
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Costa MR, Dos Santos AYI, de Miranda TB, Aires R, de Camargo Coque A, Hurtado ECP, Bernardi MM, Pecorari VGA, Andia DC, Birbrair A, Guillemin GJ, Latini A, da Silva RA. Impact of neuroinflammation on epigenetic transcriptional control of Sonic Hedgehog members in the central nervous system. Brain Res 2023; 1799:148180. [PMID: 36463954 DOI: 10.1016/j.brainres.2022.148180] [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: 08/03/2022] [Revised: 09/14/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022]
Abstract
Sonic Hedgehog (Shh) signaling plays a critical role during central nervous system (CNS) development, and its dysregulation leads to neurological disorders. Nevertheless, little is known about Shh signaling regulation in the adult brain. Here, we investigated the contribution of DNA methylation on the transcriptional control of Shh signaling pathway members and its basal distribution impact on the brain, as well as its modulation by inflammation. The methylation status of the promoter regions of these members and the transcriptional profile of DNA-modifying enzymes (DNA Methyltransferases - DNMTs and Tet Methylcytosine Dioxygenase - TETs) were investigated in a murine model of neuroinflammation by qPCR. We showed that, in the adult brain, methylation in the CpG promoter regions of the Shh signaling pathway members was critical to determine the endogenous differential transcriptional pattern observed between distinct brain regions. We also found that neuroinflammation differentially modulates gene expression of DNA-modifying enzymes. This study reveals the basal transcriptional profile of DNMTs and TETs enzymes in the CNS and demonstrates the effect of neuroinflammation on the transcriptional control of members of the Shh Signaling pathway in the adult brain.
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Affiliation(s)
| | | | | | - Rogério Aires
- Epigenetic Study Center and Gene Regulation - CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo 04026-002, São Paulo, Brazil
| | - Alex de Camargo Coque
- Epigenetic Study Center and Gene Regulation - CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo 04026-002, São Paulo, Brazil
| | - Elizabeth Cristina Perez Hurtado
- Epigenetic Study Center and Gene Regulation - CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo 04026-002, São Paulo, Brazil.
| | - Maria Martha Bernardi
- Epigenetic Study Center and Gene Regulation - CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo 04026-002, São Paulo, Brazil
| | | | - Denise Carleto Andia
- School of Dentistry, Health Science Institute, Paulista University, São Paulo 04026-002, São Paulo, Brazil.
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gilles J Guillemin
- Neuroinflammation Group, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Alexandra Latini
- Bioenergetics and Oxidative Stress Lab - LABOX, Department of Biochemistry, Center for Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Rodrigo A da Silva
- School of Dentistry, University of Taubaté, 12020-3400 Taubaté, São Paulo, Brazil; Epigenetic Study Center and Gene Regulation - CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo 04026-002, São Paulo, Brazil.
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7
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Lozano-Ureña A, Lázaro-Carot L, Jiménez-Villalba E, Montalbán-Loro R, Mateos-White I, Duart-Abadía P, Martínez-Gurrea I, Nakayama KI, Fariñas I, Kirstein M, Gil-Sanz C, Ferrón SR. IGF2 interacts with the imprinted gene Cdkn1c to promote terminal differentiation of neural stem cells. Development 2023; 150:286545. [PMID: 36633189 PMCID: PMC9903205 DOI: 10.1242/dev.200563] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 11/23/2022] [Indexed: 01/13/2023]
Abstract
Adult neurogenesis is supported by multipotent neural stem cells (NSCs) with unique properties and growth requirements. Adult NSCs constitute a reversibly quiescent cell population that can be activated by extracellular signals from the microenvironment in which they reside in vivo. Although genomic imprinting plays a role in adult neurogenesis through dose regulation of some relevant signals, the roles of many imprinted genes in the process remain elusive. Insulin-like growth factor 2 (IGF2) is encoded by an imprinted gene that contributes to NSC maintenance in the adult subventricular zone through a biallelic expression in only the vascular compartment. We show here that IGF2 additionally promotes terminal differentiation of NSCs into astrocytes, neurons and oligodendrocytes by inducing the expression of the maternally expressed gene cyclin-dependent kinase inhibitor 1c (Cdkn1c), encoding the cell cycle inhibitor p57. Using intraventricular infusion of recombinant IGF2 in a conditional mutant strain with Cdkn1c-deficient NSCs, we confirm that p57 partially mediates the differentiation effects of IGF2 in NSCs and that this occurs independently of its role in cell-cycle progression, balancing the relationship between astrogliogenesis, neurogenesis and oligodendrogenesis.
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Affiliation(s)
- Anna Lozano-Ureña
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain
| | - Laura Lázaro-Carot
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain
| | - Esteban Jiménez-Villalba
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain
| | - Raquel Montalbán-Loro
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain
| | - Isabel Mateos-White
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain
| | - Pere Duart-Abadía
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain
| | - Irene Martínez-Gurrea
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain
| | - Keiichi I. Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 819-0395, Japan
| | - Isabel Fariñas
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain
| | - Martina Kirstein
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain
| | - Cristina Gil-Sanz
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain
| | - Sacri R. Ferrón
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia 46100, Spain,Departamento de Biología Celular, Universidad de Valencia, Valencia 46100, Spain,Author for correspondence ()
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8
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Xie D, Stutz B, Li F, Chen F, Lv H, Sestan-Pesa M, Catarino J, Gu J, Zhao H, Stoddard CE, Carmichael GG, Shanabrough M, Taylor HS, Liu ZW, Gao XB, Horvath TL, Huang Y. TET3 epigenetically controls feeding and stress response behaviors via AGRP neurons. J Clin Invest 2022; 132:162365. [PMID: 36189793 PMCID: PMC9525119 DOI: 10.1172/jci162365] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
The TET family of dioxygenases promote DNA demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine (5hmC). Hypothalamic agouti-related peptide-expressing (AGRP-expressing) neurons play an essential role in driving feeding, while also modulating nonfeeding behaviors. Besides AGRP, these neurons produce neuropeptide Y (NPY) and the neurotransmitter GABA, which act in concert to stimulate food intake and decrease energy expenditure. Notably, AGRP, NPY, and GABA can also elicit anxiolytic effects. Here, we report that in adult mouse AGRP neurons, CRISPR-mediated genetic ablation of Tet3, not previously known to be involved in central control of appetite and metabolism, induced hyperphagia, obesity, and diabetes, in addition to a reduction of stress-like behaviors. TET3 deficiency activated AGRP neurons, simultaneously upregulated the expression of Agrp, Npy, and the vesicular GABA transporter Slc32a1, and impeded leptin signaling. In particular, we uncovered a dynamic association of TET3 with the Agrp promoter in response to leptin signaling, which induced 5hmC modification that was associated with a chromatin-modifying complex leading to transcription inhibition, and this regulation occurred in both the mouse models and human cells. Our results unmasked TET3 as a critical central regulator of appetite and energy metabolism and revealed its unexpected dual role in the control of feeding and other complex behaviors through AGRP neurons.
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Affiliation(s)
- Di Xie
- Department of Obstetrics, Gynecology and Reproductive Sciences.,Yale Center for Molecular and Systems Metabolism, and
| | - Bernardo Stutz
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Feng Li
- Department of Obstetrics, Gynecology and Reproductive Sciences.,Yale Center for Molecular and Systems Metabolism, and
| | - Fan Chen
- Department of Obstetrics, Gynecology and Reproductive Sciences
| | - Haining Lv
- Department of Obstetrics, Gynecology and Reproductive Sciences.,Yale Center for Molecular and Systems Metabolism, and
| | - Matija Sestan-Pesa
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jonatas Catarino
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jianlei Gu
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Christopher E Stoddard
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Gordon G Carmichael
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Marya Shanabrough
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hugh S Taylor
- Department of Obstetrics, Gynecology and Reproductive Sciences
| | - Zhong-Wu Liu
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Xiao-Bing Gao
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tamas L Horvath
- Department of Obstetrics, Gynecology and Reproductive Sciences.,Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yingqun Huang
- Department of Obstetrics, Gynecology and Reproductive Sciences.,Yale Center for Molecular and Systems Metabolism, and
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9
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Qin S, Yuan Y, Huang X, Tan Z, Hu X, Liu H, Pu Y, Ding YQ, Su Z, He C. Topoisomerase IIA in adult NSCs regulates SVZ neurogenesis by transcriptional activation of Usp37. Nucleic Acids Res 2022; 50:9319-9338. [PMID: 36029179 PMCID: PMC9458435 DOI: 10.1093/nar/gkac731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 07/31/2022] [Accepted: 08/14/2022] [Indexed: 01/27/2023] Open
Abstract
Topoisomerase IIA (TOP2a) has traditionally been known as an important nuclear enzyme that resolves entanglements and relieves torsional stress of DNA double strands. However, its function in genomic transcriptional regulation remains largely unknown, especially during adult neurogenesis. Here, we show that TOP2a is preferentially expressed in neurogenic niches in the brain of adult mice, such as the subventricular zone (SVZ). Conditional knockout of Top2a in adult neural stem cells (NSCs) of the SVZ significantly inhibits their self-renewal and proliferation, and ultimately reduces neurogenesis. To gain insight into the molecular mechanisms by which TOP2a regulates adult NSCs, we perform RNA-sequencing (RNA-Seq) plus chromatin immunoprecipitation sequencing (ChIP-Seq) and identify ubiquitin-specific protease 37 (Usp37) as a direct TOP2a target gene. Importantly, overexpression of Usp37 is sufficient to rescue the impaired self-renewal ability of adult NSCs caused by Top2a knockdown. Taken together, this proof-of-principle study illustrates a TOP2a/Usp37-mediated novel molecular mechanism in adult neurogenesis, which will significantly expand our understanding of the function of topoisomerase in the adult brain.
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Affiliation(s)
- Shangyao Qin
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Yimin Yuan
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Xiao Huang
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Zijian Tan
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Xin Hu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Hong Liu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Yingyan Pu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Yu-qiang Ding
- Department of Laboratory Animal Science, and State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhida Su
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
| | - Cheng He
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Naval Medical University, Shanghai 200433, China
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10
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Fan BF, Hao B, Dai YD, Xue L, Shi YW, Liu L, Xuan SM, Yang N, Wang XG, Zhao H. Deficiency of Tet3 in nucleus accumbens enhances fear generalization and anxiety-like behaviors in mice. Brain Pathol 2022; 32:e13080. [PMID: 35612904 PMCID: PMC9616092 DOI: 10.1111/bpa.13080] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/02/2022] [Indexed: 11/30/2022] Open
Abstract
Stress‐induced neuroepigenetic programming gains growing more and more interest in the studies of the etiology of posttraumatic stress disorder (PTSD). However, seldom attention is focused on DNA demethylation in fear memory generalization, which is the core characteristic of PTSD. Here, we show that ten‐eleven translocation protein 3 (TET3), the most abundant DNA demethylation enzyme of the TET family in neurons, senses environmental stress and bridges neuroplasticity with behavioral adaptation during fear generalization. Foot shock strength dependently induces fear generalization and TET3 expression in nucleus accumbens (NAc) in mice. Inhibition of DNA demethylation by infusing demethyltransferase inhibitors or AAV‐Tet3‐shRNA virus in NAc enhances the fear generalization and anxiety‐like behavior. Furthermore, TET3 knockdown impairs the dendritic spine density, PSD length, and thickness of neurons, decreases DNA hydroxymethylation (5hmC), reduces the expression of synaptic plasticity‐related genes including Homer1, Cdkn1a, Cdh8, Vamp8, Reln, Bdnf, while surprisingly increases immune‐related genes Stat1, B2m, H2‐Q7, H2‐M2, C3, Cd68 shown by RNA‐seq. Notably, knockdown of TET3 in NAc activates microglia and CD39‐P2Y12R signaling pathway, and inhibition of CD39 reverses the effects of TET3 knockdown on the fear memory generalization and anxiety. Overexpression of TET3 by Crispr‐dSaCas9 virus delivery to activate endogenous Tet3 in NAc increases dendritic spine density of neurons in NAc and reverses fear memory generalization and anxiety‐like behavior in mice. These results suggest that TET3 modulates fear generalization and anxiety via regulating synaptic plasticity and CD39 signaling pathway.
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Affiliation(s)
- Bu-Fang Fan
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bo Hao
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yun-Da Dai
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li Xue
- Department of Psychology, School of Public Medicine, Southern Medical University, Guangzhou, China
| | - Yan-Wei Shi
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lu Liu
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shou-Min Xuan
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ning Yang
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Guang Wang
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hu Zhao
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
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11
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Hayashi T, Eto K, Kadoya Y. Downregulation of ten-eleven translocation-2 triggers epithelial differentiation during organogenesis. Differentiation 2022; 125:45-53. [DOI: 10.1016/j.diff.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/25/2022] [Accepted: 05/02/2022] [Indexed: 11/26/2022]
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12
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New Insights into TETs in Psychiatric Disorders. Int J Mol Sci 2022; 23:ijms23094909. [PMID: 35563298 PMCID: PMC9103987 DOI: 10.3390/ijms23094909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022] Open
Abstract
Psychiatric disorders are complex and heterogeneous disorders arising from the interaction of multiple factors based on neurobiology, genetics, culture, and life experience. Increasing evidence indicates that sustained abnormalities are maintained by epigenetic modifications in specific brain regions. Over the past decade, the critical, non-redundant roles of the ten-eleven translocation (TET) family of dioxygenase enzymes have been identified in the brain during developmental and postnatal stages. Specifically, TET-mediated active demethylation, involving the iterative oxidation of 5-methylcytosine to 5-hydroxymethylcytosine and subsequent oxidative derivatives, is dynamically regulated in response to environmental stimuli such as neuronal activity, learning and memory processes, and stressor exposure. Here, we review the progress of studies designed to provide a better understanding of how profiles of TET proteins and 5hmC are powerful mechanisms by which to explain neuronal plasticity and long-term behaviors, and impact transcriptional programs operative in the brain that contribute to psychiatric disorders.
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13
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Arand J, Chiang HR, Martin D, Snyder MP, Sage J, Reijo Pera RA, Wossidlo M. Tet enzymes are essential for early embryogenesis and completion of embryonic genome activation. EMBO Rep 2021; 23:e53968. [PMID: 34866320 PMCID: PMC8811641 DOI: 10.15252/embr.202153968] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/18/2022] Open
Abstract
Mammalian development begins in transcriptional silence followed by a period of widespread activation of thousands of genes. DNA methylation reprogramming is integral to embryogenesis and linked to Tet enzymes, but their function in early development is not well understood. Here, we generate combined deficiencies of all three Tet enzymes in mouse oocytes using a morpholino‐guided knockdown approach and study the impact of acute Tet enzyme deficiencies on preimplantation development. Tet1–3 deficient embryos arrest at the 2‐cell stage with the most severe phenotype linked to Tet2. Individual Tet enzymes display non‐redundant roles in the consecutive oxidation of 5‐methylcytosine to 5‐carboxylcytosine. Gene expression analysis uncovers that Tet enzymes are required for completion of embryonic genome activation (EGA) and fine‐tuned expression of transposable elements and chimeric transcripts. Whole‐genome bisulfite sequencing reveals minor changes of global DNA methylation in Tet‐deficient 2‐cell embryos, suggesting an important role of non‐catalytic functions of Tet enzymes in early embryogenesis. Our results demonstrate that Tet enzymes are key components of the clock that regulates the timing and extent of EGA in mammalian embryos.
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Affiliation(s)
- Julia Arand
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Department of Pediatrics, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - H Rosaria Chiang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA.,Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, USA
| | - David Martin
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | | | - Julien Sage
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Department of Pediatrics, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Renee A Reijo Pera
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, USA
| | - Mark Wossidlo
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA.,Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, USA
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14
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Kozlova A, Butler RR, Zhang S, Ujas T, Zhang H, Steidl S, Sanders AR, Pang ZP, Vezina P, Duan J. Sex-specific nicotine sensitization and imprinting of self-administration in rats inform GWAS findings on human addiction phenotypes. Neuropsychopharmacology 2021; 46:1746-1756. [PMID: 34007041 PMCID: PMC8358005 DOI: 10.1038/s41386-021-01027-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/26/2021] [Accepted: 04/22/2021] [Indexed: 02/04/2023]
Abstract
Repeated nicotine exposure leads to sensitization (SST) and enhances self-administration (SA) in rodents. However, the molecular basis of nicotine SST and SA and their biological relevance to the mounting genome-wide association study (GWAS) loci of human addictive behaviors are poorly understood. Considering a gateway drug role of nicotine, we modeled nicotine SST and SA in F1 progeny of inbred rats (F344/BN) and conducted integrative genomics analyses. We unexpectedly observed male-specific nicotine SST and a parental effect of SA only present in paternal F344 crosses. Transcriptional profiling in the ventral tegmental area (VTA) and nucleus accumbens (NAc) core and shell further revealed sex- and brain region-specific transcriptomic signatures of SST and SA. We found that genes associated with SST and SA were enriched for those related to synaptic processes, myelin sheath, and tobacco use disorder or chemdependency. Interestingly, SST-associated genes were often downregulated in male VTA but upregulated in female VTA, and strongly enriched for smoking GWAS risk variants, possibly explaining the male-specific SST. For SA, we found widespread region-specific allelic imbalance of expression (AIE), of which genes showing AIE bias toward paternal F344 alleles in NAc core were strongly enriched for SA-associated genes and for GWAS risk variants of smoking initiation, likely contributing to the parental effect of SA. Our study suggests a mechanistic link between transcriptional changes underlying the NIC SST and SA and human nicotine addiction, providing a resource for understanding the neurobiology basis of the GWAS findings on human smoking and other addictive phenotypes.
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Affiliation(s)
- Alena Kozlova
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL USA
| | - Robert R. Butler
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL USA
| | - Siwei Zhang
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL USA
| | - Thomas Ujas
- grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL USA
| | - Hanwen Zhang
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL USA
| | - Stephan Steidl
- grid.164971.c0000 0001 1089 6558Department of Psychology, Loyola University Chicago, Chicago, IL USA
| | - Alan R. Sanders
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL USA
| | - Zhiping P. Pang
- grid.430387.b0000 0004 1936 8796Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers University, New Brunswick, NJ USA
| | - Paul Vezina
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA.
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA. .,Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA.
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15
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Colussi C, Grassi C. Epigenetic regulation of neural stem cells: The emerging role of nucleoporins. STEM CELLS (DAYTON, OHIO) 2021; 39:1601-1614. [PMID: 34399020 PMCID: PMC9290943 DOI: 10.1002/stem.3444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/28/2021] [Indexed: 11/06/2022]
Abstract
Nucleoporins (Nups) are components of the nuclear pore complex that, besides regulating nucleus-cytoplasmic transport, emerged as a hub for chromatin interaction and gene expression modulation. Specifically, Nups act in a dynamic manner both at specific gene level and in the topological organization of chromatin domains. As such, they play a fundamental role during development and determination of stemness/differentiation balance in stem cells. An increasing number of reports indicate the implication of Nups in many central nervous system functions with great impact on neurogenesis, neurophysiology, and neurological disorders. Nevertheless, the role of Nup-mediated epigenetic regulation in embryonic and adult neural stem cells (NSCs) is a field largely unexplored and the comprehension of their mechanisms of action is only beginning to be unveiled. After a brief overview of epigenetic mechanisms, we will present and discuss the emerging role of Nups as new effectors of neuroepigenetics and as dynamic platform for chromatin function with specific reference to the biology of NSCs.
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Affiliation(s)
- Claudia Colussi
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI)-CNR, Rome, Italy
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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16
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Dick A, Chen A. The role of TET proteins in stress-induced neuroepigenetic and behavioural adaptations. Neurobiol Stress 2021; 15:100352. [PMID: 34189192 PMCID: PMC8220100 DOI: 10.1016/j.ynstr.2021.100352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/21/2021] [Accepted: 06/05/2021] [Indexed: 12/27/2022] Open
Abstract
Over the past decade, critical, non-redundant roles of the ten-eleven translocation (TET) family of dioxygenase enzymes have been identified in the brain during developmental and postnatal stages. Specifically, TET-mediated active demethylation, involving the iterative oxidation of 5-methylcytosine to 5-hydroxymethylcytosine and subsequent oxidative derivatives, is dynamically regulated in response to environmental stimuli such as neuronal activity, learning and memory processes, and stressor exposure. Such changes may therefore perpetuate stable and dynamic transcriptional patterns within neuronal populations required for neuroplasticity and behavioural adaptation. In this review, we will highlight recent evidence supporting a role of TET protein function and active demethylation in stress-induced neuroepigenetic and behavioural adaptations. We further explore potential mechanisms by which TET proteins may mediate both the basal and pathological embedding of stressful life experiences within the brain of relevance to stress-related psychiatric disorders.
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Affiliation(s)
- Alec Dick
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
- Corresponding author.
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
- The Ruhman Family Laboratory for Research on the Neurobiology of Stress, Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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17
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Huang Y, Grand K, Kimonis V, Butler MG, Jain S, Huang AYW, Martinez-Agosto JA, Nelson SF, Sanchez-Lara PA. Mosaic de novo SNRPN gene variant associated with Prader-Willi syndrome. J Med Genet 2021; 59:719-722. [PMID: 34099539 DOI: 10.1136/jmedgenet-2020-107674] [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] [Received: 12/28/2020] [Accepted: 05/11/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Prader-Willi syndrome (PWS) is an imprinting disorder caused by the absence of paternal expressed genes in the Prader-Willi critical region (PWCR) on chromosome 15q11.2-q13. Three molecular mechanisms have been known to cause PWS, including a deletion in the PWCR, uniparental disomy 15 and imprinting defects. RESULTS We report the first case of PWS associated with a single-nucleotide SNRPN variant in a 10-year-old girl presenting with clinical features consistent with PWS, including infantile hypotonia and feeding difficulty, developmental delay with cognitive impairment, excessive eating with central obesity, sleep disturbances, skin picking and related behaviour issues. Whole-exome sequencing revealed a de novo mosaic nonsense variant of the SNRPN gene (c.73C>T, p.R25X) in 10% of DNA isolated from buccal cells and 19% of DNA from patient-derived lymphoblast cells. DNA methylation study did not detect an abnormal methylation pattern in the SNRPN locus. Parental origin studies showed a paternal source of an intronic single-nucleotide polymorphism within the locus in proximity to the SNRPN variant. CONCLUSIONS This is the first report that provides evidence of a de novo point mutation of paternal origin in SNRPN as a new disease-causing mechanism for PWS. This finding suggests that gene sequencing should be considered as part of the diagnostic workup in patients with clinical suspicion of PWS.
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Affiliation(s)
- Yue Huang
- Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Virginia Kimonis
- Department of Pediatrics, UCI and Children's Hospital of Orange County, Irvine, California, USA
| | - Merlin G Butler
- Departments of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Suparna Jain
- Pediatric Endocrinology, Department of Pediatrics, Cedar-Sinai Medical Center, Los Angeles, California, USA
| | - Alden Yen-Wen Huang
- Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Julian A Martinez-Agosto
- Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
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18
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Antunes C, Da Silva JD, Guerra-Gomes S, Alves ND, Ferreira F, Loureiro-Campos E, Branco MR, Sousa N, Reik W, Pinto L, Marques CJ. Tet3 ablation in adult brain neurons increases anxiety-like behavior and regulates cognitive function in mice. Mol Psychiatry 2021; 26:1445-1457. [PMID: 32103150 DOI: 10.1038/s41380-020-0695-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 01/16/2020] [Accepted: 02/18/2020] [Indexed: 01/25/2023]
Abstract
TET3 is a member of the ten-eleven translocation (TET) family of enzymes which oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). Tet3 is highly expressed in the brain, where 5hmC levels are most abundant. In adult mice, we observed that TET3 is present in mature neurons and oligodendrocytes but is absent in astrocytes. To investigate the function of TET3 in adult postmitotic neurons, we crossed Tet3 floxed mice with a neuronal Cre-expressing mouse line, Camk2a-CreERT2, obtaining a Tet3 conditional KO (cKO) mouse line. Ablation of Tet3 in adult mature neurons resulted in increased anxiety-like behavior with concomitant hypercorticalism, and impaired hippocampal-dependent spatial orientation. Transcriptome and gene-specific expression analysis of the hippocampus showed dysregulation of genes involved in glucocorticoid signaling pathway (HPA axis) in the ventral hippocampus, whereas upregulation of immediate early genes was observed in both dorsal and ventral hippocampal areas. In addition, Tet3 cKO mice exhibit increased dendritic spine maturation in the ventral CA1 hippocampal subregion. Based on these observations, we suggest that TET3 is involved in molecular alterations that govern hippocampal-dependent functions. These results reveal a critical role for epigenetic modifications in modulating brain functions, opening new insights into the molecular basis of neurological disorders.
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Affiliation(s)
- Cláudia 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
| | - Jorge D Da Silva
- 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
| | - Sónia Guerra-Gomes
- 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
| | - Nuno D Alves
- 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
| | - Fábio Ferreira
- 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
| | - Eduardo Loureiro-Campos
- 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
| | - 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
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,The Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - 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.
| | - C Joana Marques
- Department of Genetics, Faculty of Medicine, University of Porto (FMUP), 4200-319, Porto, Portugal. .,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.
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19
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Montalbán-Loro R, Lassi G, Lozano-Ureña A, Perez-Villalba A, Jiménez-Villalba E, Charalambous M, Vallortigara G, Horner AE, Saksida LM, Bussey TJ, Trejo JL, Tucci V, Ferguson-Smith AC, Ferrón SR. Dlk1 dosage regulates hippocampal neurogenesis and cognition. Proc Natl Acad Sci U S A 2021; 118:e2015505118. [PMID: 33712542 PMCID: PMC7980393 DOI: 10.1073/pnas.2015505118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Neurogenesis in the adult brain gives rise to functional neurons, which integrate into neuronal circuits and modulate neural plasticity. Sustained neurogenesis throughout life occurs in the subgranular zone (SGZ) of the dentate gyrus in the hippocampus and is hypothesized to be involved in behavioral/cognitive processes such as memory and in diseases. Genomic imprinting is of critical importance to brain development and normal behavior, and exemplifies how epigenetic states regulate genome function and gene dosage. While most genes are expressed from both alleles, imprinted genes are usually expressed from either the maternally or the paternally inherited chromosome. Here, we show that in contrast to its canonical imprinting in nonneurogenic regions, Delta-like homolog 1 (Dlk1) is expressed biallelically in the SGZ, and both parental alleles are required for stem cell behavior and normal adult neurogenesis in the hippocampus. To evaluate the effects of maternally, paternally, and biallelically inherited mutations within the Dlk1 gene in specific behavioral domains, we subjected Dlk1-mutant mice to a battery of tests that dissociate and evaluate the effects of Dlk1 dosage on spatial learning ability and on anxiety traits. Importantly, reduction in Dlk1 levels triggers specific cognitive abnormalities that affect aspects of discriminating differences in environmental stimuli, emphasizing the importance of selective absence of imprinting in this neurogenic niche.
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Affiliation(s)
- Raquel Montalbán-Loro
- ERI Biotecmed-Departamento de Biología Celular, Universidad de Valencia, 46010 Valencia,Spain
| | - Glenda Lassi
- Genetics and Epigenetics of Behaviour (GEB) Laboratory, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Translational Science and Experimental Medicine Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Anna Lozano-Ureña
- ERI Biotecmed-Departamento de Biología Celular, Universidad de Valencia, 46010 Valencia,Spain
| | - Ana Perez-Villalba
- ERI Biotecmed-Departamento de Biología Celular, Universidad de Valencia, 46010 Valencia,Spain
- Faculty of Psychology, Laboratory of Animal Behavior Phenotype (LABP), Universidad Católica de Valencia, 46100 Valencia, Spain
| | | | - Marika Charalambous
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | | | - Alexa E Horner
- Synome Ltd, Babraham, Cambridge CB22 3AT, United Kingdom
| | - Lisa M Saksida
- Department of Psychology, Medical Research Council and Wellcome Trust Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge CB2 3EB, United Kingdom
- Molecular Medicine Research Laboratories, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5K8, Canada
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- The Brain and Mind Institute, Western University, London, ON N6A 5B7, Canada
| | - Timothy J Bussey
- Department of Psychology, Medical Research Council and Wellcome Trust Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge CB2 3EB, United Kingdom
- Molecular Medicine Research Laboratories, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5K8, Canada
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- The Brain and Mind Institute, Western University, London, ON N6A 5B7, Canada
| | - José Luis Trejo
- Department of Translational Neuroscience, Cajal Institute, The Spanish National Research Council, Madrid 28002, Spain
| | - Valter Tucci
- Genetics and Epigenetics of Behaviour (GEB) Laboratory, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | | | - Sacri R Ferrón
- ERI Biotecmed-Departamento de Biología Celular, Universidad de Valencia, 46010 Valencia,Spain;
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20
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TETology: Epigenetic Mastermind in Action. Appl Biochem Biotechnol 2021; 193:1701-1726. [PMID: 33694104 DOI: 10.1007/s12010-021-03537-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
Cytosine methylation is a well-explored epigenetic modification mediated by DNA methyltransferases (DNMTs) which are considered "methylation writers"; cytosine methylation is a reversible process. The process of removal of methyl groups from DNA remained unelucidated until the discovery of ten-eleven translocation (TET) proteins which are now considered "methylation editors." TET proteins are a family of Fe(II) and alpha-ketoglutarate-dependent 5-methyl cytosine dioxygenases-they convert 5-methyl cytosine to 5-hydroxymethyl cytosine, and to further oxidized derivatives. In humans, there are three TET paralogs with tissue-specific expression, namely TET1, TET2, and TET3. Among the TETs, TET2 is highly expressed in hematopoietic stem cells where it plays a pleiotropic role. The paralogs also differ in their structure and DNA binding. TET2 lacks the CXXC domain which mediates DNA binding in the other paralogs; thus, TET2 requires interactions with other proteins containing DNA-binding domains for effectively binding to DNA to bring about the catalysis. In addition to its role as methylation editor of DNA, TET2 also serves as methylation editor of RNA. Thus, TET2 is involved in epigenetics as well as epitranscriptomics. TET2 mutations have been found in various malignant hematological disorders like acute myeloid leukemia, and non-malignant hematological disorders like myelodysplastic syndromes. Increasing evidence shows that TET2 plays an important role in the non-hematopoietic system as well. Hepatocellular carcinoma, gastric cancer, prostate cancer, and melanoma are some non-hematological malignancies in which a role of TET2 has been implicated. Loss of TET2 is also associated with atherosclerotic vascular lesions and endometriosis. The current review elaborates on the role of structure, catalysis, physiological functions, pathological alterations, and methods to study TET2, with specific emphasis on epigenomics and epitranscriptomics.
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21
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Sun J, Yang J, Miao X, Loh HH, Pei D, Zheng H. Proteins in DNA methylation and their role in neural stem cell proliferation and differentiation. CELL REGENERATION (LONDON, ENGLAND) 2021; 10:7. [PMID: 33649938 PMCID: PMC7921253 DOI: 10.1186/s13619-020-00070-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/25/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND Epigenetic modifications, namely non-coding RNAs, DNA methylation, and histone modifications such as methylation, phosphorylation, acetylation, ubiquitylation, and sumoylation play a significant role in brain development. DNA methyltransferases, methyl-CpG binding proteins, and ten-eleven translocation proteins facilitate the maintenance, interpretation, and removal of DNA methylation, respectively. Different forms of methylation, including 5-methylcytosine, 5-hydroxymethylcytosine, and other oxidized forms, have been detected by recently developed sequencing technologies. Emerging evidence suggests that the diversity of DNA methylation patterns in the brain plays a key role in fine-tuning and coordinating gene expression in the development, plasticity, and disorders of the mammalian central nervous system. Neural stem cells (NSCs), originating from the neuroepithelium, generate neurons and glial cells in the central nervous system and contribute to brain plasticity in the adult mammalian brain. MAIN BODY Here, we summarized recent research in proteins responsible for the establishment, maintenance, interpretation, and removal of DNA methylation and those involved in the regulation of the proliferation and differentiation of NSCs. In addition, we discussed the interactions of chemicals with epigenetic pathways to regulate NSCs as well as the connections between proteins involved in DNA methylation and human diseases. CONCLUSION Understanding the interplay between DNA methylation and NSCs in a broad biological context can facilitate the related studies and reduce potential misunderstanding.
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Affiliation(s)
- Jiaqi Sun
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China.
| | - Junzheng Yang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China
| | - Xiaoli Miao
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China
| | - Horace H Loh
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China
| | - Duanqing Pei
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China.,CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, 510530, China.,Institutes for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,School of Life Science, Westlake University, Hangzhou, 310024, China
| | - Hui Zheng
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #188 Kaiyuan Ave., Science City, Huangpu District, Guangzhou, 510700, China. .,CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, 510530, China. .,Institutes for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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22
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Morris-Blanco KC, Chokkalla AK, Bertogliat MJ, Vemuganti R. TET3 regulates DNA hydroxymethylation of neuroprotective genes following focal ischemia. J Cereb Blood Flow Metab 2021; 41:590-603. [PMID: 32380888 PMCID: PMC7922754 DOI: 10.1177/0271678x20912965] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 5-hydroxymethylcytosine (5hmC) epigenetic modification is highly enriched in the CNS and a critical modulator of neuronal function and development. We found that cortical 5hmC was enhanced from 5 min to three days of reperfusion following focal ischemia in adult mice. Blockade of the 5hmC-producing enzyme ten-eleven translocase 3 (TET3) increased edema, infarct volume, and motor function impairments. To determine the mechanism by which TET3 provides ischemic neuroprotection, we assessed the genomic regions where TET3 modulates 5hmC. Genome-wide sequencing analysis of differentially hydroxymethylated regions (DhMRs) revealed that focal ischemia robustly increased 5hmC at the promoters of thousands of genes in a TET3-dependent manner. TET3 inhibition reduced 5hmC at the promoters of neuroprotective genes involved in cell survival, angiogenesis, neurogenesis, antioxidant defense, DNA repair, and metabolism demonstrating a role for TET3 in endogenous protection against stroke. The mRNA expression of several genes with known involvement in ischemic neuroprotection were also reduced with TET3 knockdown in both male and female mice, establishing a correlation between decreased promoter 5hmC levels and decreased gene expression. Collectively, our results indicate that TET3 globally increases 5hmC at regulatory regions and overwhelmingly modulates 5hmC in several neuroprotective pathways that may improve outcome after ischemic injury.
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Affiliation(s)
- Kahlilia C Morris-Blanco
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA.,Department of Research, William S. Middleton Veterans Administration Hospital, Madison, WI, USA
| | - Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA.,Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Mario J Bertogliat
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA.,Department of Research, William S. Middleton Veterans Administration Hospital, Madison, WI, USA.,Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
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23
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MacArthur IC, Dawlaty MM. TET Enzymes and 5-Hydroxymethylcytosine in Neural Progenitor Cell Biology and Neurodevelopment. Front Cell Dev Biol 2021; 9:645335. [PMID: 33681230 PMCID: PMC7930563 DOI: 10.3389/fcell.2021.645335] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/01/2021] [Indexed: 12/19/2022] Open
Abstract
Studies of tissue-specific epigenomes have revealed 5-hydroxymethylcytosine (5hmC) to be a highly enriched and dynamic DNA modification in the metazoan nervous system, inspiring interest in the function of this epigenetic mark in neurodevelopment and brain function. 5hmC is generated by oxidation of 5-methylcytosine (5mC), a process catalyzed by the ten–eleven translocation (TET) enzymes. 5hmC serves not only as an intermediate in DNA demethylation but also as a stable epigenetic mark. Here, we review the known functions of 5hmC and TET enzymes in neural progenitor cell biology and embryonic and postnatal neurogenesis. We also discuss how TET enzymes and 5hmC regulate neuronal activity and brain function and highlight their implications in human neurodevelopmental and neurodegenerative disorders. Finally, we present outstanding questions in the field and envision new research directions into the roles of 5hmC and TET enzymes in neurodevelopment.
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Affiliation(s)
- Ian C MacArthur
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Meelad M Dawlaty
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, United States
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24
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Tsiouplis NJ, Bailey DW, Chiou LF, Wissink FJ, Tsagaratou A. TET-Mediated Epigenetic Regulation in Immune Cell Development and Disease. Front Cell Dev Biol 2021; 8:623948. [PMID: 33520997 PMCID: PMC7843795 DOI: 10.3389/fcell.2020.623948] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
TET proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidation products in DNA. The oxidized methylcytosines (oxi-mCs) facilitate DNA demethylation and are also novel epigenetic marks. TET loss-of-function is strongly associated with cancer; TET2 loss-of-function mutations are frequently observed in hematological malignancies that are resistant to conventional therapies. Importantly, TET proteins govern cell fate decisions during development of various cell types by activating a cell-specific gene expression program. In this review, we seek to provide a conceptual framework of the mechanisms that fine tune TET activity. Then, we specifically focus on the multifaceted roles of TET proteins in regulating gene expression in immune cell development, function, and disease.
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Affiliation(s)
- Nikolas James Tsiouplis
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States
| | - David Wesley Bailey
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States.,University of North Carolina Center of Translational Immunology, Chapel Hill, NC, United States.,University of North Carolina Institute of Inflammatory Disease, Chapel Hill, NC, United States
| | - Lilly Felicia Chiou
- University of North Carolina Curriculum in Genetics and Molecular Biology, Chapel Hill, NC, United States
| | - Fiona Jane Wissink
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States
| | - Ageliki Tsagaratou
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States.,University of North Carolina Center of Translational Immunology, Chapel Hill, NC, United States.,University of North Carolina Institute of Inflammatory Disease, Chapel Hill, NC, United States.,University of North Carolina Curriculum in Genetics and Molecular Biology, Chapel Hill, NC, United States.,University of North Carolina Department of Genetics, Chapel Hill, NC, United States.,University of North Carolina Department of Microbiology and Immunology, Chapel Hill, NC, United States
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25
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Liu X, Fan B, Chopp M, Zhang Z. Epigenetic Mechanisms Underlying Adult Post Stroke Neurogenesis. Int J Mol Sci 2020; 21:E6179. [PMID: 32867041 PMCID: PMC7504398 DOI: 10.3390/ijms21176179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022] Open
Abstract
Stroke remains the leading cause of adult disability. Post-stroke neurogenesis contributes to functional recovery. As an intrinsic neurorestorative process, it is important to elucidate the molecular mechanism underlying stroke-induced neurogenesis and to develop therapies designed specifically to augment neurogenesis. Epigenetic mechanisms include DNA methylation, histone modification and its mediation by microRNAs and long-non-coding RNAs. In this review, we highlight how epigenetic factors including DNA methylation, histone modification, microRNAs and long-non-coding RNAs mediate stroke-induced neurogenesis including neural stem cell self-renewal and cell fate determination. We also summarize therapies targeting these mechanisms in the treatment of stroke.
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Affiliation(s)
- Xianshuang Liu
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA; (B.F.); (M.C.); (Z.Z.)
| | - Baoyan Fan
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA; (B.F.); (M.C.); (Z.Z.)
| | - Michael Chopp
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA; (B.F.); (M.C.); (Z.Z.)
- Department of Physics, Oakland University, Rochester, MI 48309, USA
| | - Zhenggang Zhang
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA; (B.F.); (M.C.); (Z.Z.)
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26
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Yang D, Wu X, Zhou Y, Wang W, Wang Z. The microRNA/TET3/REST axis is required for olfactory globose basal cell proliferation and male behavior. EMBO Rep 2020; 21:e49431. [PMID: 32677323 DOI: 10.15252/embr.201949431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 06/14/2020] [Accepted: 06/18/2020] [Indexed: 12/16/2022] Open
Abstract
In the main olfactory epithelium (MOE), new olfactory sensory neurons (OSNs) are persistently generated to replace lost neurons throughout an organism's lifespan. This process predominantly depends on the proliferation of globose basal cells (GBCs), the actively dividing stem cells in the MOE. Here, by using CRISPR/Cas9 and RNAi coupled with adeno-associated virus (AAV) nose delivery approaches, we demonstrated that knockdown of miR-200b/a in the MOE resulted in supernumerary Mash1-marked GBCs and decreased numbers of differentiated OSNs, accompanied by abrogation of male behaviors. We further showed that in the MOE, miR-200b/a targets the ten-eleven translocation methylcytosine dioxygenase TET3, which cooperates with RE1-silencing transcription factor (REST) to exert their functions. Deficiencies including proliferation, differentiation, and behaviors illustrated in miR-200b/a knockdown mice were rescued by suppressing either TET3 or REST. Our work describes a mechanism of coordination of GBC proliferation and differentiation in the MOE and olfactory male behaviors through miR-200/TET3/REST signaling.
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Affiliation(s)
- Dong Yang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Xiangbo Wu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Yanfen Zhou
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Weina Wang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Zhenshan Wang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
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27
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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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28
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Hepatic TET3 contributes to type-2 diabetes by inducing the HNF4α fetal isoform. Nat Commun 2020; 11:342. [PMID: 31953394 PMCID: PMC6969024 DOI: 10.1038/s41467-019-14185-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023] Open
Abstract
Precise control of hepatic glucose production (HGP) is pivotal to maintain systemic glucose homeostasis. HNF4α functions to stimulate transcription of key gluconeogenic genes. HNF4α harbors two promoters (P2 and P1) thought to be primarily active in fetal and adult livers, respectively. Here we report that the fetal version of HNF4α is required for HGP in the adult liver. This isoform is acutely induced upon fasting and chronically increased in type-2 diabetes (T2D). P2 isoform induction occurs in response to glucagon-stimulated upregulation of TET3, not previously shown to be involved in HGP. TET3 is recruited to the P2 promoter by FOXA2, leading to promoter demethylation and increased transcription. While TET3 overexpression augments HGP, knockdown of either TET3 or the P2 isoform alone in the liver improves glucose homeostasis in dietary and genetic mouse models of T2D. These studies unmask an unanticipated, conserved regulatory mechanism in HGP and offer potential therapeutic targets for T2D. The HNF4α gene contains two promoters, which are thought to be active in the fetal and adult liver, the latter contributing to hepatic glucose production. Here the authors show that the fetal isoform of HNF4a is induced in mouse livers upon fasting and in type-2 diabetes in a manner regulated by TET3.
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