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Faillace MP, Ortiz J, Rocco L, Bernabeu R. Histone Methyltransferase G9a Plays an Essential Role on Nicotine Preference in Zebrafish. Mol Neurobiol 2024; 61:6245-6263. [PMID: 38289455 DOI: 10.1007/s12035-024-03961-8] [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: 07/07/2023] [Accepted: 01/12/2024] [Indexed: 08/22/2024]
Abstract
Psychostimulants regulate behavioral responses in zebrafish via epigenetic mechanisms. We have previously shown that DNA methylation and histone deacetylase (HDAC) inhibition abolish nicotine-induced conditioned place preference (CPP) but little is known about the role of histone methylation in addictive-like behaviors. To assess the influence of histone methylation on nicotine-CPP, zebrafish were treated with a histone (H3) lysine-9 (K9) dimethyltransferase G9a/GLP inhibitor, BIX-01294 (BIX), which was administered before conditioning sessions. We observed a dual effect of the inhibitor BIX: at high doses inhibited while at low doses potentiated nicotine reward. Transcriptional expression of α6 and α7 subunits of the nicotinic acetylcholine receptor and of G9a, DNA methyl transferase-3, and HDAC-1 was upregulated in zebrafish with positive scores for nicotine-CPP. Changes in relative levels of these mRNA molecules reflected the effects of BIX on nicotine reward. BIX treatment per sé did not affect transcriptional levels of epigenetic enzymes that regulate trimethylation or demethylation of H3. BIX reduced H3K9me2 protein levels in a dose-dependent manner in key structures of the reward pathway. Thus, our findings indicated that different doses of BIX differentially affect nicotine CPP via strong or weak inhibition of G9a/GLP activity. Additionally, we found that the lysine demethylase inhibitor daminozide abolished nicotine-CPP and drug seeking. Our data demonstrate that H3 methylation catalyzed by G9a/GLP is involved in nicotine-CPP induction. Dimethylation of K9 at H3 is an important epigenetic modification that should be considered as a potential therapeutic target to treat nicotine reward and perhaps other drug addictions.
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Affiliation(s)
- Maria Paula Faillace
- Department of Physiology and Institute of Physiology and Biophysics (IFIBIO-Houssay, UBA-CONICET), School of Medicine, University of Buenos Aires, Paraguay 2155 7th floor (C1121ABG), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Joaquin Ortiz
- Department of Physiology and Institute of Physiology and Biophysics (IFIBIO-Houssay, UBA-CONICET), School of Medicine, University of Buenos Aires, Paraguay 2155 7th floor (C1121ABG), Ciudad Autónoma de Buenos Aires, Argentina
| | - Leandro Rocco
- Department of Physiology and Institute of Physiology and Biophysics (IFIBIO-Houssay, UBA-CONICET), School of Medicine, University of Buenos Aires, Paraguay 2155 7th floor (C1121ABG), Ciudad Autónoma de Buenos Aires, Argentina
| | - Ramon Bernabeu
- Department of Physiology and Institute of Physiology and Biophysics (IFIBIO-Houssay, UBA-CONICET), School of Medicine, University of Buenos Aires, Paraguay 2155 7th floor (C1121ABG), Ciudad Autónoma de Buenos Aires, Argentina.
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Negi CK, Bláhová L, Phan A, Bajard L, Blaha L. Triphenyl Phosphate Alters Methyltransferase Expression and Induces Genome-Wide Aberrant DNA Methylation in Zebrafish Larvae. Chem Res Toxicol 2024. [PMID: 39205618 DOI: 10.1021/acs.chemrestox.4c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Emerging environmental contaminants, organophosphate flame retardants (OPFRs), pose significant threats to ecosystems and human health. Despite numerous studies reporting the toxic effects of OPFRs, research on their epigenetic alterations remains limited. In this study, we investigated the effects of exposure to 2-ethylhexyl diphenyl phosphate (EHDPP), tricresyl phosphate (TMPP), and triphenyl phosphate (TPHP) on DNA methylation patterns during zebrafish embryonic development. We assessed general toxicity and morphological changes, measured global DNA methylation and hydroxymethylation levels, and evaluated DNA methyltransferase (DNMT) enzyme activity, as well as mRNA expression of DNMTs and ten-eleven translocation (TET) methylcytosine dioxygenase genes. Additionally, we analyzed genome-wide methylation patterns in zebrafish larvae using reduced-representation bisulfite sequencing. Our morphological assessment revealed no general toxicity, but a statistically significant yet subtle decrease in body length following exposure to TMPP and EHDPP, along with a reduction in head height after TPHP exposure, was observed. Eye diameter and head width were unaffected by any of the OPFRs. There were no significant changes in global DNA methylation levels in any exposure group, and TMPP showed no clear effect on DNMT expression. However, EHDPP significantly decreased only DNMT1 expression, while TPHP exposure reduced the expression of several DNMT orthologues and TETs in zebrafish larvae, leading to genome-wide aberrant DNA methylation. Differential methylation occurred primarily in introns (43%) and intergenic regions (37%), with 9% and 10% occurring in exons and promoter regions, respectively. Pathway enrichment analysis of differentially methylated region-associated genes indicated that TPHP exposure enhanced several biological and molecular functions corresponding to metabolism and neurological development. KEGG enrichment analysis further revealed TPHP-mediated potential effects on several signaling pathways including TGFβ, cytokine, and insulin signaling. This study identifies specific changes in DNA methylation in zebrafish larvae after TPHP exposure and brings novel insights into the epigenetic mode of action of TPHP.
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Affiliation(s)
- Chander K Negi
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Lucie Bláhová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Audrey Phan
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Lola Bajard
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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Castilho RM, Castilho LS, Palomares BH, Squarize CH. Determinants of Chromatin Organization in Aging and Cancer-Emerging Opportunities for Epigenetic Therapies and AI Technology. Genes (Basel) 2024; 15:710. [PMID: 38927646 PMCID: PMC11202709 DOI: 10.3390/genes15060710] [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: 03/31/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
This review article critically examines the pivotal role of chromatin organization in gene regulation, cellular differentiation, disease progression and aging. It explores the dynamic between the euchromatin and heterochromatin, coded by a complex array of histone modifications that orchestrate essential cellular processes. We discuss the pathological impacts of chromatin state misregulation, particularly in cancer and accelerated aging conditions such as progeroid syndromes, and highlight the innovative role of epigenetic therapies and artificial intelligence (AI) in comprehending and harnessing the histone code toward personalized medicine. In the context of aging, this review explores the use of AI and advanced machine learning (ML) algorithms to parse vast biological datasets, leading to the development of predictive models for epigenetic modifications and providing a framework for understanding complex regulatory mechanisms, such as those governing cell identity genes. It supports innovative platforms like CEFCIG for high-accuracy predictions and tools like GridGO for tailored ChIP-Seq analysis, which are vital for deciphering the epigenetic landscape. The review also casts a vision on the prospects of AI and ML in oncology, particularly in the personalization of cancer therapy, including early diagnostics and treatment optimization for diseases like head and neck and colorectal cancers by harnessing computational methods, AI advancements and integrated clinical data for a transformative impact on healthcare outcomes.
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Affiliation(s)
- Rogerio M. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
| | - Leonard S. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
| | - Bruna H. Palomares
- Oral Diagnosis Department, Piracicaba School of Dentistry, State University of Campinas, Piracicaba 13414-903, Sao Paulo, Brazil;
| | - Cristiane H. Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
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Xia Y, Chen K, Yang Q, Chen Z, Jin L, Zhang L, Yu X, Wang L, Xie C, Zhao Y, Shen Y, Tong J. Methylation in cornea and corneal diseases: a systematic review. Cell Death Discov 2024; 10:169. [PMID: 38589350 PMCID: PMC11002037 DOI: 10.1038/s41420-024-01935-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024] Open
Abstract
Corneal diseases are among the primary causes of blindness and vision loss worldwide. However, the pathogenesis of corneal diseases remains elusive, and diagnostic and therapeutic tools are limited. Thus, identifying new targets for the diagnosis and treatment of corneal diseases has gained great interest. Methylation, a type of epigenetic modification, modulates various cellular processes at both nucleic acid and protein levels. Growing evidence shows that methylation is a key regulator in the pathogenesis of corneal diseases, including inflammation, fibrosis, and neovascularization, making it an attractive potential therapeutic target. In this review, we discuss the major alterations of methylation and demethylation at the DNA, RNA, and protein levels in corneal diseases and how these dynamics contribute to the pathogenesis of corneal diseases. Also, we provide insights into identifying potential biomarkers of methylation that may improve the diagnosis and treatment of corneal diseases.
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Affiliation(s)
- Yutong Xia
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Kuangqi Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Qianjie Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Zhitong Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Le Jin
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyue Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Xin Yu
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyin Wang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Chen Xie
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Yuan Zhao
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Ye Shen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
| | - Jianping Tong
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
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Rajanala K, Upadhyay A. Epigenetic Switches in Retinal Homeostasis and Target for Drug Development. Int J Mol Sci 2024; 25:2840. [PMID: 38474086 DOI: 10.3390/ijms25052840] [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: 01/22/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Retinal homeostasis, a tightly regulated process maintaining the functional integrity of the retina, is vital for visual function. Emerging research has unveiled the critical role of epigenetic regulation in controlling gene expression patterns during retinal development, maintenance, and response to mutational loads and injuries. Epigenetic switches, including DNA methylation, histone modifications, and non-coding RNAs, play pivotal roles in orchestrating retinal gene expression and cellular responses through various intracellular, extracellular, and environmental modulators. This review compiles the current knowledge on epigenetic switches in retinal homeostasis, providing a deeper understanding of their impact on retinal structural integrity and function and using them as potential targets for therapeutic interventions.
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Affiliation(s)
| | - Arun Upadhyay
- Ocugen Inc., 11 Great Valley Parkway, Malvern, PA 19355, USA
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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [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: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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Rajesh V, Divya PK. Embryonic exposure to decitabine induces multiple neural tube defects in developing zebrafish. FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:1357-1379. [PMID: 37982970 DOI: 10.1007/s10695-023-01261-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 11/01/2023] [Indexed: 11/21/2023]
Abstract
Neural tube defects are severe congenital disorders of the central nervous system that originate during embryonic development when the neural tube fails to close completely. It affects one to two infants per 1000 births. The aetiology is multifactorial with contributions from both genetic and environmental factors. Dysregulated epigenetic mechanisms, in particular the abnormal genome-wide methylation during embryogenesis, have been linked to developmental abnormalities including neural tube defects. The current study investigated the influence of decitabine (DCT), a DNA methylation inhibitor, on embryonic development in zebrafish, with a focus on neural tube formation. The developing zebrafish embryos were exposed to graded concentrations of decitabine (from 13.69 μM to 1 mM) before the onset of neurulation. The developmental process was monitored at regular time intervals post fertilization. At 120 h post fertilization, the developing embryos were inspected individually to determine the incidence and severity of neural tube defects. Using alizarin red staining, the cranial and caudal neural tube morphology was examined in formaldehyde fixed larvae. Anomalies in neural tube and somite development, as well as a delay in hatching, were discovered at an early stage of development. As development continued, neural tube defects became increasingly evident, and there was a concentration-dependent rise in the prevalence and severity of various neural tube defects. 90% of growing embryos in the group exposed to decitabine 1 mM had multiple neural tube malformations, and 10% had isolated neural tube defects. With several abnormalities, the caudal region of the neural tube was seriously compromised. The histopathological studies supported the malformations in neural tube. Our study revealed the harmful impact of decitabine on the development of the neural tube in growing zebrafish. Moreover, these findings support the hypothesis that the hypomethylation during embryonic development causes neural tube defects.
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Affiliation(s)
- Venugopalan Rajesh
- Department of Pharmacology, The Erode College of Pharmacy and Research Institute affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Veppampalayam, Vallipurathampalayam (Po), Erode, Chennai, Tamil Nadu, 638112, India.
| | - Pachangattupalayam Karuppusamy Divya
- Department of Pharmacology, The Erode College of Pharmacy and Research Institute affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Veppampalayam, Vallipurathampalayam (Po), Erode, Chennai, Tamil Nadu, 638112, India
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Motaghed M, Sanooghi D, Bagher Z, Faghihi F, Lotfi A, Shahbazi A, Jogataei MT. In Vitro Assessment of the Gene Expression of EZH-2 and P300 During Motor Neuron Differentiation of Human Umbilical Cord Blood Mesenchymal Stem Cells. Basic Clin Neurosci 2022; 13:709-718. [PMID: 37313026 PMCID: PMC10258600 DOI: 10.32598/bcn.2021.2997.1] [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: 11/04/2020] [Revised: 03/10/2021] [Accepted: 04/01/2021] [Indexed: 11/02/2023] Open
Abstract
Introduction Maintenance of neurogenesis depends on the function of some histone-modifying enzymes; including Enhancer of zeste homolog 2 (EZH2) and histone acetyltransferases (P300). The mechanism of epigenetic regulation and gene expression underlying the transition of human umbilical cord blood mesenchymal stem cells (hUCB-MSCs) into MNs has not been fully clarified. Methods Two morphogens; sonic hedgehog (Shh: 100 ng/mL) and retinoic acid (RA: 0.01 mM) were involved in the specification of hUCB-MSCs into MNs after MSC characterization using Flow cytometry. Real time-quantitative PCR and immunocytochemistry were performed to find the expression of the genes at the level of mRNA and protein. Results The expression of MN-related markers was confirmed at the level of mRNA and protein by induction of differentiation. The results were confirmed by immunocytochemistry and showed those mean cell percentages of 55.33%±15.885% and 49.67%±13.796% could express Islet-1 and ChAT, respectively. The gene expression level of Islet-1 and ChAT was significantly increased in the first and second week of exposure, respectively. After two weeks, the expression level of P300 and EZH-2 genes increased remarkably. No significant expression of Mnx-1 was detected when compared to the control sample. Conclusion MN-related markers, Islet-1 and ChAT, were detected in differentiated cells of hUCB-MSCs, supporting the potency of cord blood cells in the regeneration of MN-related disorders. Assessing these epigenetic regulatory genes at the protein level can be suggested to confirm their functional epigenetic modifying effects during motor neuron differentiation.
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Affiliation(s)
- Marjaneh Motaghed
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
- International Campus, Iran University of Medical Sciences, Tehran, Iran
| | - Davood Sanooghi
- Department of Genetics, School of Biological Sciences, Shahid Beheshti University, Tehran, Iran
| | - Zohreh Bagher
- ENT and Head and Neck Research Center and Department, Five Senses Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Faezeh Faghihi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Lotfi
- Damavand Agricultural College, Technical and Vocational University, Tehran, Iran
| | - Ali Shahbazi
- Department of Neuroscience, School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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Sanooghi D, Vahdani P, Bagher Z, Faghihi F, Lotfi A. In vitro characterization of human bone marrow mesenchymal stem cell-derived motor neurons induced by epigenetic modifiers. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00171-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Motor neurons (MNs) are distinct types of cells in the dorso-ventral axis of the spinal cord. These cells are developed in the presence of two main morphogens, including Sonic hedgehog (Shh) and retinoic acid (RA). On the other hand, human bone marrow mesenchymal stem cells (hBM-MSCs) are known as a multipotent type of cells with neural differentiation capacity. In this regard, the aim of this study was to quantitatively evaluate the expression of MN-related genes and the potent epigenetic regulatory genes involved in neurogenesis, including Enhancer of zeste homolog 2 (EZH-2) and P300, during hBM-MSC differentiation into MN-like cells, using RA and Shh. After isolating and inducing the cells with Shh and RA, the results were evaluated using immunocytochemistry and qRT-PCR.
Results
Our findings showed that the treated cells could express choline acetyltransferase (ChAT) and insulin gene enhancer binding protein-1 (Islet-1) antigens at the protein level, 2 weeks after induction. Moreover, at the second week after induction, the induced cells expressed MN-related genes (ChAT and ISLET-1) and epigenetic regulatory genes (EZH-2 and P300) at significant levels compared to the control (non-treated BM-MSCs) and to the induced cells at the first week (day 7). In addition, the expression of EZH-2, as a histone-modifying gene, was also significantly upregulated at the first week compared to the control. No significant upregulation was detected in the expression of motor neuron and pancreas homeobox 1 (MNX-1) in the treated groups compared to the control group.
Conclusion
We concluded that epigenetic modifiers, P300 and EZH-2, are important mediators for regulating the process of motor neuron differentiation induced by RA and Shh.
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Wu J, Liu LL, Cao M, Hu A, Hu D, Luo Y, Wang H, Zhong JN. DNA methylation plays important roles in retinal development and diseases. Exp Eye Res 2021; 211:108733. [PMID: 34418429 DOI: 10.1016/j.exer.2021.108733] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/16/2022]
Abstract
DNA methylation is important in developing and post-mitotic cells in various tissues. Recent studies have shown that DNA methylation is highly dynamic, and plays important roles during retinal development and aging. In addition, the dynamic regulation of DNA methylation is involved in the occurrence and development of age-related macular degeneration and diabetic retinopathy and shows potential in disease diagnoses and prognoses. This review introduces the epigenetic concepts of DNA methylation and demethylation with an emphasis on their regulatory roles in retinal development and related diseases. Moreover, we propose exciting ideas such as its crosstalk with other epigenetic modifications and retinal regeneration, to provide a potential direction for understanding retinal diseases from the epigenetic perspective.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, Lishui Municipal Central Hospital, Lishui, 323000, Zhejiang Province, China
| | - Lin-Lin Liu
- Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Miao Cao
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Ang Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Die Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Yan Luo
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Hui Wang
- Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China.
| | - Jia-Ning Zhong
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China.
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Marchione AD, Thompson Z, Kathrein KL. DNA methylation and histone modifications are essential for regulation of stem cell formation and differentiation in zebrafish development. Brief Funct Genomics 2021:elab022. [PMID: 33782688 DOI: 10.1093/bfgp/elab022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 01/21/2023] Open
Abstract
The complex processes necessary for embryogenesis require a gene regulatory network that is complex and systematic. Gene expression regulates development and organogenesis, but this process is altered and fine-tuned by epigenetic regulators that facilitate changes in the chromatin landscape. Epigenetic regulation of embryogenesis adjusts the chromatin structure by modifying both DNA through methylation and nucleosomes through posttranslational modifications of histone tails. The zebrafish is a well-characterized model organism that is a quintessential tool for studying developmental biology. With external fertilization, low cost and high fecundity, the zebrafish are an efficient tool for studying early developmental stages. Genetic manipulation can be performed in vivo resulting in quick identification of gene function. Large-scale genome analyses including RNA sequencing, chromatin immunoprecipitation and chromatin structure all are feasible in the zebrafish. In this review, we highlight the key events in zebrafish development where epigenetic regulation plays a critical role from the early stem cell stages through differentiation and organogenesis.
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Raeisossadati R, Ferrari MFR, Kihara AH, AlDiri I, Gross JM. Epigenetic regulation of retinal development. Epigenetics Chromatin 2021; 14:11. [PMID: 33563331 PMCID: PMC7871400 DOI: 10.1186/s13072-021-00384-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/28/2021] [Indexed: 01/10/2023] Open
Abstract
In the developing vertebrate retina, retinal progenitor cells (RPCs) proliferate and give rise to terminally differentiated neurons with exquisite spatio-temporal precision. Lineage commitment, fate determination and terminal differentiation are controlled by intricate crosstalk between the genome and epigenome. Indeed, epigenetic regulation plays pivotal roles in numerous cell fate specification and differentiation events in the retina. Moreover, aberrant chromatin structure can contribute to developmental disorders and retinal pathologies. In this review, we highlight recent advances in our understanding of epigenetic regulation in the retina. We also provide insight into several aspects of epigenetic-related regulation that should be investigated in future studies of retinal development and disease. Importantly, focusing on these mechanisms could contribute to the development of novel treatment strategies targeting a variety of retinal disorders.
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Affiliation(s)
- Reza Raeisossadati
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Merari F R Ferrari
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil
| | | | - Issam AlDiri
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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Pisera-Fuster A, Zwiller J, Bernabeu R. Methionine Supplementation Abolishes Nicotine-Induced Place Preference in Zebrafish: a Behavioral and Molecular Analysis. Mol Neurobiol 2021; 58:2590-2607. [PMID: 33475949 DOI: 10.1007/s12035-020-02260-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/10/2020] [Indexed: 12/26/2022]
Abstract
In zebrafish, nicotine is known to regulate sensitivity to psychostimulants via epigenetic mechanisms. Little however is known about the regulation of addictive-like behavior by DNA methylation processes. To evaluate the influence of DNA methylation on nicotine-induced conditioned place preference (CPP), zebrafish were exposed to methyl supplementation through oral L-methionine (Met) administration. Met was found to reduce dramatically nicotine-induced CPP as well as behaviors associated with drug reward. The reduction was associated with the upregulation of DNA methyltransferases (DNMT1 and 3) as well as with the downregulation of methyl-cytosine dioxygenase-1 (TET1) and of nicotinic receptor subunits. Met also increased the expression of histone methyltransferases in nicotine-induced CPP groups. It reversed the nicotine-induced reduction in the methylation at α7 and NMDAR1 gene promoters. Treatment with the DNMT inhibitor 5-aza-2'-deoxycytidine (AZA) was found to reverse the effects of Met in structures of the reward pathway. Interestingly, Met did not modify the amount of the phospho-form of CREB (pCREB), a key factor establishing nicotine conditioning, whereas AZA increased pCREB levels. Our data suggest that nicotine-seeking behavior is partially dependent on DNA methylation occurring probably at specific gene loci, such as α7 and NMDAR1 receptor gene promoters. Overall, they suggest that Met should be considered as a potential therapeutic drug to treat nicotine addiction.
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Affiliation(s)
- Antonella Pisera-Fuster
- Department of Physiology and Institute of Physiology and Biophysics, School of Medicine, University of Buenos Aires, Paraguay 2155 7thfloor (C1121ABG), Ciudad Autónoma de Buenos Aires, Argentina
| | - Jean Zwiller
- Laboratoire de Neurosciences Cognitives et Adaptatives, Université de Strasbourg, Strasbourg, France
| | - Ramon Bernabeu
- Department of Physiology and Institute of Physiology and Biophysics, School of Medicine, University of Buenos Aires, Paraguay 2155 7thfloor (C1121ABG), Ciudad Autónoma de Buenos Aires, Argentina.
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14
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Li P, Quan W, Wang Z, Chen Y, Zhang H, Zhou Y. AD7c-NTP Impairs Adult Striatal Neurogenesis by Affecting the Biological Function of MeCP2 in APP/PSl Transgenic Mouse Model of Alzheimer's Disease. Front Aging Neurosci 2021; 12:616614. [PMID: 33551790 PMCID: PMC7855712 DOI: 10.3389/fnagi.2020.616614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022] Open
Abstract
The processes by which neural stem cells (NSCs) and neural precursor cells (NPCs) transform into the characteristic lineages observed in Alzheimer's disease (AD) are poorly characterized. Understanding these processes is of critical importance due to the increased prevalence of AD and the lack of effective AD strategies. Here, we used immunohistochemistry and Western blot to find out if MeCP2 was phosphorylated at a specific amino acid residue, Serine 421 (S421), and activated in response to AD-induced damage in amyloid precursor protein (APP)/PSl transgenic mice, altering its nuclear to cytoplasmic shuttling. Epigenetic examinations combined with chromatin immunoprecipitation and methylated DNA immunoprecipitation revealed that the translocation of MeCP2 from the nucleus to cytoplasm led to the loss of lineage-specific gene promoters (such as Gfap, Nestin, and Dcx), decreased transcriptional repression, and the activation of gene expression. Immunofluorescence data demonstrated that neurogenic progenitors with high levels of active phosphorylated MeCP2 at S421 (MeCP2 pS421) possessed a high probability of development into doublecortin (DCX)-expressing cells. AD7c-NTP will control neurogenic progenitor regeneration through its effects on MeCP2 pS421, leading to altered lineage-specific gene expression. This adds to the growing list of biological effects of AD7c-NTP in the brain and highlights MeCP2 as relevant to the plasticity of neural cells in the AD mice striatum.
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Affiliation(s)
- Pan Li
- Department of Neurology, Tianjin Huanhu Hospital Affiliated to Nankai University, Tianjin, China.,Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgery Institute, Tianjin Huanhu Hospital Affiliated to Nankai University, Tianjin, China
| | - Wei Quan
- Department of Neurosurgery, General Hospital of Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin Neurological Institute, Tianjin, China
| | - Zengguang Wang
- Department of Neurosurgery, General Hospital of Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin Neurological Institute, Tianjin, China
| | - Yuan Chen
- Department of Neurology, Tianjin Huanhu Hospital Affiliated to Nankai University, Tianjin, China.,Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgery Institute, Tianjin Huanhu Hospital Affiliated to Nankai University, Tianjin, China
| | - Huihong Zhang
- Department of Neurology, Tianjin Huanhu Hospital Affiliated to Nankai University, Tianjin, China.,Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgery Institute, Tianjin Huanhu Hospital Affiliated to Nankai University, Tianjin, China
| | - Yuying Zhou
- Department of Neurology, Tianjin Huanhu Hospital Affiliated to Nankai University, Tianjin, China.,Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgery Institute, Tianjin Huanhu Hospital Affiliated to Nankai University, Tianjin, China
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15
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Ross SE, Angeloni A, Geng FS, de Mendoza A, Bogdanovic O. Developmental remodelling of non-CG methylation at satellite DNA repeats. Nucleic Acids Res 2020; 48:12675-12688. [PMID: 33271598 PMCID: PMC7736785 DOI: 10.1093/nar/gkaa1135] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022] Open
Abstract
In vertebrates, DNA methylation predominantly occurs at CG dinucleotides however, widespread non-CG methylation (mCH) has been reported in mammalian embryonic stem cells and in the brain. In mammals, mCH is found at CAC trinucleotides in the nervous system, where it is associated with transcriptional repression, and at CAG trinucleotides in embryonic stem cells, where it positively correlates with transcription. Moreover, CAC methylation appears to be a conserved feature of adult vertebrate brains. Unlike any of those methylation signatures, here we describe a novel form of mCH that occurs in the TGCT context within zebrafish mosaic satellite repeats. TGCT methylation is inherited from both male and female gametes, remodelled during mid-blastula transition, and re-established during gastrulation in all embryonic layers. Moreover, we identify DNA methyltransferase 3ba (Dnmt3ba) as the primary enzyme responsible for the deposition of this mCH mark. Finally, we observe that TGCT-methylated repeats are specifically associated with H3K9me3-marked heterochromatin suggestive of a functional interplay between these two gene-regulatory marks. Altogether, this work provides insight into a novel form of vertebrate mCH and highlights the substrate diversity of vertebrate DNA methyltransferases.
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Affiliation(s)
- Samuel E Ross
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Allegra Angeloni
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Fan-Suo Geng
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Alex de Mendoza
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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16
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Oliveira CCV, Fatsini E, Fernández I, Anjos C, Chauvigné F, Cerdà J, Mjelle R, Fernandes JMO, Cabrita E. Kisspeptin Influences the Reproductive Axis and Circulating Levels of microRNAs in Senegalese Sole. Int J Mol Sci 2020; 21:E9051. [PMID: 33260781 PMCID: PMC7730343 DOI: 10.3390/ijms21239051] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
Kisspeptin regulates puberty and reproduction onset, acting upstream of the brain-pituitary-gonad (HPG) axis. This study aimed to test a kisspeptin-based hormonal therapy on cultured Senegalese sole (G1) breeders, known to have reproductive dysfunctions. A single intramuscular injection of KISS2-10 decapeptide (250 µg/kg) was tested in females and males during the reproductive season, and gonad maturation, sperm motility, plasma levels of gonadotropins (Fsh and Lh) and sex steroids (11-ketotestosterone, testosterone and estradiol), as well as changes in small non-coding RNAs (sncRNAs) in plasma, were investigated. Fsh, Lh, and testosterone levels increased after kisspeptin injection in both sexes, while sperm analysis did not show differences between groups. Let7e, miR-199a-3p and miR-100-5p were differentially expressed in females, while miR-1-3p miRNA was up-regulated in kisspeptin-treated males. In silico prediction of mRNAs targeted by miRNAs revealed that kisspeptin treatment might affect paracellular transporters, regulate structural and functional polarity of cells, neural networks and intracellular trafficking in Senegalese sole females; also, DNA methylation and sphingolipid metabolism might be altered in kisspeptin-treated males. Results demonstrated that kisspeptin stimulated gonadotropin and testosterone secretion in both sexes and induced an unanticipated alteration of plasma miRNAs, opening new research venues to understand how this neuropeptide impacts in fish HPG axis.
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Affiliation(s)
- Catarina C. V. Oliveira
- Center of Marine Sciences-CCMAR, University of Algarve, 8005-139 Faro, Portugal; (E.F.); (C.A.)
| | - Elvira Fatsini
- Center of Marine Sciences-CCMAR, University of Algarve, 8005-139 Faro, Portugal; (E.F.); (C.A.)
| | - Ignacio Fernández
- Aquaculture Research Center, Agrarian Technological Institute of Castile and Leon, Ctra. Arévalo, s/n, 40196 Segovia, Spain;
| | - Catarina Anjos
- Center of Marine Sciences-CCMAR, University of Algarve, 8005-139 Faro, Portugal; (E.F.); (C.A.)
| | - François Chauvigné
- IRTA-Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, 08193 Barcelona, Spain; (F.C.); (J.C.)
| | - Joan Cerdà
- IRTA-Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, 08193 Barcelona, Spain; (F.C.); (J.C.)
| | - Robin Mjelle
- Faculty of Bioscience and Aquaculture, Nord University, 8049 Bodø, Norway; (R.M.); (J.M.O.F.)
| | - Jorge M. O. Fernandes
- Faculty of Bioscience and Aquaculture, Nord University, 8049 Bodø, Norway; (R.M.); (J.M.O.F.)
| | - Elsa Cabrita
- Center of Marine Sciences-CCMAR, University of Algarve, 8005-139 Faro, Portugal; (E.F.); (C.A.)
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17
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Mu X, Chen X, Liu J, Yuan L, Wang D, Qian L, Qian Y, Shen G, Huang Y, Li X, Li Y, Lin X. A multi-omics approach reveals molecular mechanisms by which phthalates induce cardiac defects in zebrafish (Danio rerio). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:113876. [PMID: 32806432 DOI: 10.1016/j.envpol.2019.113876] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 06/11/2023]
Abstract
The potential risks of phthalates affecting human and animal health as well as the environment are emerging as serious concerns worldwide. However, the mechanism by which phthalates induce developmental effects is under debate. Herein, we found that embryonic exposure of zebrafish to di-(2-ethylhexyl) phthalate (DEHP) and di-butyl phthalate (DBP) increased the rate of heart defects including abnormal heart rate and pericardial edema. Changes in the transcriptional profile demonstrated that genes involved in the development of the heart, such as tbx5b, nppa, ctnt, my17, cmlc1, were significantly altered by DEHP and DBP at 50 μg/L, which agreed with the abnormal cardiac outcomes. Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) further showed that significant hypomethylation of nppa and ctnt was identified after DEHP and DBP exposure, which was consistent with the up-regulation of these genes. Notably, hypermethylation on the promoter region (<1 kb) of tbx5b was found after DEHP and DBP exposure, which might be responsible for its decrease in transcription. In conclusion, phthalates have the potential to induce cardiac birth defects, which might be associated with the transcriptional regulation of the involved developmental factors such as tbx5b. These findings would contribute to understand the molecular pathways that mediated the cardiac defects caused by phthalates.
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Affiliation(s)
- Xiyan Mu
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China.
| | - Xiaofeng Chen
- College of Sciences, China Agricultural University, People's Republic of China
| | - Jia Liu
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Lilai Yuan
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Donghui Wang
- College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Le Qian
- College of Sciences, China Agricultural University, People's Republic of China
| | - Yu Qian
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Gongming Shen
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Ying Huang
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Xuxing Li
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Yingren Li
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Xiangming Lin
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
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18
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Kenney MC, Nashine S. Further understanding of epigenetic dysfunction of the retinal pigment epithelium in AMD. EXPERT REVIEW OF OPHTHALMOLOGY 2020; 15:221-231. [PMID: 33732291 DOI: 10.1080/17469899.2020.1767597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Introduction Modulation of epigenetic mechanisms that contribute to retinal development may render the eye susceptible to age-related macular degeneration (AMD). Progression of AMD involves alterations of epigenome such as CpG methylation and histone modifications, and study of the epigenetic regulation of molecular/ cellular pathways associated with AMD might identify target epigenetic markers for treatment of AMD. Areas covered In this review, we provide an overview of the influence of epigenetic factors on signaling pathways/ related genes associated with AMD, mainly hypoxia, angiogenesis, inflammation, complement, and oxidative stress; and discuss the critical role of microRNAs in AMD. Expert Opinion Better understanding of epigenetic-mediated and microRNA-mediated regulation of the AMD disease-related pathways would help to assess the risk of developing AMD besides providing valuable insight on potential target candidates for AMD therapy.
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Affiliation(s)
- Maria Cristina Kenney
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, USA.,Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, USA
| | - Sonali Nashine
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, USA
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19
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Akdogan-Ozdilek B, Duval KL, Goll MG. Chromatin dynamics at the maternal to zygotic transition: recent advances from the zebrafish model. F1000Res 2020; 9. [PMID: 32528656 PMCID: PMC7262572 DOI: 10.12688/f1000research.21809.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Early animal development is characterized by intense reorganization of the embryonic genome, including large-scale changes in chromatin structure and in the DNA and histone modifications that help shape this structure. Particularly profound shifts in the chromatin landscape are associated with the maternal-to-zygotic transition, when the zygotic genome is first transcribed and maternally loaded transcripts are degraded. The accessibility of the early zebrafish embryo facilitates the interrogation of chromatin during this critical window of development, making it an important model for early chromatin regulation. Here, we review our current understanding of chromatin dynamics during early zebrafish development, highlighting new advances as well as similarities and differences between early chromatin regulation in zebrafish and other species.
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Affiliation(s)
| | | | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, GA, USA
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20
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Raja DA, Subramaniam Y, Aggarwal A, Gotherwal V, Babu A, Tanwar J, Motiani RK, Sivasubbu S, Gokhale RS, Natarajan VT. Histone variant dictates fate biasing of neural crest cells to melanocyte lineage. Development 2020; 147:dev.182576. [PMID: 32098766 DOI: 10.1242/dev.182576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022]
Abstract
In the neural crest lineage, progressive fate restriction and stem cell assignment are crucial for both development and regeneration. Whereas fate commitment events have distinct transcriptional footprints, fate biasing is often transitory and metastable, and is thought to be moulded by epigenetic programmes. Therefore, the molecular basis of specification is difficult to define. In this study, we established a role for a histone variant, H2a.z.2, in specification of the melanocyte lineage from multipotent neural crest cells. H2a.z.2 silencing reduces the number of melanocyte precursors in developing zebrafish embryos and from mouse embryonic stem cells in vitro We demonstrate that this histone variant occupies nucleosomes in the promoter of the key melanocyte determinant mitf, and enhances its induction. CRISPR/Cas9-based targeted mutagenesis of this gene in zebrafish drastically reduces adult melanocytes, as well as their regeneration. Thereby, our study establishes the role of a histone variant upstream of the core gene regulatory network in the neural crest lineage. This epigenetic mark is a key determinant of cell fate and facilitates gene activation by external instructive signals, thereby establishing melanocyte fate identity.
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Affiliation(s)
- Desingu Ayyappa Raja
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Yogaspoorthi Subramaniam
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Ayush Aggarwal
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishvabandhu Gotherwal
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Aswini Babu
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Jyoti Tanwar
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Rajender K Motiani
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Sridhar Sivasubbu
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Rajesh S Gokhale
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Vivek T Natarajan
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India .,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
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21
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Balasubramanian S, Raghunath A, Perumal E. Role of epigenetics in zebrafish development. Gene 2019; 718:144049. [DOI: 10.1016/j.gene.2019.144049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
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22
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Wu T, Sun XY, Yang X, Liu L, Tong K, Gao Y, Hao JR, Cao J, Gao C. Histone H3K9 Trimethylation Downregulates the Expression of Brain-Derived Neurotrophic Factor in the Dorsal Hippocampus and Impairs Memory Formation During Anaesthesia and Surgery. Front Mol Neurosci 2019; 12:246. [PMID: 31708739 PMCID: PMC6823536 DOI: 10.3389/fnmol.2019.00246] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/24/2019] [Indexed: 01/01/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is essential for cognitive and memory functions. Abnormal BDNF expression in the central nervous system may impair these functions. Anaesthesia and surgery can induce perioperative neurocognitive disorders (PND). Clinical studies show that BDNF expression is decreased in patients presenting with cognitive impairment after anaesthesia and surgery. However, the molecular mechanism is still unclear. Epigenetic regulation plays an important role in cognition. The hypermethylation of H3K9 is crucial for transcriptional silencing and the onset of cognitive disorders. Here, we hypothesised that H3K9 trimethylation repressed BDNF expression and impaired memory formation or recall during anaesthesia and surgery. Laparotomy under isoflurane inhalation anaesthesia, behavioural tests, Western blotting, quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR), chromatin immunoprecipitation (ChIP), and immunohistochemistry were used in this study. BDNF expression was decreased in the hippocampus after anaesthesia and surgery. Cognitive impairment affected memory formation but not recall. The trimethylation of H3K9 downregulated BDNF expression. The overexpression of BDNF or use of exogenous BDNF improved the impairment of memory formation caused by anaesthesia and surgery. Therefore, inhibiting H3K9 trimethylation and increasing the expression of BDNF may help prevent PND in the clinical setting.
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Affiliation(s)
- Tong Wu
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China.,Department of Anesthesia, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Xiao-Yu Sun
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Xiu Yang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Le Liu
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Kun Tong
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Ya Gao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Jing-Ru Hao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
| | - Jing Cao
- Department of Anesthesia, Xuzhou Central Hospital, The Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
| | - Can Gao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, China
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23
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Seelan RS, Pisano M, Greene RM. Nucleic acid methylation and orofacial morphogenesis. Birth Defects Res 2019; 111:1593-1610. [PMID: 31385455 DOI: 10.1002/bdr2.1564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
Abstract
In this review, we highlight the current state of knowledge of the diverse roles nucleic acid methylation plays in the embryonic development of the orofacial region and how aberrant methylation may contribute to orofacial clefts. We also consider the role of methylation in the regulation of neural crest cell function as it pertains to orofacial ontogeny. Changes in DNA methylation, as a consequence of environmental effects, have been observed in the regulatory regions of several genes, potentially identifying new candidate genes for orofacial clefting and opening promising new avenues for further research. While the focus of this review is primarily on the nonsyndromic forms of orofacial clefting, syndromic forms are briefly discussed in the context of aberrant nucleic acid methylation.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
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24
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Nashine S, Nesburn AB, Kuppermann BD, Kenney MC. Age-related macular degeneration (AMD) mitochondria modulate epigenetic mechanisms in retinal pigment epithelial cells. Exp Eye Res 2019; 189:107701. [PMID: 31226340 DOI: 10.1016/j.exer.2019.107701] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023]
Abstract
Mitochondrial damage and epigenetic modifications have been implicated in the pathogenesis of Age-related Macular Degeneration (AMD). This study was designed to investigate the effects of AMD/normal mitochondria on epigenetic regulation in human transmitochondrial retinal pigment epithelial (RPE) cells in vitro. Human RPE cybrid cell lines were created by fusing mitochondria-deficient (Rho0) ARPE-19 cells with platelets obtained from either AMD patients (AMD cybrids) or normal subjects (normal cybrids). Therefore, all cybrids had identical nuclei (derived from ARPE-19 cells) but mitochondria derived from either AMD patients or age-matched normal subjects. AMD cybrids demonstrated increased RNA/protein levels for five methylation-related and four acetylation-related genes, along with lower levels of two methylation and three acetylation genes compared to normal cybrids. Demethylation using 5-Aza-2'-deoxycytidine (DAC) led to decreased expression of VEGF-A gene in AMD cells. Trichostatin A (TSA), an HDAC inhibitor, also influenced protein levels of VEGF-A, HIF1α, NFκB, and CFH in AMD cells. Our findings suggest that retrograde signaling leads to mitochondria-nucleus interactions that influence the epigenetic status of the RPE cells and this may help in the identification of future potential therapeutic targets for AMD.
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Affiliation(s)
- Sonali Nashine
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, USA
| | - Anthony B Nesburn
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, USA; Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Baruch D Kuppermann
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, USA
| | - M Cristina Kenney
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, USA; Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, USA.
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25
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Epigenetic Regulation of Organ Regeneration in Zebrafish. J Cardiovasc Dev Dis 2018; 5:jcdd5040057. [PMID: 30558240 PMCID: PMC6306890 DOI: 10.3390/jcdd5040057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023] Open
Abstract
The zebrafish is broadly used for investigating de novo organ regeneration, because of its strong regenerative potential. Over the past two decades of intense study, significant advances have been made in identifying both the regenerative cell sources and molecular signaling pathways in a variety of organs in adult zebrafish. Epigenetic regulation has gradually moved into the center-stage of this research area, aided by comprehensive work demonstrating that DNA methylation, histone modifications, chromatin remodeling complexes, and microRNAs are essential for organ regeneration. Here, we present a brief review of how these epigenetic components are induced upon injury, and how they are involved in sophisticated organ regeneration. In addition, we highlight several prospective research directions and their potential implications for regenerative medicine.
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26
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Anderson EM, Penrod RD, Barry SM, Hughes BW, Taniguchi M, Cowan CW. It is a complex issue: emerging connections between epigenetic regulators in drug addiction. Eur J Neurosci 2018; 50:2477-2491. [PMID: 30251397 DOI: 10.1111/ejn.14170] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/04/2018] [Accepted: 09/11/2018] [Indexed: 02/06/2023]
Abstract
Drug use leads to addiction in some individuals, but the underlying brain mechanisms that control the transition from casual drug use to an intractable substance use disorder (SUD) are not well understood. Gene x environment interactions such as the frequency of drug use and the type of substance used likely to promote maladaptive plastic changes in brain regions that are critical for controlling addiction-related behavior. Epigenetics encompasses a broad spectrum of mechanisms important for regulating gene transcription that are not dependent on changes in DNA base pair sequences. This review focuses on the proteins and complexes contributing to epigenetic modifications in the nucleus accumbens (NAc) following drug experience. We discuss in detail the three major mechanisms: histone acetylation and deacetylation, histone methylation, and DNA methylation. We discuss how drug use alters the regulation of the associated proteins regulating these processes and highlight how experimental manipulations of these proteins in the NAc can alter drug-related behaviors. Finally, we discuss the ways that histone modifications and DNA methylation coordinate actions by recruiting large epigenetic enzyme complexes to aid in transcriptional repression. Targeting these multiprotein epigenetic enzyme complexes - and the individual proteins that comprise them - might lead to effective therapeutics to reverse or treat SUDs in patients.
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Affiliation(s)
- Ethan M Anderson
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Rachel D Penrod
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Sarah M Barry
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Brandon W Hughes
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Makoto Taniguchi
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
| | - Christopher W Cowan
- Departments of Neuroscience and Psychiatry and Behavioral Sciences, Medical University of South Carolina, 173 Ashley Ave, MSC 510, Charleston, SC, 29425-2030, USA
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27
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Alata Jimenez N, Torres Pérez SA, Sánchez-Vásquez E, Fernandino JI, Strobl-Mazzulla PH. Folate deficiency prevents neural crest fate by disturbing the epigenetic Sox2 repression on the dorsal neural tube. Dev Biol 2018; 444 Suppl 1:S193-S201. [PMID: 30098999 DOI: 10.1016/j.ydbio.2018.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 08/03/2018] [Accepted: 08/03/2018] [Indexed: 12/22/2022]
Abstract
Folate deficiency has been known to contribute to neural tube and neural crest defects, but why these tissues are particularly affected, and which are the molecular mechanisms involved in those abnormalities are important human health questions that remain unanswered. Here we study the function of two of the main folate transporters, FolR1 and Rfc1, which are robustly expressed in these tissues. Folate is the precursor of S-adenosylmethionine, which is the main donor for DNA, protein and RNA methylation. Our results show that knockdown of FolR1 and/or Rfc1 reduced the abundance of histone H3 lysine and DNA methylation, two epigenetic modifications that play an important role during neural and neural crest development. Additionally, by knocking down folate transporter or pharmacologically inhibiting folate transport and metabolism, we observed ectopic Sox2 expression at the expense of neural crest markers in the dorsal neural tube. This is correlated with neural crest associated defects, with particular impact on orofacial formation. By using bisulfite sequencing, we show that this phenotype is consequence of reduced DNA methylation on the Sox2 locus at the dorsal neural tube, which can be rescued by the addition of folinic acid. Taken together, our in vivo results reveal the importance of folate as a source of the methyl groups necessary for the establishment of the correct epigenetic marks during neural and neural crest fate-restriction.
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Affiliation(s)
- Nagif Alata Jimenez
- Laboratory of Developmental Biology, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Int Marino 8200, Chascomús 7130, Argentina
| | - Sergio A Torres Pérez
- Laboratory of Developmental Biology, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Int Marino 8200, Chascomús 7130, Argentina
| | - Estefanía Sánchez-Vásquez
- Laboratory of Developmental Biology, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Int Marino 8200, Chascomús 7130, Argentina
| | - Juan I Fernandino
- Laboratory of Developmental Biology, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Int Marino 8200, Chascomús 7130, Argentina
| | - Pablo H Strobl-Mazzulla
- Laboratory of Developmental Biology, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Int Marino 8200, Chascomús 7130, Argentina.
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28
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Corso-Díaz X, Jaeger C, Chaitankar V, Swaroop A. Epigenetic control of gene regulation during development and disease: A view from the retina. Prog Retin Eye Res 2018; 65:1-27. [PMID: 29544768 PMCID: PMC6054546 DOI: 10.1016/j.preteyeres.2018.03.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/01/2018] [Accepted: 03/08/2018] [Indexed: 12/20/2022]
Abstract
Complex biological processes, such as organogenesis and homeostasis, are stringently regulated by genetic programs that are fine-tuned by epigenetic factors to establish cell fates and/or to respond to the microenvironment. Gene regulatory networks that guide cell differentiation and function are modulated and stabilized by modifications to DNA, RNA and proteins. In this review, we focus on two key epigenetic changes - DNA methylation and histone modifications - and discuss their contribution to retinal development, aging and disease, especially in the context of age-related macular degeneration (AMD) and diabetic retinopathy. We highlight less-studied roles of DNA methylation and provide the RNA expression profiles of epigenetic enzymes in human and mouse retina in comparison to other tissues. We also review computational tools and emergent technologies to profile, analyze and integrate epigenetic information. We suggest implementation of editing tools and single-cell technologies to trace and perturb the epigenome for delineating its role in transcriptional regulation. Finally, we present our thoughts on exciting avenues for exploring epigenome in retinal metabolism, disease modeling, and regeneration.
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Affiliation(s)
- Ximena Corso-Díaz
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Catherine Jaeger
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vijender Chaitankar
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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29
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Moreno-Villanueva M, Bürkle A. Epigenetic and redox biomarkers: Novel insights from the MARK-AGE study. Mech Ageing Dev 2018; 177:128-134. [PMID: 29969595 DOI: 10.1016/j.mad.2018.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/12/2018] [Accepted: 06/29/2018] [Indexed: 02/07/2023]
Abstract
Ageing is a multifactorial process that affects most, if not all, of the body's tissues and organs and can be defined as the accumulation of physical and psychological changes in a human being over time. The rate of ageing differs between individuals of the same chronological age, meaning that 'biological age' of a person may be different from 'chronological age'. Furthermore, ageing represents a very potent risk factor for diseases and disability in humans. Therefore, establishment of markers of biological ageing is important for preventing age-associated diseases and extending health span. MARK-AGE, a large-scale European study, aimed at identifying a set of biomarkers which, as a combination of parameters with appropriate weighting, would measure biological age better than any marker in isolation. But beyond the identification of useful biomarkers, MARK-AGE provided new insights in age-associated specific cellular processes, such as DNA methylation, oxidative stress and the regulation of zinc homeostasis.
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Affiliation(s)
- Maria Moreno-Villanueva
- Molecular Toxicology Group, Dept. of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Alexander Bürkle
- Molecular Toxicology Group, Dept. of Biology, University of Konstanz, D-78457 Konstanz, Germany.
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30
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Vieira GC, D'Ávila MF, Zanini R, Deprá M, da Silva Valente VL. Evolution of DNMT2 in drosophilids: Evidence for positive and purifying selection and insights into new protein (pathways) interactions. Genet Mol Biol 2018; 41:215-234. [PMID: 29668012 PMCID: PMC5913717 DOI: 10.1590/1678-4685-gmb-2017-0056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/18/2017] [Indexed: 12/03/2022] Open
Abstract
The DNA methyltransferase 2 (DNMT2) protein is the most conserved member of the
DNA methyltransferase family. Nevertheless, its substrate specificity is still
controversial and elusive. The genomic role and determinants of DNA methylation
are poorly understood in invertebrates, and several mechanisms and associations
are suggested. In Drosophila, the only known DNMT gene is
Dnmt2. Here we present our findings from a wide search for
Dnmt2 homologs in 68 species of Drosophilidae. We
investigated its molecular evolution, and in our phylogenetic analyses the main
clades of Drosophilidae species were recovered. We tested whether the
Dnmt2 has evolved neutrally or under positive selection
along the subgenera Drosophila and Sophophora
and investigated positive selection in relation to several physicochemical
properties. Despite of a major selective constraint on Dnmt2,
we detected six sites under positive selection. Regarding the DNMT2 protein, 12
sites under positive-destabilizing selection were found, which suggests a
selection that favors structural and functional shifts in the protein. The
search for new potential protein partners with DNMT2 revealed 15 proteins with
high evolutionary rate covariation (ERC), indicating a plurality of DNMT2
functions in different pathways. These events might represent signs of molecular
adaptation, with molecular peculiarities arising from the diversity of
evolutionary histories experienced by drosophilids.
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Affiliation(s)
- Gilberto Cavalheiro Vieira
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Marícia Fantinel D'Ávila
- Departamento de Zoologia e Ciências Biológicas, Universidade Federal de Santa Maria (UFSM), Palmeira das Missões, RS, Brazil
| | - Rebeca Zanini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Maríndia Deprá
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Vera Lúcia da Silva Valente
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Departamento de Zoologia e Ciências Biológicas, Universidade Federal de Santa Maria (UFSM), Palmeira das Missões, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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31
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Jessop P, Ruzov A, Gering M. Developmental Functions of the Dynamic DNA Methylome and Hydroxymethylome in the Mouse and Zebrafish: Similarities and Differences. Front Cell Dev Biol 2018; 6:27. [PMID: 29616219 PMCID: PMC5869911 DOI: 10.3389/fcell.2018.00027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/05/2018] [Indexed: 12/25/2022] Open
Abstract
5-methylcytosine (5mC) is the best understood DNA modification and is generally believed to be associated with repression of gene expression. Over the last decade, sequentially oxidized forms of 5mC (oxi-mCs) have been discovered within the genomes of vertebrates. Their discovery was accompanied by that of the ten-eleven translocation (TET) methylcytosine dioxygenases, the enzymes that catalyze the formation of the oxi-mCs. Although a number of studies performed on different vertebrate models and embryonic stem cells demonstrated that both TET enzymes and oxi-mCs are likely to be important for several developmental processes it is currently unclear whether their developmental roles are conserved among vertebrates. Here, we summarize recent developments in this field suggesting that biological roles of TETs/oxi-mCs may significantly differ between mice and zebrafish. Thus, although the role of TET proteins in late organogenesis has been documented for both these systems; unlike in mice the enzymatic oxidation of 5mC does not seem to be involved in zygotic reprogramming or gastrulation in zebrafish. Our analysis may provide an insight into the general principles of epigenetic regulation of animal development and cellular differentiation.
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Affiliation(s)
- Peter Jessop
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Alexey Ruzov
- Division of Cancer and Stem Cells, Centre for Biomolecular Sciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Martin Gering
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
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32
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Epigenetics in teleost fish: From molecular mechanisms to physiological phenotypes. Comp Biochem Physiol B Biochem Mol Biol 2018; 224:210-244. [PMID: 29369794 DOI: 10.1016/j.cbpb.2018.01.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 02/07/2023]
Abstract
While the field of epigenetics is increasingly recognized to contribute to the emergence of phenotypes in mammalian research models across different developmental and generational timescales, the comparative biology of epigenetics in the large and physiologically diverse vertebrate infraclass of teleost fish remains comparatively understudied. The cypriniform zebrafish and the salmoniform rainbow trout and Atlantic salmon represent two especially important teleost orders, because they offer the unique possibility to comparatively investigate the role of epigenetic regulation in 3R and 4R duplicated genomes. In addition to their sequenced genomes, these teleost species are well-characterized model species for development and physiology, and therefore allow for an investigation of the role of epigenetic modifications in the emergence of physiological phenotypes during an organism's lifespan and in subsequent generations. This review aims firstly to describe the evolution of the repertoire of genes involved in key molecular epigenetic pathways including histone modifications, DNA methylation and microRNAs in zebrafish, rainbow trout, and Atlantic salmon, and secondly, to discuss recent advances in research highlighting a role for molecular epigenetics in shaping physiological phenotypes in these and other teleost models. Finally, by discussing themes and current limitations of the emerging field of teleost epigenetics from both theoretical and technical points of view, we will highlight future research needs and discuss how epigenetics will not only help address basic research questions in comparative teleost physiology, but also inform translational research including aquaculture, aquatic toxicology, and human disease.
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33
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Madakashira B, Corbett L, Zhang C, Paoli P, Casement JW, Mann J, Sadler KC, Mann DA. Variant Histone H2afv reprograms DNA methylation during early zebrafish development. Epigenetics 2017; 12:811-824. [PMID: 29099280 PMCID: PMC5739095 DOI: 10.1080/15592294.2017.1359382] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The DNA methylome is re-patterned during discrete phases of vertebrate development. In zebrafish, there are 2 waves of global DNA demethylation and re-methylation: the first occurs before gastrulation when the parental methylome is changed to the zygotic pattern and the second occurs after formation of the embryonic body axis, during organ specification. The occupancy of the histone variant H2A.Z and regions of DNA methylation are generally anti-correlated, and it has been proposed that H2A.Z restricts the boundaries of highly methylated regions. While many studies have described the dynamics of methylome changes during early zebrafish development, the factors involved in establishing the DNA methylation landscape in zebrafish embryos have not been identified. We test the hypothesis that the zebrafish ortholog of H2A.Z (H2afv) restricts DNA methylation during development. We find that, in control embryos, bulk genome methylation decreases after gastrulation, with a nadir at the bud stage, and peaks during mid-somitogenesis; by 24 hours post -fertilization, total DNA methylation levels return to those detected in gastrula. Early zebrafish embryos depleted of H2afv have significantly more bulk DNA methylation during somitogenesis, suggesting that H2afv limits methylation during this stage of development. H2afv deficient embryos are small, with multisystemic abnormalities. Genetic interaction experiments demonstrate that these phenotypes are suppressed by depletion of DNA methyltransferase 1 (Dnmt1). This work demonstrates that H2afv is essential for global DNA methylation reprogramming during early vertebrate development and that embryonic development requires crosstalk between H2afv and Dnmt1.
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Affiliation(s)
- Bhavani Madakashira
- a Program in Biology , New York University Abu Dhabi , Abu Dhabi , United Arab Emirates
| | - Laura Corbett
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
| | - Chi Zhang
- a Program in Biology , New York University Abu Dhabi , Abu Dhabi , United Arab Emirates
| | - Pier Paoli
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
| | - John W Casement
- c Bioinformatics Support Unit, Faculty of Medical Sciences , Newcastle University , Newcastle Upon Tyne , NE24HH
| | - Jelena Mann
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
| | - Kirsten C Sadler
- a Program in Biology , New York University Abu Dhabi , Abu Dhabi , United Arab Emirates.,d Department of Medicine/Division of Liver Diseases, Department of Developmental and Regenerative Biology , Icahn School of Medicine at Mount Sinai , New York , New York
| | - Derek A Mann
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
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34
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Adamkova K, Yi YJ, Petr J, Zalmanova T, Hoskova K, Jelinkova P, Moravec J, Kralickova M, Sutovsky M, Sutovsky P, Nevoral J. SIRT1-dependent modulation of methylation and acetylation of histone H3 on lysine 9 (H3K9) in the zygotic pronuclei improves porcine embryo development. J Anim Sci Biotechnol 2017; 8:83. [PMID: 29118980 PMCID: PMC5664433 DOI: 10.1186/s40104-017-0214-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/25/2017] [Indexed: 12/31/2022] Open
Abstract
Background The histone code is an established epigenetic regulator of early embryonic development in mammals. The lysine residue K9 of histone H3 (H3K9) is a prime target of SIRT1, a member of NAD+-dependent histone deacetylase family of enzymes targeting both histone and non-histone substrates. At present, little is known about SIRT1-modulation of H3K9 in zygotic pronuclei and its association with the success of preimplantation embryo development. Therefore, we evaluated the effect of SIRT1 activity on H3K9 methylation and acetylation in porcine zygotes and the significance of H3K9 modifications for early embryonic development. Results Our results show that SIRT1 activators resveratrol and BML-278 increased H3K9 methylation and suppressed H3K9 acetylation in both the paternal and maternal pronucleus. Inversely, SIRT1 inhibitors nicotinamide and sirtinol suppressed methylation and increased acetylation of pronuclear H3K9. Evaluation of early embryonic development confirmed positive effect of selective SIRT1 activation on blastocyst formation rate (5.2 ± 2.9% versus 32.9 ± 8.1% in vehicle control and BML-278 group, respectively; P ≤ 0.05). Stimulation of SIRT1 activity coincided with fluorometric signal intensity of ooplasmic ubiquitin ligase MDM2, a known substrate of SIRT1 and known limiting factor of epigenome remodeling. Conclusions We conclude that SIRT1 modulates zygotic histone code, obviously through direct deacetylation and via non-histone targets resulting in increased H3K9me3. These changes in zygotes lead to more successful pre-implantation embryonic development and, indeed, the specific SIRT1 activation due to BML-278 is beneficial for in vitro embryo production and blastocyst achievement.
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Affiliation(s)
- Katerina Adamkova
- Department of Veterinary Sciences, Faculty of Agriculture, Food and Natural Resources, Czech University of Life Sciences Prague, 6-Suchdol, Prague, Czech Republic
| | - Young-Joo Yi
- Division of Biotechnology, Safety, Environment and Life Science Institute, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, 54596 South Korea
| | - Jaroslav Petr
- Institute of Animal Science, 10-Uhrineves, Prague, Czech Republic
| | - Tereza Zalmanova
- Department of Veterinary Sciences, Faculty of Agriculture, Food and Natural Resources, Czech University of Life Sciences Prague, 6-Suchdol, Prague, Czech Republic.,Institute of Animal Science, 10-Uhrineves, Prague, Czech Republic
| | - Kristyna Hoskova
- Department of Veterinary Sciences, Faculty of Agriculture, Food and Natural Resources, Czech University of Life Sciences Prague, 6-Suchdol, Prague, Czech Republic.,Institute of Animal Science, 10-Uhrineves, Prague, Czech Republic
| | - Pavla Jelinkova
- Department of Veterinary Sciences, Faculty of Agriculture, Food and Natural Resources, Czech University of Life Sciences Prague, 6-Suchdol, Prague, Czech Republic
| | - Jiri Moravec
- Proteomic Laboratory, Biomedical Center of Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Milena Kralickova
- Laboratory of Reproductive Medicine of Biomedical Center, Charles University, Pilsen, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Miriam Sutovsky
- Division of Animal Science, University of Missouri, Columbia, MO USA
| | - Peter Sutovsky
- Division of Animal Science, University of Missouri, Columbia, MO USA.,Departments of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO USA
| | - Jan Nevoral
- Department of Veterinary Sciences, Faculty of Agriculture, Food and Natural Resources, Czech University of Life Sciences Prague, 6-Suchdol, Prague, Czech Republic.,Laboratory of Reproductive Medicine of Biomedical Center, Charles University, Pilsen, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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35
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Feng C, Pettersson M, Lamichhaney S, Rubin CJ, Rafati N, Casini M, Folkvord A, Andersson L. Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate. eLife 2017; 6:e23907. [PMID: 28665273 PMCID: PMC5524536 DOI: 10.7554/elife.23907] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 06/28/2017] [Indexed: 12/23/2022] Open
Abstract
The Atlantic herring is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (π = 0.3%), only three-fold higher than in human. Here, we present a pedigree-based estimation of the mutation rate in this species. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 2.0 × 10-9 per base per generation. We observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development. The estimated mutation rate - the lowest among vertebrates analyzed to date - partially explains the discrepancy between the rather low nucleotide diversity in herring and its huge census population size. But a species like the herring will never reach its expected nucleotide diversity because of fluctuations in population size over the millions of years it takes to build up high nucleotide diversity.
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Affiliation(s)
- Chungang Feng
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mats Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sangeet Lamichhaney
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carl-Johan Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Nima Rafati
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Michele Casini
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, Sweden
| | - Arild Folkvord
- Department of Biology, University of Bergen and the Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway
- Institute of Marine Research, Bergen, Norway
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, United States
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36
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Transgenerational inheritance of neurobehavioral and physiological deficits from developmental exposure to benzo[a]pyrene in zebrafish. Toxicol Appl Pharmacol 2017; 329:148-157. [PMID: 28583304 DOI: 10.1016/j.taap.2017.05.033] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 12/11/2022]
Abstract
Benzo[a]pyrene (B[a]P) is a well-known genotoxic polycylic aromatic compound whose toxicity is dependent on signaling via the aryl hydrocarbon receptor (AHR). It is unclear to what extent detrimental effects of B[a]P exposures might impact future generations and whether transgenerational effects might be AHR-dependent. This study examined the effects of developmental B[a]P exposure on 3 generations of zebrafish. Zebrafish embryos were exposed from 6 to 120h post fertilization (hpf) to 5 and 10μM B[a]P and raised in chemical-free water until adulthood (F0). Two generations were raised from F0 fish to evaluate transgenerational inheritance. Morphological, physiological and neurobehavioral parameters were measured at two life stages. Juveniles of the F0 and F2 exhibited hyper locomotor activity, decreased heartbeat and mitochondrial function. B[a]P exposure during development resulted in decreased global DNA methylation levels and generally reduced expression of DNA methyltransferases in wild type zebrafish, with the latter effect largely reversed in an AHR2-null background. Adults from the F0 B[a]P exposed lineage displayed social anxiety-like behavior. Adults in the F2 transgeneration manifested gender-specific increased body mass index (BMI), increased oxygen consumption and hyper-avoidance behavior. Exposure to benzo[a]pyrene during development resulted in transgenerational inheritance of neurobehavioral and physiological deficiencies. Indirect evidence suggested the potential for an AHR2-dependent epigenetic route.
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Deimling SJ, Olsen JB, Tropepe V. The expanding role of the Ehmt2/G9a complex in neurodevelopment. NEUROGENESIS 2017; 4:e1316888. [PMID: 28596979 DOI: 10.1080/23262133.2017.1316888] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/22/2017] [Accepted: 03/30/2017] [Indexed: 10/19/2022]
Abstract
Epigenetic regulators play a crucial role in neurodevelopment. One such epigenetic complex, Ehmt1/2 (G9a/GLP), is essential for repressing gene transcription by methylating H3K9 in a highly tissue- and temporal-specific manner. Recently, data has emerged suggesting that this complex plays additional roles in regulating the activity of numerous other non-histone proteins. While much is known about the downstream effects of Ehmt1/2 function, evidence is only beginning to come to light suggesting the control of Ehmt1/2 function may be, at least in part, due to context-dependent binding partners. Here we review emerging roles for the Ehmt1/2 complex suggesting that it may play a much larger role than previously recognized, and discuss binding partners that we and others have recently characterized which act to coordinate its activity during early neurodevelopment.
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Affiliation(s)
- Steven J Deimling
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Jonathan B Olsen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Vincent Tropepe
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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38
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Kamstra JH, Sales LB, Aleström P, Legler J. Differential DNA methylation at conserved non-genic elements and evidence for transgenerational inheritance following developmental exposure to mono(2-ethylhexyl) phthalate and 5-azacytidine in zebrafish. Epigenetics Chromatin 2017; 10:20. [PMID: 28413451 PMCID: PMC5389146 DOI: 10.1186/s13072-017-0126-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/04/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Exposure to environmental stressors during development may lead to latent and transgenerational adverse health effects. To understand the role of DNA methylation in these effects, we used zebrafish as a vertebrate model to investigate heritable changes in DNA methylation following chemical-induced stress during early development. We exposed zebrafish embryos to non-embryotoxic concentrations of the biologically active phthalate metabolite mono(2-ethylhexyl) phthalate (MEHP, 30 µM) and the DNA methyltransferase 1 inhibitor 5-azacytidine (5AC, 10 µM). Direct, latent and transgenerational effects on DNA methylation were assessed using global, genome-wide and locus-specific DNA methylation analyses. RESULTS Following direct exposure in zebrafish embryos from 0 to 6 days post-fertilization, genome-wide analysis revealed a multitude of differentially methylated regions, strongly enriched at conserved non-genic elements for both compounds. Pathways involved in adipogenesis were enriched with the putative obesogenic compound MEHP. Exposure to 5AC resulted in enrichment of pathways involved in embryonic development and transgenerational effects on larval body length. Locus-specific methylation analysis of 10 differentially methylated sites revealed six of these loci differentially methylated in sperm sampled from adult zebrafish exposed during development to 5AC, and in first and second generation larvae. With MEHP, consistent changes were found at 2 specific loci in first and second generation larvae. CONCLUSIONS Our results suggest a functional role for DNA methylation on cis-regulatory conserved elements following developmental exposure to compounds. Effects on these regions are potentially transferred to subsequent generations.
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Affiliation(s)
- Jorke H. Kamstra
- Faculty of Veterinary Medicine, Department of Basic Sciences and Aquatic Medicine, CoE CERAD, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway
| | - Liana Bastos Sales
- Institute for Environmental Studies, VU University Amsterdam, Amsterdam, The Netherlands
| | - Peter Aleström
- Faculty of Veterinary Medicine, Department of Basic Sciences and Aquatic Medicine, CoE CERAD, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway
| | - Juliette Legler
- Institute for Environmental Studies, VU University Amsterdam, Amsterdam, The Netherlands
- Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
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39
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Testicular Dnmt3 expression and global DNA methylation are down-regulated by gonadotropin releasing hormones in the ricefield eel Monopterus albus. Sci Rep 2017; 7:43158. [PMID: 28225069 PMCID: PMC5320511 DOI: 10.1038/srep43158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/19/2017] [Indexed: 02/06/2023] Open
Abstract
In vertebrates, DNA methyltransferase 3 (Dnmt3) homologues are responsible for de novo DNA methylation and play important roles in germ cell development. In the present study, four dnmt3 genes, dnmt3aa, dnmt3ab, dnmt3ba and dnmt3bb.1, were identified in ricefield eels. Real-time quantitative PCR analysis showed that all four dnmt3 mRNAs were detected broadly in tissues examined, with testicular expression at relatively high levels. In the testis, immunostaining for all four Dnmt3 forms was mainly localized to spermatocytes, which also contained highly methylated DNA. All three forms of Gonadotropin-releasing hormone (Gnrh) in the ricefield eel were shown to decrease the expression of dnmt3 genes in the in vitro incubated testicular fragments through cAMP and IP3/Ca2+ pathways. Moreover, in vivo treatment of male fish with three forms of Gnrh decreased significantly the testicular Dnmt3 expression at both mRNA and protein levels, and the global DNA methylation levels. These results suggest that the expression of Dnmt3 and global DNA methylation in the testis of ricefield eels are potentially down-regulated by Gnrh, and reveal a novel regulatory mechanism of testicular Dnmt3 expression in vertebrates.
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40
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Hoang TV, Horowitz ER, Chaffee BR, Qi P, Flake RE, Bruney DG, Rasor BJ, Rosalez SE, Wagner BD, Robinson ML. Lens development requires DNMT1 but takes place normally in the absence of both DNMT3A and DNMT3B activity. Epigenetics 2017; 12:27-40. [PMID: 27824296 PMCID: PMC5270636 DOI: 10.1080/15592294.2016.1253651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/14/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022] Open
Abstract
Despite the wealth of knowledge of transcription factors involved in lens development, little information exists about the role of DNA methylation in this process. Here, we investigated the role of DNA methylation in lens development and fiber cell differentiation using mice conditionally lacking maintenance or de novo methyltransferases in the lens lineage. We found that while Dnmt1 inactivation at the lens placode stage (via the Le-Cre transgene) led to lens DNA hypomethylation and severe lens epithelial apoptosis, lens fiber cell differentiation remained largely unaffected. The simultaneous deletion of phosphatase and tensin homolog (Pten) elevated the level of phosphorylated AKT and rescued many of the morphological defects and cell death in DNMT1-deficient lenses. With a different Cre driver (MLR10) we demonstrated that a small number of lens epithelial cells escaped Dnmt1-deletion and over-proliferated to compensate for the loss of Dnmt1-deleted cells, suggesting that lens epithelium possess a substantial capacity for self-renewal. Unlike lenses deficient for Dnmt1, inactivation of both Dnmt3a and Dnmt3b by either the Le-Cre or MLR10-Cre transgene did not result in any obvious lens phenotype prior to 10 months of age. Taken together, while lens epithelial cell survival requires DNMT1, morphologically normal lenses develop in the absence of both DNMT3A and DNMT3B.
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Affiliation(s)
- Thanh V. Hoang
- Department of Biology, Miami University, Oxford, OH, USA
| | | | | | - Peipei Qi
- Department of Biology, Miami University, Oxford, OH, USA
| | | | | | - Blake J. Rasor
- Department of Biology, Miami University, Oxford, OH, USA
| | | | - Brad D. Wagner
- Department of Biology, Miami University, Oxford, OH, USA
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41
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Kong EY, Cheng SH, Yu KN. Zebrafish as an In Vivo Model to Assess Epigenetic Effects of Ionizing Radiation. Int J Mol Sci 2016; 17:ijms17122108. [PMID: 27983682 PMCID: PMC5187908 DOI: 10.3390/ijms17122108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/01/2016] [Accepted: 12/09/2016] [Indexed: 12/14/2022] Open
Abstract
Exposure to ionizing radiations (IRs) is ubiquitous in our environment and can be categorized into “targeted” effects and “non-targeted” effects. In addition to inducing deoxyribonucleic acid (DNA) damage, IR exposure leads to epigenetic alterations that do not alter DNA sequence. Using an appropriate model to study the biological effects of radiation is crucial to better understand IR responses as well as to develop new strategies to alleviate exposure to IR. Zebrafish, Danio rerio, is a scientific model organism that has yielded scientific advances in several fields and recent studies show the usefulness of this vertebrate model in radiation biology. This review briefly describes both “targeted” and “non-targeted” effects, describes the findings in radiation biology using zebrafish as a model and highlights the potential of zebrafish to assess the epigenetic effects of IR, including DNA methylation, histone modifications and miRNA expression. Other in vivo models are included to compare observations made with zebrafish, or to illustrate the feasibility of in vivo models when the use of zebrafish was unavailable. Finally, tools to study epigenetic modifications in zebrafish, including changes in genome-wide DNA methylation, histone modifications and miRNA expression, are also described in this review.
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Affiliation(s)
- Eva Yi Kong
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, China.
| | - Shuk Han Cheng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China.
| | - Kwan Ngok Yu
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China.
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42
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Reyes-Aguirre LI, Lamas M. Oct4 Methylation-Mediated Silencing As an Epigenetic Barrier Preventing Müller Glia Dedifferentiation in a Murine Model of Retinal Injury. Front Neurosci 2016; 10:523. [PMID: 27895551 PMCID: PMC5108807 DOI: 10.3389/fnins.2016.00523] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/28/2016] [Indexed: 11/29/2022] Open
Abstract
Müller glia (MG) is the most abundant glial type in the vertebrate retina. Among its many functions, it is capable of responding to injury by dedifferentiating, proliferating, and differentiating into every cell types lost to damage. This regenerative ability is notoriously absent in mammals. We have previously reported that cultured mammalian MG undergoes a partial dedifferentiation, but fails to fully acquire a progenitor phenotype and differentiate into neurons. This might be explained by a mnemonic mechanism comprised by epigenetic traits, such as DNA methylation. To achieve a better understanding of this epigenetic memory, we studied the expression of pluripotency-associated genes, such as Oct4, Nanog, and Lin28, which have been reported as necessary for regeneration in fish, at early times after NMDA-induced retinal injury in a mouse experimental model. We found that although Oct4 is expressed rapidly after damage (4 hpi), it is silenced at 24 hpi. This correlates with a significant decrease in the DNA methyltransferase Dnmt3b expression, which returns to basal levels at 24 hpi. By MS-PCR, we observed a decrease in Oct4 methylation levels at 4 and 12 hpi, before returning to a fully methylated state at 24 hpi. To demonstrate that these changes are restricted to MG, we separated these cells using a GLAST antibody coupled with magnetic beads. Finally, intravitreous administration of the DNA-methyltransferase inhibitor SGI-1027 induced Oct4 expression at 24 hpi in MG. Our results suggest that mammalian MG injury-induced dedifferentiation could be restricted by DNA methylation, which rapidly silences Oct4 expression, preventing multipotency acquisition.
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Affiliation(s)
- Luis I Reyes-Aguirre
- Departamento de Farmacobiología, Centro de Investigación y de Estudios Avanzados-Sede Sur México, Mexico
| | - Monica Lamas
- Departamento de Farmacobiología, Centro de Investigación y de Estudios Avanzados-Sede Sur México, Mexico
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43
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Dorts J, Falisse E, Schoofs E, Flamion E, Kestemont P, Silvestre F. DNA methyltransferases and stress-related genes expression in zebrafish larvae after exposure to heat and copper during reprogramming of DNA methylation. Sci Rep 2016; 6:34254. [PMID: 27731414 PMCID: PMC5059630 DOI: 10.1038/srep34254] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/08/2016] [Indexed: 12/23/2022] Open
Abstract
DNA methylation, a well-studied epigenetic mark, is important for gene regulation in adulthood and for development. Using genetic and epigenetic approaches, the present study aimed at evaluating the effects of heat stress and copper exposure during zebrafish early embryogenesis when patterns of DNA methylation are being established, a process called reprogramming. Embryos were exposed to 325 μg Cu/L from fertilization (<1 h post fertilization - hpf) to 4 hpf at either 26.5 °C or 34 °C, followed by incubation in clean water at 26.5 °C till 96 hpf. Significant increased mortality rates and delayed hatching were observed following exposure to combined high temperature and Cu. Secondly, both stressors, alone or in combination, significantly upregulated the expression of de novo DNA methyltransferase genes (dnmt3) along with no differences in global cytosine methylation level. Finally, Cu exposure significantly increased the expression of metallothionein (mt2) and heat shock protein (hsp70), the latter being also increased following exposure to high temperature. These results highlighted the sensitivity of early embryogenesis and more precisely of the reprogramming period to environmental challenges, in a realistic situation of combined stressors.
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Affiliation(s)
- Jennifer Dorts
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Elodie Falisse
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Emilie Schoofs
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Enora Flamion
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Patrick Kestemont
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Frédéric Silvestre
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
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44
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Olsen JB, Wong L, Deimling S, Miles A, Guo H, Li Y, Zhang Z, Greenblatt JF, Emili A, Tropepe V. G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis. Stem Cell Reports 2016; 7:454-470. [PMID: 27546533 PMCID: PMC5031922 DOI: 10.1016/j.stemcr.2016.06.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 01/05/2023] Open
Abstract
Proliferating progenitor cells undergo changes in competence to give rise to post-mitotic progeny of specialized function. These cell-fate transitions typically involve dynamic regulation of gene expression by histone methyltransferase (HMT) complexes. However, the composition, roles, and regulation of these assemblies in regulating cell-fate decisions in vivo are poorly understood. Using unbiased affinity purification and mass spectrometry, we identified the uncharacterized C2H2-like zinc finger protein ZNF644 as a G9a/GLP-interacting protein and co-regulator of histone methylation. In zebrafish, functional characterization of ZNF644 orthologs, znf644a and znf644b, revealed complementary roles in regulating G9a/H3K9me2-mediated gene silencing during neurogenesis. The non-overlapping requirements for znf644a and znf644b during retinal differentiation demarcate critical aspects of retinal differentiation programs regulated by differential G9a-ZNF644 associations, such as transitioning proliferating progenitor cells toward differentiation. Collectively, our data point to ZNF644 as a critical co-regulator of G9a/H3K9me2-mediated gene silencing during neuronal differentiation.
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Affiliation(s)
- Jonathan B Olsen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada
| | - Loksum Wong
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Steven Deimling
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Amanda Miles
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Hongbo Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Yue Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada.
| | - Vincent Tropepe
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada.
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45
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Landgraf K, Strobach A, Kiess W, Körner A. Loss of mtch2 function impairs early development of liver, intestine and visceral adipocytes in zebrafish larvae. FEBS Lett 2016; 590:2852-61. [PMID: 27468124 DOI: 10.1002/1873-3468.12330] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/15/2016] [Accepted: 07/20/2016] [Indexed: 01/28/2023]
Abstract
The mitochondrial carrier homologue 2 (MTCH2) has been shown to be essential for embryogenesis in mice, and variants in the MTCH2 locus have been linked to obesity in humans. Here, we investigated the importance of mtch2 for embryogenesis and adipocyte formation in zebrafish in vivo. We show that mtch2 is conserved in zebrafish and broadly expressed during embryogenesis. Knock-down of mtch2 results in impaired development of liver and intestine, and is associated with a reduced number of adipocytes and impaired postembryonic growth. The findings indicate an essential role for mtch2 during organ development and adipogenesis in vivo.
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Affiliation(s)
- Kathrin Landgraf
- Center for Pediatric Research Leipzig (CPL), University Hospital for Children and Adolescents, University of Leipzig, Germany.,Medical Center AdiposityDiseases (IFB), University of Leipzig, Germany
| | - Ariane Strobach
- Center for Pediatric Research Leipzig (CPL), University Hospital for Children and Adolescents, University of Leipzig, Germany
| | - Wieland Kiess
- Center for Pediatric Research Leipzig (CPL), University Hospital for Children and Adolescents, University of Leipzig, Germany
| | - Antje Körner
- Center for Pediatric Research Leipzig (CPL), University Hospital for Children and Adolescents, University of Leipzig, Germany.,Medical Center AdiposityDiseases (IFB), University of Leipzig, Germany
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46
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Abstract
Genomic DNA methylation functions to repress gene expression by interfering with transcription factor binding and/or recruiting repressive chromatin machinery. Recent data support contribution of regulated DNA methylation to embryonic pluripotency, development, and tissue differentiation; this important epigenetic mark is chemically stable yet enzymatically reversible-and heritable through the germline. Importantly, all the major components involved in dynamic DNA methylation are conserved in zebrafish, including the factors that "write, read, and erase" this mark. Therefore, the zebrafish has become an excellent model for studying most biological processes associated with DNA methylation in mammals. Here we briefly review the zebrafish model for studying DNA methylation and describe a series of methods for performing genome-wide DNA methylation analysis. We address and provide methods for methylated DNA immunoprecipitation followed by sequencing (MeDIP-Seq), bisulfite sequencing (BS-Seq), and reduced representation bisulfite sequencing (RRBS-Seq).
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Affiliation(s)
- P J Murphy
- University of Utah School of Medicine, Salt Lake City, UT, United States
| | - B R Cairns
- University of Utah School of Medicine, Salt Lake City, UT, United States
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47
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Miles A, Tropepe V. Coordinating progenitor cell cycle exit and differentiation in the developing vertebrate retina. NEUROGENESIS 2016; 3:e1161697. [PMID: 27604453 PMCID: PMC4974023 DOI: 10.1080/23262133.2016.1161697] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/09/2016] [Accepted: 02/29/2016] [Indexed: 02/06/2023]
Abstract
The proper development of the vertebrate retina relies heavily on producing the correct number and type of differentiated retinal cell types. To achieve this, proliferating retinal progenitor cells (RPCs) must exit the cell cycle at an appropriate time and correctly express a subset of differentiation markers that help specify retinal cell fate. Homeobox genes, which encode a family of transcription factors, have been accredited to both these processes, implicated in the transcriptional regulation of important cell cycle components, such as cyclins and cyclin-dependent kinases, and proneural genes. This dual regulation of homeobox genes allows these factors to help co-ordinate the transition from the proliferating RPC to postmitotic, differentiated cell. However, understanding the exact molecular targets of these factors remains a challenging task. This commentary highlights the current knowledge we have about how these factors regulate cell cycle progression and differentiation, with particular emphasis on a recent discovery from our lab demonstrating an antagonistic relationship between Vsx2 and Dmbx1 to control RPC proliferation. Future studies should aim to further understand the direct transcriptional targets of these genes, additional co-factors/interacting proteins and the possible recruitment of epigenetic machinery by these homeobox genes.
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Affiliation(s)
- Amanda Miles
- Department of Cell & Systems Biology, University of Toronto , Toronto, Ontario, Canada
| | - Vincent Tropepe
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada; Department of Ophthalmology & Vision Sciences; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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48
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49
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Kent B, Magnani E, Walsh MJ, Sadler KC. UHRF1 regulation of Dnmt1 is required for pre-gastrula zebrafish development. Dev Biol 2016; 412:99-113. [PMID: 26851214 DOI: 10.1016/j.ydbio.2016.01.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 12/16/2022]
Abstract
Landmark epigenetic events underlie early embryonic development, yet how epigenetic modifiers are regulated to achieve rapid epigenome re-patterning is not known. Uhrf1 and DNA methyltransferase 1 (Dnmt1) are known to largely mediate maintenance DNA methylation and Uhrf1 is also required for both Dnmt1 localization and stability. Here, we investigate how these two key epigenetic modifiers regulate early zebrafish development and characterize the developmental consequences of disrupting their homeostatic relationship. Unlike Uhrf1 knockdown, which causes developmental arrest and death prior to gastrulation, overexpression of human UHRF1 (WT-UHRF1) caused asymmetric epiboly, inefficient gastrulation and multi-systemic defects. UHRF1 phosphorylation was previously demonstrated as essential for zebrafish embryogenesis, and we found that penetrance of the asymmetric epiboly phenotype was significantly increased in embryos injected with mRNA encoding non-phosphorylatable UHRF1 (UHRF1(S661A)). Surprisingly, both WT-UHRF1 and UHRF1(S661A) overexpression caused DNA hypomethylation. However, since other approaches that caused an equivalent degree of DNA hypomethylation did not cause the asymmetric epiboly phenotype, we conclude that bulk DNA methylation is not the primary mechanism. Instead, UHRF1(S661A) overexpression resulted in accumulation of Dnmt1 protein and the overexpression of both WT and a catalytically inactive Dnmt1 phenocopied the assymetric epiboly phenotype. Dnmt1 knockdown suppressed the phenotype caused by UHRF1(S661A) overexpression, and Uhrf1 knockdown suppressed the effect of Dnmt1 overexpression. Therefore, we conclude that the interaction between these two proteins is the mechanism underlying the gastrulation defects. This indicates that Dnmt1 stability requires UHRF1 phosphorylation and that crosstalk between the proteins is essential for the function of these two important epigenetic regulators during gastrulation.
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Affiliation(s)
- Brandon Kent
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States
| | - Elena Magnani
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States
| | - Martin J Walsh
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States
| | - Kirsten C Sadler
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States.
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Gore AV, Athans B, Iben JR, Johnson K, Russanova V, Castranova D, Pham VN, Butler MG, Williams-Simons L, Nichols JT, Bresciani E, Feldman B, Kimmel CB, Liu PP, Weinstein BM. Epigenetic regulation of hematopoiesis by DNA methylation. eLife 2016; 5:e11813. [PMID: 26814702 PMCID: PMC4744183 DOI: 10.7554/elife.11813] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/06/2015] [Indexed: 11/13/2022] Open
Abstract
During embryonic development, cell type-specific transcription factors promote cell identities, while epigenetic modifications are thought to contribute to maintain these cell fates. Our understanding of how genetic and epigenetic modes of regulation work together to establish and maintain cellular identity is still limited, however. Here, we show that DNA methyltransferase 3bb.1 (dnmt3bb.1) is essential for maintenance of hematopoietic stem and progenitor cell (HSPC) fate as part of an early Notch-runx1-cmyb HSPC specification pathway in the zebrafish. Dnmt3bb.1 is expressed in HSPC downstream from Notch1 and runx1, and loss of Dnmt3bb.1 activity leads to reduced cmyb locus methylation, reduced cmyb expression, and gradual reduction in HSPCs. Ectopic overexpression of dnmt3bb.1 in non-hematopoietic cells is sufficient to methylate the cmyb locus, promote cmyb expression, and promote hematopoietic development. Our results reveal an epigenetic mechanism supporting the maintenance of hematopoietic cell fate via DNA methylation-mediated perdurance of a key transcription factor in HSPCs. DOI:http://dx.doi.org/10.7554/eLife.11813.001 The cells in our blood are constantly being replaced with new cells that are produced by stem cells called hematopoietic stem and progenitor cells (or HSPCs for short). The HSPCs form early on in the development of the embryo and continue in the same role throughout the life of the animal. A gene called runx1 is required for HSPCs to form, but is not required for these cells to maintain their role (cell identity) in the long term. In mice, this gene is only expressed for a brief period of time as the HSPCs form, and is switched off in the mature stem cells. Another gene called cmyb – which is switched on by runx1 – is also required for HSPCs to form. However, unlike runx1, cmyb continues to be expressed in mature HSPCs and is required to maintain HSPC identity. It is not known how the temporary activation of runx1 causes the long-term expression of cmyb. One possible explanation is that the cmyb gene may be subject to a process called DNA methylation. This process is carried out by enzymes called DNA methyltransferases and can have long-term effects on the expression of genes by modifying the structure of the DNA that encodes them. Here, Gore et al. investigate the role of a particular DNA methyltransferase in the formation of HSPCs in zebrafish embryos. The experiments show that this enzyme is activated in developing HSPCs in response to an increase in runx1 expression. The loss of this enzyme’s activity reduces both the amount that cmyb is methylated and its level of expression, which results in a gradual decline in the number of HSPCs in zebrafish. Further experiments show that if the DNA methyltransferase is artificially activated in cells that don’t normally form blood cells, these cells change their identity to do so. This switch is accompanied by methylation of cmyb and an increase in its expression. Gore et al.’s findings reveal that the temporary activation of runx1 triggers the production of an enzyme that methylates cmyb to maintain the identity of HSPCs. Future studies should help to reveal exactly how runx1 promotes DNA methylation, and whether this process can be harnessed to promote HSPC formation for research or medical treatments. DOI:http://dx.doi.org/10.7554/eLife.11813.002
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Affiliation(s)
- Aniket V Gore
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Brett Athans
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - James R Iben
- Program in Developmental Endocrinology and Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Kristin Johnson
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Valya Russanova
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Daniel Castranova
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Van N Pham
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Matthew G Butler
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Lisa Williams-Simons
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - James T Nichols
- Institute of Neuroscience, University of Oregon, Eugene, United States
| | - Erica Bresciani
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Bejamin Feldman
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Charles B Kimmel
- Institute of Neuroscience, University of Oregon, Eugene, United States
| | - Paul P Liu
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Brant M Weinstein
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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