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Bozdemir N, Kablan T, Altintas MO, Sukur G, Cinar O, Uysal F. Altered DNA methylation and Dnmt expression in obese uterus may cause implantation failure. J Mol Histol 2024; 55:427-436. [PMID: 38850446 DOI: 10.1007/s10735-024-10212-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Obesity is defined by increased adipose tissue volume and has become a major risk factor for reproduction. Recent studies have revealed a substantial link between obesity and epigenetics. The epigenome is dynamically regulated mainly by DNA methylation. DNA methylation, which is controlled by DNA methyltransferases (Dnmts), has been widely studied because it is essential for imprinting and regulation of gene expression. In our previous study, we showed that the levels of Dnmt1, Dnmt3a and global DNA methylation was dramatically altered in the testis and ovary of high-fat diet (HFD)-induced obese mice. However, the effect of HFD on Dnmts and global DNA methylation in mouse uterus has not yet been demonstrated. Therefore, in the present study, we aimed to evaluate the effect of HFD on the level of Dnmt1, Dnmt3a, Dnmt3b, Dnmt3l and global DNA methylation in uterus. Our results showed that HFD significantly altered the levels of Dnmts and global DNA methylation in the uterus. The total expression of Dnmt1, Dnmt3a and Dnmt3b was significantly upregulated, while level of Dnmt3l and global DNA methylation were dramatically decreased (p < 0.05). Furthermore, we observed that the expression of Dnmt3b and Dnmt3l was significantly increased in endometrium including gland and epithelium (p < 0.05). Although Dnmt3b was the only protein whose expression significantly increased, the level of global DNA methylation and Dnmt3l significantly decreased in stroma and myometrium (p < 0.05). In conclusion, our results show for the first time that obesity dramatically alters global DNA methylation and expression of Dnmts, and decreased DNA methylation and Dnmt expression may cause abnormal gene expression, especially in the endometrium.
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Affiliation(s)
- Nazlican Bozdemir
- Department of Histology and Embryology, Ankara Medipol University School of Medicine, Ankara, 06050, Turkey
| | - Tuba Kablan
- Department of Histology and Embryology, Ankara Medipol University School of Medicine, Ankara, 06050, Turkey
| | - Mehmet Ozgen Altintas
- Department of Physiology, Ankara Medipol University School of Medicine, Ankara, Turkey
- Department of Physiology, Istanbul Medipol University Institute of Health Sciences, Istanbul, Turkey
| | - Gozde Sukur
- Department of Histology and Embryology, Ankara University School of Medicine, Ankara, Turkey
| | - Ozgur Cinar
- Department of Histology and Embryology, Ankara University School of Medicine, Ankara, Turkey
| | - Fatma Uysal
- Department of Histology and Embryology, Ankara Medipol University School of Medicine, Ankara, 06050, Turkey.
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2
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Aanniz T, Bouyahya A, Balahbib A, El Kadri K, Khalid A, Makeen HA, Alhazmi HA, El Omari N, Zaid Y, Wong RSY, Yeo CI, Goh BH, Bakrim S. Natural bioactive compounds targeting DNA methyltransferase enzymes in cancer: Mechanisms insights and efficiencies. Chem Biol Interact 2024; 392:110907. [PMID: 38395253 DOI: 10.1016/j.cbi.2024.110907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
The regulation of gene expression is fundamental to health and life and is essentially carried out at the promoter region of the DNA of each gene. Depending on the molecular context, this region may be accessible or non-accessible (possibility of integration of RNA polymerase or not at this region). Among enzymes that control this process, DNA methyltransferase enzymes (DNMTs), are responsible for DNA demethylation at the CpG islands, particularly at the promoter regions, to regulate transcription. The aberrant activity of these enzymes, i.e. their abnormal expression or activity, can result in the repression or overactivation of gene expression. Consequently, this can generate cellular dysregulation leading to instability and tumor development. Several reports highlighted the involvement of DNMTs in human cancers. The inhibition or activation of DNMTs is a promising therapeutic approach in many human cancers. In the present work, we provide a comprehensive and critical summary of natural bioactive molecules as primary inhibitors of DNMTs in human cancers. The active compounds hold the potential to be developed as anti-cancer epidrugs targeting DNMTs.
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Affiliation(s)
- Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, B.P, 6203, Morocco.
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, 10106, Morocco.
| | - Abdelaali Balahbib
- High Institute of Nursing Professions and Health Techniques of Errachidia, Errachidia, Morocco.
| | - Kawtar El Kadri
- High Institute of Nursing Professions and Health Techniques of Errachidia, Errachidia, Morocco
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan, Saudi Arabia; Medicinal and Aromatic Plants Research Institute, National Center for Research, P.O. Box: 2424, Khartoum, 11111, Sudan.
| | - Hafiz A Makeen
- Pharmacy Practice Research Unit, Clinical Pharmacy Department, Faculty of Pharmacy, Jazan University, Jazan, Saudi Arabia.
| | - Hassan A Alhazmi
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan, Saudi Arabia; Pharmacy Practice Research Unit, Clinical Pharmacy Department, Faculty of Pharmacy, Jazan University, Jazan, Saudi Arabia.
| | - Nasreddine El Omari
- High Institute of Nursing Professions and Health Techniques of Tetouan, Tetouan, Morocco.
| | - Younes Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Morocco.
| | - Rebecca Shin-Yee Wong
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia; Department of Medical Education, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia.
| | - Chien Ing Yeo
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia.
| | - Bey Hing Goh
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia; Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Malaysia; College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Saad Bakrim
- Geo-Bio-Environment Engineering and Innovation Laboratory, Molecular Engineering, Biotechnology and Innovation Team, Polydisciplinary Faculty of Taroudant, Ibn Zohr University, Agadir, 80000, Morocco.
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Rajeev R, Mishra RK, Khosla S. DNMT3L interacts with Piwi and modulates the expression of piRNAs in transgenic Drosophila. Epigenomics 2024; 16:375-388. [PMID: 38440884 DOI: 10.2217/epi-2023-0405] [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] [Indexed: 03/06/2024] Open
Abstract
Aim: To explore the role of Piwi protein and piRNAs in DNMT3L-mediated epigenetic inheritance. Materials & methods: Transgenic Drosophila were used to examine the effect of ectopically expressed DNMT3L on the profile of piRNAs by sequencing of small RNAs. Results & conclusion: Our previous work showed accumulation and inheritance of epimutations across multiple generations in transgenic DNMT3L Drosophila. Here, we show interaction of DNMT3L with Piwi and a significant alteration in the piRNA profile across multiple generations in transgenic Drosophila. In the light of its interaction with histone H1, we propose that in addition to its role of modulating core histone modifications, DNMT3L allows for inheritance of epigenetic information through its collaboration with Piwi, piRNAs and histone H1.
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Affiliation(s)
- Ramisetti Rajeev
- Centre for DNA Fingerprinting & Diagnostics, Hyderabad, 500 039, India
- Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular & Molecular Biology, Hyderabad, 500 007, India
| | - Sanjeev Khosla
- Centre for DNA Fingerprinting & Diagnostics, Hyderabad, 500 039, India
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
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Djihinto OY, Meacci D, Medjigodo AA, Bernardini F, Djogbénou LS. Relative expression of key genes involved in nucleic acids methylation in Anopheles gambiae sensu stricto. MEDICAL AND VETERINARY ENTOMOLOGY 2023; 37:754-766. [PMID: 37417368 DOI: 10.1111/mve.12681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
In vertebrates, enzymes responsible for DNA methylation, one of the epigenetic mechanisms, are encoded by genes falling into the cytosine methyltransferases genes family (Dnmt1, Dnmt3a,b and Dnmt3L). However, in Diptera, only the methyltransferase Dnmt2 was found, suggesting that DNA methylation might act differently for species in this order. Moreover, genes involved in epigenetic dynamics, such as Ten-eleven Translocation dioxygenases (TET) and Methyl-CpG-binding domain (MBDs), present in vertebrates, might play a role in insects. This work aimed at investigating nucleic acids methylation in the malaria vector Anopheles gambiae (Diptera: Culicidae) by analysing the expression of Dnmt2, TET2 and MBDs genes using quantitative real-time polymerase chain reaction (qRT-PCR) at pre-immature stages and in reproductive tissues of adult mosquitoes. In addition, the effect of two DNA methylation inhibitors on larval survival was evaluated. The qPCR results showed an overall low expression of Dnmt2 at all developmental stages and in adult reproductive tissues. In contrast, MBD and TET2 showed an overall higher expression. In adult mosquito reproductive tissues, the expression level of the three genes in males' testes was significantly higher than that in females' ovaries. The chemical treatments did not affect larval survival. The findings suggest that mechanisms other than DNA methylation underlie epigenetic regulation in An. gambiae.
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Affiliation(s)
- Oswald Y Djihinto
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Dario Meacci
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Adandé A Medjigodo
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Luc S Djogbénou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
- Institut Régional de Santé Publique (IRSP), University of Abomey-Calavi, Ouidah, Benin
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Zou YC, Wang ZJ, Shao LC, Xia ZH, Lan YF, Yu ZH, Yao JY, Luo ZR. DNA methylation of DKK-1 may correlate with pathological bone formation in ankylosing spondylitis. Immun Inflamm Dis 2023; 11:e911. [PMID: 37506134 PMCID: PMC10326833 DOI: 10.1002/iid3.911] [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: 02/08/2023] [Revised: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 07/30/2023] Open
Abstract
OBJECTIVE To investigate DNA methylation (DNAm) status of dickkopf-associated protein 1 (DKK-1) in ossified hip capsule synovium and serum among patients with ankylosing spondylitis (AS). METHODS Western blot was applied to detect the level of DKK-1 protein expression in hip joint capsule tissues from four patients with AS as well as four patients with femoral neck fracture (FNF) caused by trauma as control. DKK-1 gene promoter methylation (GPM) was examined by methylation-specific polymerase chain reaction. Reverse transcription-polymerase chain reaction was performed to examine the messenger RNA (mRNA) levels of DKK-1, β-catenin, and Wnt3a in both tissue and serum. The DNAm status of serum DKK-1 was measured among 36 patients with AS and syndesmophytes (AS + syndesmophytes group), 40 patients with AS but no syndesmophyte (AS group), and 42 healthy individuals (control group). Also, the serum levels of DKK-1 were measured by enzyme-linked immunosorbent assay. The modified New York criteria (mNYC) together with the modified Stoke Ankylosing Spondylitis Spinal Score (mSASSS) were adopted to examine the radiographic progression of AS. The receiver operating characteristic (ROC) curve was applied to investigate the diagnostic value of the methylation rate of DKK-1 with regard to radiographic progression. RESULTS The expressions of DKK-1 protein and mRNA in hip joint capsule tissues of AS patients were significantly lower, while DKK-1 GPM rate, β-catenin mRNA, and Wnt3a mRNA were markedly higher when compared with FNF group. For serum samples, the DKK-1 methylation rate was significantly higher in AS+ syndesmophytes group in contrast to AS group and healthy controls. Serum levels of DKK-1 protein and mRNA in AS with syndesmophytes group were markedly decreased, while β-catenin mRNA and Wnt3a mRNA expressions were significantly increased than AS with no syndesmophyte group and the healthy control group. AS patients in Grade 4 showed a significantly higher serum DKK-1 GPM rate than those in Grade 3 based on mNYC. Serum DKK-1 GPM level was markedly and positively correlated with mSASSS. Serum levels of DKK-1 in AS+ syndesmophytes group were markedly lower compared with AS but no syndesmophyte group and healthy controls. ROC curve analysis indicated that serum DKK-1 methylation rate serves as a decent indicator for AS radiographic progression. CONCLUSION DNAm of DKK-1 may correlate with pathological bone formation in AS, which may provide new strategies for the treatment of AS abnormal bone formation.
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Affiliation(s)
- Yu-Cong Zou
- Department of Rehabilitation, The 5th People's Hospital of Foshan City, Foshan, Guangdong Province, China
- Deaprtment of Rehabilitation, The 5th Affiliated Hospital of Foshan University, Foshan, Guangdong Province, China
| | - Zhi-Jun Wang
- Department of Rehabilitation, The 5th People's Hospital of Foshan City, Foshan, Guangdong Province, China
| | - Li-Cheng Shao
- Department of Internal Medicine, The 5th People's Hospital of Foshan City, Foshan, Guangdong Province, China
| | - Zhi-Hong Xia
- Department of Internal Medicine, The 5th People's Hospital of Foshan City, Foshan, Guangdong Province, China
| | - Yi-Feng Lan
- Department of Radiology, The 5th People's Hospital of Foshan City, Foshan, Guangdong Province, China
| | - Zhi-Hui Yu
- Department of Laboratory medicine, The 5th People's Hospital of Foshan City, Foshan, Guangdong Province, China
| | - Jia-Yu Yao
- Department of Internal Medicine, The 5th People's Hospital of Foshan City, Foshan, Guangdong Province, China
| | - Zi-Rui Luo
- Department of Rehabilitation, The 5th People's Hospital of Foshan City, Foshan, Guangdong Province, China
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Stamidis N, Żylicz JJ. RNA-mediated heterochromatin formation at repetitive elements in mammals. EMBO J 2023; 42:e111717. [PMID: 36847618 PMCID: PMC10106986 DOI: 10.15252/embj.2022111717] [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: 05/20/2022] [Revised: 12/12/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
The failure to repress transcription of repetitive genomic elements can lead to catastrophic genome instability and is associated with various human diseases. As such, multiple parallel mechanisms cooperate to ensure repression and heterochromatinization of these elements, especially during germline development and early embryogenesis. A vital question in the field is how specificity in establishing heterochromatin at repetitive elements is achieved. Apart from trans-acting protein factors, recent evidence points to a role of different RNA species in targeting repressive histone marks and DNA methylation to these sites in mammals. Here, we review recent discoveries on this topic and predominantly focus on the role of RNA methylation, piRNAs, and other localized satellite RNAs.
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Affiliation(s)
- Nikolaos Stamidis
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Jan Jakub Żylicz
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
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7
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MeCP2 Is an Epigenetic Factor That Links DNA Methylation with Brain Metabolism. Int J Mol Sci 2023; 24:ijms24044218. [PMID: 36835623 PMCID: PMC9966807 DOI: 10.3390/ijms24044218] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
DNA methylation, one of the most well-studied epigenetic modifications, is involved in a wide spectrum of biological processes. Epigenetic mechanisms control cellular morphology and function. Such regulatory mechanisms involve histone modifications, chromatin remodeling, DNA methylation, non-coding regulatory RNA molecules, and RNA modifications. One of the most well-studied epigenetic modifications is DNA methylation that plays key roles in development, health, and disease. Our brain is probably the most complex part of our body, with a high level of DNA methylation. A key protein that binds to different types of methylated DNA in the brain is the methyl-CpG binding protein 2 (MeCP2). MeCP2 acts in a dose-dependent manner and its abnormally high or low expression level, deregulation, and/or genetic mutations lead to neurodevelopmental disorders and aberrant brain function. Recently, some of MeCP2-associated neurodevelopmental disorders have emerged as neurometabolic disorders, suggesting a role for MeCP2 in brain metabolism. Of note, MECP2 loss-of-function mutation in Rett Syndrome is reported to cause impairment of glucose and cholesterol metabolism in human patients and/or mouse models of disease. The purpose of this review is to outline the metabolic abnormalities in MeCP2-associated neurodevelopmental disorders that currently have no available cure. We aim to provide an updated overview into the role of metabolic defects associated with MeCP2-mediated cellular function for consideration of future therapeutic strategies.
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8
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Young plasma transfer recovers decreased sperm counts and restores epigenetics in aged testis. Exp Gerontol 2023; 172:112042. [PMID: 36481396 DOI: 10.1016/j.exger.2022.112042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM Aging is one of the causes of male infertility, and abnormal global DNA methylation and imprinting defects have been characterized in testis during biological aging. One of the important emerging approaches aims to take advantage of the healing properties of young blood plasma to limit the progression of aging in various organs in the body. We aimed to show whether blood plasma transfer has an effect on DNA methylation and spermatogenetic cell development. In addition, we aimed to show whether the young plasma transfer to old mice has an effect on the rejuvenation of the old and whether the impaired DNA methylation and PCNA expression in old age can be restored. METHODS Groups were (i) young control, (ii) young plasma transfer to aged, (iii) aged control, (iv) aged plasma transfer to young. We utilized IHC and WB in protein level of Dnmts. For the global DNA methylation level, we used 5-methylcytosine staining. We also analyzed PCNA protein expressions in all groups by IHC. RESULTS We found that transfusion of young plasma into the old animal restored DNA methylation and PCNA expression as it did in the young animal. Most importantly, we observed an increase in spermatogonia and spermatid counts in older animals after young blood plasma transfer. CONCLUSIONS Our findings show that young plasma transfer can restore epigenetic disorders that occur with aging and solve infertility problems by increasing the sperm count that decreases. It needs to be supported by different studies, especially human studies.
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Barbero G, de Sousa Serro MG, Perez Lujan C, Vitullo AD, González CR, González B. Transcriptome profiling of histone writers/erasers enzymes across spermatogenesis, mature sperm and pre-cleavage embryo: Implications in paternal epigenome transitions and inheritance mechanisms. Front Cell Dev Biol 2023; 11:1086573. [PMID: 36776561 PMCID: PMC9911891 DOI: 10.3389/fcell.2023.1086573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/04/2023] [Indexed: 01/28/2023] Open
Abstract
Accumulating evidence points out that sperm carry epigenetic instructions to embryo in the form of retained histones marks and RNA cargo that can transmit metabolic and behavioral traits to offspring. However, the mechanisms behind epigenetic inheritance of paternal environment are still poorly understood. Here, we curated male germ cells RNA-seq data and analyzed the expression profile of all known histone lysine writers and erasers enzymes across spermatogenesis, unraveling the developmental windows at which they are upregulated, and the specific activity related to canonical and non-canonical histone marks deposition and removal. We also characterized the epigenetic enzymes signature in the mature sperm RNA cargo, showing most of them positive translation at pre-cleavage zygote, suggesting that paternally-derived enzymes mRNA cooperate with maternal factors to embryo chromatin assembly. Our study shows several histone modifying enzymes not described yet in spermatogenesis and even more, important mechanistic aspects behind transgenerational epigenetics. Epigenetic enzymes not only can respond to environmental stressors, but could function as vectors of epigenetic information and participate in chromatin organization during maternal-to-zygote transition.
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Affiliation(s)
- Gastón Barbero
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Maximiliano G. de Sousa Serro
- Instituto de Investigaciones Farmacológicas (Universidad de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Camila Perez Lujan
- Instituto de Investigaciones Farmacológicas (Universidad de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Alfredo D. Vitullo
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Candela R. González
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Betina González
- Instituto de Investigaciones Farmacológicas (Universidad de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina,*Correspondence: Betina González,
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10
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Kim M, Delgado E, Ko S. DNA methylation in cell plasticity and malignant transformation in liver diseases. Pharmacol Ther 2023; 241:108334. [PMID: 36535346 PMCID: PMC9841769 DOI: 10.1016/j.pharmthera.2022.108334] [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: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The liver possesses extraordinary regenerative capacity mainly attributable to the ability of hepatocytes (HCs) and biliary epithelial cells (BECs) to self-replicate. This ability is left over from their bipotent parent cell, the hepatoblast, during development. When this innate regeneration is compromised due to the absence of proliferative parenchymal cells, such as during cirrhosis, HCs and BEC can transdifferentiate; thus, adding another layer of complexity to the process of liver repair. In addition, dysregulated lineage maintenance in these two cell populations has been shown to promote malignant growth in experimental conditions. Here, malignant transformation, driven in part by insufficient maintenance of lineage reprogramming, contributes to end-stage liver disease. Epigenetic changes are key drivers for cell fate decisions as well as transformation by finetuning overall transcription and gene expression. In this review, we address how altered DNA methylation contributes to the initiation and progression of hepatic cell fate conversion and cancer formation. We also discussed the diagnostic and therapeutic potential of targeting DNA methylation in liver cancer, its current limitations, and what future research is necessary to facilitate its contribution to clinical translation.
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Affiliation(s)
- Minwook Kim
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Evan Delgado
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Sungjin Ko
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America.
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11
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Micale V, Di Bartolomeo M, Di Martino S, Stark T, Dell'Osso B, Drago F, D'Addario C. Are the epigenetic changes predictive of therapeutic efficacy for psychiatric disorders? A translational approach towards novel drug targets. Pharmacol Ther 2023; 241:108279. [PMID: 36103902 DOI: 10.1016/j.pharmthera.2022.108279] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 02/06/2023]
Abstract
The etiopathogenesis of mental disorders is not fully understood and accumulating evidence support that clinical symptomatology cannot be assigned to a single gene mutation, but it involves several genetic factors. More specifically, a tight association between genes and environmental risk factors, which could be mediated by epigenetic mechanisms, may play a role in the development of mental disorders. Several data suggest that epigenetic modifications such as DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA) may modify the severity of the disease and the outcome of the therapy. Indeed, the study of these mechanisms may help to identify patients particularly vulnerable to mental disorders and may have potential utility as biomarkers to facilitate diagnosis and treatment of psychiatric disorders. This article summarizes the most relevant preclinical and human data showing how epigenetic modifications can be central to the therapeutic efficacy of antidepressant and/or antipsychotic agents, as possible predictor of drugs response.
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Affiliation(s)
- Vincenzo Micale
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy.
| | - Martina Di Bartolomeo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Serena Di Martino
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy
| | - Tibor Stark
- Department of Pharmacology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; Scientific Core Unit Neuroimaging, Max Planck Institute of Psychiatry, Munich, Germany
| | - Bernardo Dell'Osso
- Department of Biomedical and Clinical Sciences 'Luigi Sacco', University of Milan, Milan, Italy, Department of Mental Health, ASST Fatebenefratelli-Sacco, Milan, Italy; "Aldo Ravelli" Research Center for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, University of Milan Medical School, Milan, Italy; Department of Psychiatry and Behavioral Sciences, Stanford University, CA, USA
| | - Filippo Drago
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy.
| | - Claudio D'Addario
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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Hatmal MM, Al-Hatamleh MAI, Olaimat AN, Alshaer W, Hasan H, Albakri KA, Alkhafaji E, Issa NN, Al-Holy MA, Abderrahman SM, Abdallah AM, Mohamud R. Immunomodulatory Properties of Human Breast Milk: MicroRNA Contents and Potential Epigenetic Effects. Biomedicines 2022; 10:biomedicines10061219. [PMID: 35740242 PMCID: PMC9219990 DOI: 10.3390/biomedicines10061219] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Infants who are exclusively breastfed in the first six months of age receive adequate nutrients, achieving optimal immune protection and growth. In addition to the known nutritional components of human breast milk (HBM), i.e., water, carbohydrates, fats and proteins, it is also a rich source of microRNAs, which impact epigenetic mechanisms. This comprehensive work presents an up-to-date overview of the immunomodulatory constituents of HBM, highlighting its content of circulating microRNAs. The epigenetic effects of HBM are discussed, especially those regulated by miRNAs. HBM contains more than 1400 microRNAs. The majority of these microRNAs originate from the lactating gland and are based on the remodeling of cells in the gland during breastfeeding. These miRNAs can affect epigenetic patterns by several mechanisms, including DNA methylation, histone modifications and RNA regulation, which could ultimately result in alterations in gene expressions. Therefore, the unique microRNA profile of HBM, including exosomal microRNAs, is implicated in the regulation of the genes responsible for a variety of immunological and physiological functions, such as FTO, INS, IGF1, NRF2, GLUT1 and FOXP3 genes. Hence, studying the HBM miRNA composition is important for improving the nutritional approaches for pregnancy and infant's early life and preventing diseases that could occur in the future. Interestingly, the composition of miRNAs in HBM is affected by multiple factors, including diet, environmental and genetic factors.
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Affiliation(s)
- Ma’mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
- Correspondence: (M.M.H.); (R.M.)
| | - Mohammad A. I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
| | - Amin N. Olaimat
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (A.N.O.); (M.A.A.-H.)
| | - Walhan Alshaer
- Cell Therapy Center (CTC), The University of Jordan, Amman 11942, Jordan;
| | - Hanan Hasan
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan;
| | - Khaled A. Albakri
- Faculty of Medicine, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Enas Alkhafaji
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan;
| | - Nada N. Issa
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Murad A. Al-Holy
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (A.N.O.); (M.A.A.-H.)
| | - Salim M. Abderrahman
- Department of Biology and Biotechnology, Faculty of Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Atiyeh M. Abdallah
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha 2713, Qatar;
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
- Correspondence: (M.M.H.); (R.M.)
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13
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Uysal F, Sukur G, Cinar O. DNMT enzymes differentially alter global DNA methylation in a stage‐dependent manner during spermatogenesis. Andrologia 2022; 54:e14357. [DOI: 10.1111/and.14357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/02/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology Ankara Medipol University School of Medicine Ankara Turkey
| | - Gozde Sukur
- Ankara University Biotechnology Institute Ankara Turkey
| | - Ozgur Cinar
- Department of Histology and Embryology Ankara University School of Medicine Ankara Turkey
- Center for Assisted Reproduction Ankara University School of Medicine Ankara Turkey
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14
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Muscles in Winter: The Epigenetics of Metabolic Arrest. EPIGENOMES 2021; 5:epigenomes5040028. [PMID: 34968252 PMCID: PMC8715459 DOI: 10.3390/epigenomes5040028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022] Open
Abstract
The winter months are challenging for many animal species, which often enter a state of dormancy or hypometabolism to “wait out” the cold weather, food scarcity, reduced daylight, and restricted mobility that can characterize the season. To survive, many species use metabolic rate depression (MRD) to suppress nonessential metabolic processes, conserving energy and limiting tissue atrophy particularly of skeletal and cardiac muscles. Mammalian hibernation is the best recognized example of winter MRD, but some turtle species spend the winter unable to breathe air and use MRD to survive with little or no oxygen (hypoxia/anoxia), and various frogs endure the freezing of about two-thirds of their total body water as extracellular ice. These winter survival strategies are highly effective, but create physiological and metabolic challenges that require specific biochemical adaptive strategies. Gene-related processes as well as epigenetic processes can lower the risk of atrophy during prolonged inactivity and limited nutrient stores, and DNA modifications, mRNA storage, and microRNA action are enacted to maintain and preserve muscle. This review article focuses on epigenetic controls on muscle metabolism that regulate MRD to avoid muscle atrophy and support winter survival in model species of hibernating mammals, anoxia-tolerant turtles and freeze-tolerant frogs. Such research may lead to human applications including muscle-wasting disorders such as sarcopenia, or other conditions of limited mobility.
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15
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Woźniak E, Owczarczyk-Saczonek A, Placek W. Psychological Stress, Mast Cells, and Psoriasis-Is There Any Relationship? Int J Mol Sci 2021; 22:ijms222413252. [PMID: 34948049 PMCID: PMC8705845 DOI: 10.3390/ijms222413252] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/06/2021] [Indexed: 12/19/2022] Open
Abstract
Psoriasis vulgaris is a common inflammatory skin disease with still unknown pathogenesis. In recent years, genetic and environmental factors have been mentioned as the main causes. Among environmental factors, many researchers are trying to investigate the role of mental health and its importance in the development of many diseases. In the pathophysiology of psoriasis, the role of the interaction between the nervous, endocrine, and immune systems are often emphasized. So far, no one has clearly indicated where the pathological process begins. One of the hypotheses is that chronic stress influences the formation of hormonal changes (lowering the systemic cortisol level), which favors the processes of autoimmunity. In inflammatory skin conditions, mast cells (MCs) are localized close to blood vessels and peripheral nerves, where they probably play an important role in the response to environmental stimuli and emotional stress. They are usually connected with a fast immune response, not only in allergies but also a protective response to microbial antigens. Among many cells of the immune system, MCs have receptors for the hormones of the hypothalamic-pituitary-adrenal (HPA) axis on their surface. In this review, we will try to take a closer look at the role of MCs in the pathophysiology of psoriasis. This knowledge may give the opportunity to search for therapeutic solutions.
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16
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Mensah IK, Norvil AB, AlAbdi L, McGovern S, Petell CJ, He M, Gowher H. Misregulation of the expression and activity of DNA methyltransferases in cancer. NAR Cancer 2021; 3:zcab045. [PMID: 34870206 PMCID: PMC8634572 DOI: 10.1093/narcan/zcab045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In mammals, DNA methyltransferases DNMT1 and DNMT3's (A, B and L) deposit and maintain DNA methylation in dividing and nondividing cells. Although these enzymes have an unremarkable DNA sequence specificity (CpG), their regional specificity is regulated by interactions with various protein factors, chromatin modifiers, and post-translational modifications of histones. Changes in the DNMT expression or interacting partners affect DNA methylation patterns. Consequently, the acquired gene expression may increase the proliferative potential of cells, often concomitant with loss of cell identity as found in cancer. Aberrant DNA methylation, including hypermethylation and hypomethylation at various genomic regions, therefore, is a hallmark of most cancers. Additionally, somatic mutations in DNMTs that affect catalytic activity were mapped in Acute Myeloid Leukemia cancer cells. Despite being very effective in some cancers, the clinically approved DNMT inhibitors lack specificity, which could result in a wide range of deleterious effects. Elucidating distinct molecular mechanisms of DNMTs will facilitate the discovery of alternative cancer therapeutic targets. This review is focused on: (i) the structure and characteristics of DNMTs, (ii) the prevalence of mutations and abnormal expression of DNMTs in cancer, (iii) factors that mediate their abnormal expression and (iv) the effect of anomalous DNMT-complexes in cancer.
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Affiliation(s)
- Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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17
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Zou Y, Li JJ, Xue W, Kong X, Duan H, Li Y, Wei L. Epigenetic Modifications and Therapy in Uveitis. Front Cell Dev Biol 2021; 9:758240. [PMID: 34869347 PMCID: PMC8636745 DOI: 10.3389/fcell.2021.758240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022] Open
Abstract
Uveitis is a sight-threatening intraocular inflammation, and the exact pathogenesis of uveitis is not yet clear. Recent studies, including multiple genome-wide association studies (GWASs), have identified genetic variations associated with the onset and progression of different types of uveitis, such as Vogt–Koyanagi–Harada (VKH) disease and Behcet’s disease (BD). However, epigenetic regulation has been shown to play key roles in the immunoregulation of uveitis, and epigenetic therapies are promising treatments for intraocular inflammation. In this review, we summarize recent advances in identifying epigenetic programs that cooperate with the physiology of intraocular immune responses and the pathology of intraocular inflammation. These attempts to understand the epigenetic mechanisms of uveitis may provide hope for the future development of epigenetic therapies for these devastating intraocular inflammatory conditions.
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Affiliation(s)
- Yanli Zou
- Department of Ophthalmology, Affiliated Foshan Hospital, Southern Medical University, Foshan, China.,State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Jing Jing Li
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Wei Xue
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Xiangbin Kong
- Department of Ophthalmology, Affiliated Foshan Hospital, Southern Medical University, Foshan, China
| | - Hucheng Duan
- Department of Ophthalmology, Affiliated Foshan Hospital, Southern Medical University, Foshan, China
| | - Yiqun Li
- Department of Orthopaedics, Affiliated Foshan Hospital, Southern Medical University, Foshan, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
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18
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Uysal F, Cinar O, Can A. Knockdown of Dnmt1 and Dnmt3a gene expression disrupts preimplantation embryo development through global DNA methylation. J Assist Reprod Genet 2021; 38:3135-3144. [PMID: 34533678 DOI: 10.1007/s10815-021-02316-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/08/2021] [Indexed: 11/24/2022] Open
Abstract
PURPOSE DNA methylation is one of the epigenetic mechanisms that plays critical roles in preimplantation embryo development executed by DNA methyltransferase (Dnmt) enzymes. Dnmt1, responsible for the maintenance of methylation, and Dnmt3a, for de novo methylation, are gradually erased from the zygote in succeeding stages and then reestablished in the blastocyst. This study was designed to address the vital role of Dnmt1 and Dnmt3a enzymes by silencing their gene expressions in embryonic development in mice. METHODS Groups were (i) control, (ii) Dnmt1-siRNA, (iii) Dnmt3a-siRNA, and (iv) non-targeted (NT) siRNA. Knockdown of Dnmt genes using siRNAs was confirmed by measuring the targeted proteins using Western blot and immunofluorescence. Following knockdown of Dnmt1 and Dnmt3a in zygotes, the developmental competence and global DNA methylation levels were analyzed after 96 h in embryo cultures. RESULTS A significant number of embryos arrested at the 2-cell stage or had undergone degeneration in the Dnmt1 and Dnmt3a knocked-down groups. By 3D observations in super-resolution microscopy, we noted that Dnmt1 was exclusively found in juxtanuclear cytoplasm, while the Dnmt3a signal was preferentially localized in the nucleus, both in trophoblasts (TBs) and embryoblasts (EBs). Interestingly, the global DNA methylation level decreased in the Dnmt1 knockdown group, while it increased in the Dnmt3a knockdown group. CONCLUSION Precisely aligned expression of Dnmt genes is highly essential for the fate of an embryo in the early developmental period. Our data indicates that further analysis is mandatory to designate the specific targets of these methylation/demethylation processes in mouse and human preimplantation embryos.
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Affiliation(s)
- Fatma Uysal
- Laboratory for Stem Cells and Reproductive Cell Biology, Department of Histology and Embryology, Ankara University School of Medicine, Ankara, Turkey
| | - Ozgur Cinar
- Laboratory for Stem Cells and Reproductive Cell Biology, Department of Histology and Embryology, Ankara University School of Medicine, Ankara, Turkey
| | - Alp Can
- Laboratory for Stem Cells and Reproductive Cell Biology, Department of Histology and Embryology, Ankara University School of Medicine, Ankara, Turkey.
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19
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Tessier SN, Ingelson-Filpula WA, Storey KB. Epigenetic regulation by DNA methyltransferases during torpor in the thirteen-lined ground squirrel Ictidomys tridecemlineatus. Mol Cell Biochem 2021; 476:3975-3985. [PMID: 34191233 DOI: 10.1007/s11010-021-04214-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 06/21/2021] [Indexed: 12/31/2022]
Abstract
The thirteen-lined ground squirrel, Ictidomys tridecemlineatus, is a mammal capable of lowering its Tb to almost 0 °C while undergoing deep torpor bouts over the winter. To decrease its metabolic rate to such a drastic extent, the squirrel must undergo multiple physiological, biological, and molecular alterations including downregulation of almost all nonessential processes. Epigenetic regulation allows for a dynamic range of transient phenotypes, allowing the squirrel to downregulate energy-expensive and nonessential pathways during torpor. DNA methylation is a prominent form of epigenetic regulation; therefore, the DNA methyltransferase (DNMT) family of enzymes were studied by measuring expression and activity levels of the five major proteins during torpor bouts. Additionally, specific cytosine marks on genomic DNA were quantified to further elucidate DNA methylation during hibernation. A tissue-specific response was observed that highlighted variant degrees of DNA methylation and DNMT expression/activity, demonstrating that DNA methylation is a highly complex form of epigenetic regulation and likely one of many regulatory mechanisms that enables metabolic rate depression in response to torpor.
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Affiliation(s)
- Shannon N Tessier
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.,BioMEMS Resource Center & Center for Engineering in Medicine, Massachusetts General Hospital & Harvard Medical School, 114 16th Street, Charlestown, MA, 02129, USA
| | - W Aline Ingelson-Filpula
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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20
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De Dieuleveult M, Bizet M, Colin L, Calonne E, Bachman M, Li C, Stancheva I, Miotto B, Fuks F, Deplus R. The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome. Epigenetics 2021; 17:422-443. [PMID: 33960278 DOI: 10.1080/15592294.2021.1917152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) in vivo and in vitro. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of Lsh leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon Lsh knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.
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Affiliation(s)
- Maud De Dieuleveult
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium.,Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Laurence Colin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Martin Bachman
- Medicines Discovery Catapult, Alderley Park, Macclesfield, UK
| | - Chao Li
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Irina Stancheva
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Benoit Miotto
- Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
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21
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Qin L, Qiao C, Sheen V, Wang Y, Lu J. DNMT3L promotes neural differentiation by enhancing STAT1 and STAT3 phosphorylation independent of DNA methylation. Prog Neurobiol 2021; 201:102028. [PMID: 33636226 DOI: 10.1016/j.pneurobio.2021.102028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/10/2021] [Accepted: 02/21/2021] [Indexed: 01/13/2023]
Abstract
Previously, we reported global hypermethylation in DS might be attributed to the overexpression of HSA21 gene DNMT3L, which can enhance DNMT3A and DNMT3B activities in DNA methylation. To test this hypothesis, we compared the DNA methylation and RNA expression profiles of early-differentiated human neuroprogenitors with and without DNMT3L overexpression. We found DNMT3L overexpression only moderately increased the DNA methylation of limited genes, yet significantly altered global RNA expression of genes involved in neural differentiation. We further found that DNMT3L bound STAT1 or STAT3, and increased its phosphorylation and nuclear translocation, which in turn activated the expression of transcription factors including HES3, ASCL1, NEUROD2 and NEUROG2 and CDK inhibitor CDKN1A, which promoted cell cycle exit and neural differentiation. This phenomenon was also confirmed in Dnmt3l conditional knockin mice, which could be rescued by STAT1 and STAT3 phosphorylation inhibitors (Fludarabine and SH-4-54) but not DNA methylation inhibitor (Decitabine). These results suggest that DNMT3L play an important role during neurodevelopment independent of DNA methylation, which may contribute to the abnormal phenotypes observed in Down syndrome cortex.
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Affiliation(s)
- Lin Qin
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, 110122, China; Department of Obstetrics & Gynecology, Shenyang Women & Children's Hospital, Shenyang, Liaoning Province, 110121, China.
| | - Chong Qiao
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, 110004, China.
| | - Volney Sheen
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
| | - Yu Wang
- Department of Obstetrics & Gynecology, Shenyang Women & Children's Hospital, Shenyang, Liaoning Province, 110121, China.
| | - Jie Lu
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, 110122, China.
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22
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Al-Yozbaki M, Jabre I, Syed NH, Wilson CM. Targeting DNA methyltransferases in non-small-cell lung cancer. Semin Cancer Biol 2021; 83:77-87. [PMID: 33486076 DOI: 10.1016/j.semcancer.2021.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/14/2021] [Accepted: 01/17/2021] [Indexed: 12/30/2022]
Abstract
Despite the advances in treatment using chemotherapy or targeted therapies, due to static survival rates, non-small cell lung cancer (NSCLC) is the major cause of cancer-related deaths worldwide. Epigenetic-based therapies have been developed for NSCLC by targeting DNA methyltransferases (DNMTs) and histone-modifying enzymes. However, treatment using single epigenetic agents on solid tumours has been inadequate; whereas, treatment with a combination of DNMTs inhibitors with chemotherapy and immunotherapy has shown great promise. Dietary sources of phytochemicals could also inhibit DNMTs and cancer stem cells, representing a novel and promising way to prevent and treat cancer. Herein, we will discuss the different DNMTs, DNA methylation profiling in NSCLC as well as current demethylating agents in ongoing clinical trials. Therefore, providing a concise overview of future developments in the field of epigenetic therapy in NSCLC.
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Affiliation(s)
- Minnatallah Al-Yozbaki
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
| | - Ibtissam Jabre
- Dept. of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Naeem H Syed
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
| | - Cornelia M Wilson
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK; University of Liverpool, Institute of Translation Medicine, Dept of Molecular & Clinical Cancer Medicine, UK.
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23
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Klutstein M. Cause and effect in epigenetics - where lies the truth, and how can experiments reveal it?: Epigenetic self-reinforcing loops obscure causation in cancer and aging. Bioessays 2020; 43:e2000262. [PMID: 33236359 DOI: 10.1002/bies.202000262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Epigenetic changes are implicated in aging and cancer. Sometimes, it is clear whether the causing agent of the condition is a genetic factor or epigenetic. In other cases, the causative factor is unclear, and could be either genetic or epigenetic. Is there a general role for epigenetic changes in cancer and aging? Here, I present the paradigm of causative roles executed by epigenetic changes. I discuss cases with clear roles of the epigenome in cancer and aging, and other cases showing involvement of other factors. I also present the possibility that sometimes causality is difficult to assign because of the presence of self-reinforcing loops in epigenetic regulation. Such loops hinder the identification of the causative factor. I provide an experimental framework by which the role of the epigenome can be examined in a better setting and where the presence of such loops could be investigated in more detail.
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Affiliation(s)
- Michael Klutstein
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
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24
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de Oliveira DT, Guerra-Sá R. Uncovering epigenetic landscape: a new path for biomarkers identification and drug development. Mol Biol Rep 2020; 47:9097-9122. [PMID: 33089404 DOI: 10.1007/s11033-020-05916-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/10/2020] [Indexed: 12/31/2022]
Abstract
Scientific advances in recent decades have revealed an incredible degree of plasticity in gene expression in response to various environmental, nutritional, physiological, pathological, and behavioral conditions. Epigenetics emerges in this sense, as the link between the internal (genetic) and external (environmental) factors underlying the expression of the phenotype. Methylation of DNA and histone post-translationa modifications are canonical epigenetic events. Additionally, noncoding RNAs molecules (microRNAs and lncRNAs) have also been proposed as another layer of epigenetic regulation. Together, these events are responsible for regulating gene expression throughout life, controlling cellular fate in both normal and pathological development. Despite being a relatively recent science, epigenetics has been arousing the interest of researchers from different segments of the life sciences and the general public. This review highlights the recent advances in the characterization of the epigenetic events and points promising use of these brands for the diagnosis, prognosis, and therapy of diseases. We also present several classes of epigenetic modifying compounds with therapeutic applications (so-call epidrugs) and their current status in clinical trials and approved by the FDA. In summary, hopefully, we provide the reader with theoretical bases for a better understanding of the epigenetic mechanisms and of the promising application of these marks and events in the medical clinic.
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Affiliation(s)
- Daiane Teixeira de Oliveira
- Programa de Pós-graduação em Ciências Farmacêuticas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
| | - Renata Guerra-Sá
- Programa de Pós-graduação em Ciências Farmacêuticas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.,Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
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From 1957 to Nowadays: A Brief History of Epigenetics. Int J Mol Sci 2020; 21:ijms21207571. [PMID: 33066397 PMCID: PMC7588895 DOI: 10.3390/ijms21207571] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 01/01/2023] Open
Abstract
Due to the spectacular number of studies focusing on epigenetics in the last few decades, and particularly for the last few years, the availability of a chronology of epigenetics appears essential. Indeed, our review places epigenetic events and the identification of the main epigenetic writers, readers and erasers on a historic scale. This review helps to understand the increasing knowledge in molecular and cellular biology, the development of new biochemical techniques and advances in epigenetics and, more importantly, the roles played by epigenetics in many physiological and pathological situations.
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Gatta E, Saudagar V, Auta J, Grayson DR, Guidotti A. Epigenetic landscape of stress surfeit disorders: Key role for DNA methylation dynamics. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:127-183. [PMID: 33461662 DOI: 10.1016/bs.irn.2020.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chronic exposure to stress throughout lifespan alters brain structure and function, inducing a maladaptive response to environmental stimuli, that can contribute to the development of a pathological phenotype. Studies have shown that hypothalamic-pituitary-adrenal (HPA) axis dysfunction is associated with various neuropsychiatric disorders, including major depressive, alcohol use and post-traumatic stress disorders. Downstream actors of the HPA axis, glucocorticoids are critical mediators of the stress response and exert their function through specific receptors, i.e., the glucocorticoid receptor (GR), highly expressed in stress/reward-integrative pathways. GRs are ligand-activated transcription factors that recruit epigenetic actors to regulate gene expression via DNA methylation, altering chromatin structure and thus shaping the response to stress. The dynamic interplay between stress response and epigenetic modifiers suggest DNA methylation plays a key role in the development of stress surfeit disorders.
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Affiliation(s)
- Eleonora Gatta
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States
| | - Vikram Saudagar
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States
| | - James Auta
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States
| | - Dennis R Grayson
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States
| | - Alessandro Guidotti
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States.
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Uysal F, Ozturk S. The loss of global DNA methylation due to decreased DNMT expression in the postnatal mouse ovaries may associate with infertility emerging during ovarian aging. Histochem Cell Biol 2020; 154:301-314. [PMID: 32514790 DOI: 10.1007/s00418-020-01890-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Ovarian aging is one of the main causes of female infertility, and its molecular background is still largely unknown. As DNA methylation regulates many oogenesis/folliculogenesis-related genes, the expression levels and cellular localizations of DNA methyltransferases (DNMTs) playing key roles in this process is important in the ovaries from early to aged terms. In the present study, we aimed to evaluate the spatial and temporal expression of the Dnmt1, Dnmt3a, Dnmt3b, and Dnmt3l genes as well as global DNA methylation levels in the mouse ovaries during aging. For this purpose, the following groups were created: young (1- and 2-week old; n = 3 from each week), prepubertal (3- and 4-week-old; n = 3 from each week), pubertal (5- and 6-week-old; n = 3 from each week), postpubertal (16- and 18-week-old; n = 3 from each week), and aged (52-, 60- and 72-week-old; n = 3 from each week). We found here that Dnmt1, Dnmt3a, and Dnmt3l genes' expression at mRNA and protein levels as well as global DNA methylation profiles were gradually and significantly decreased in the postnatal ovaries from young to aged groups (P < 0.05). In contrast, there was a remarkable increase of Dnmt3b expression in the pubertal, postpubertal and aged groups (P < 0.05). Our findings suggest that the significantly altered DNMT expression and global DNA methylation levels during ovarian aging may contribute to female infertility development at the later terms of lifespan. Also, new researches are required to determine the molecular biological mechanism(s) that how altered DNMT expression and decreased DNA methylation lead to ovarian aging.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, Akdeniz University School of Medicine, 07070, Antalya, Turkey
- Department of Histology and Embryology, Ankara University School of Medicine, 06100, Ankara, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, 07070, Antalya, Turkey.
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Haws SA, Leech CM, Denu JM. Metabolism and the Epigenome: A Dynamic Relationship. Trends Biochem Sci 2020; 45:731-747. [DOI: 10.1016/j.tibs.2020.04.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022]
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García-Guede Á, Vera O, Ibáñez-de-Caceres I. When Oxidative Stress Meets Epigenetics: Implications in Cancer Development. Antioxidants (Basel) 2020; 9:antiox9060468. [PMID: 32492865 PMCID: PMC7346131 DOI: 10.3390/antiox9060468] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide and it can affect any part of the organism. It arises as a consequence of the genetic and epigenetic changes that lead to the uncontrolled growth of the cells. The epigenetic machinery can regulate gene expression without altering the DNA sequence, and it comprises methylation of the DNA, histones modifications, and non-coding RNAs. Alterations of these gene-expression regulatory elements can be produced by an imbalance of the intracellular environment, such as the one derived by oxidative stress, to promote cancer development, progression, and resistance to chemotherapeutic treatments. Here we review the current literature on the effect of oxidative stress in the epigenetic machinery, especially over the largely unknown ncRNAs and its consequences toward cancer development and progression.
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Affiliation(s)
- Álvaro García-Guede
- Epigenetics Laboratory, INGEMM, Hospital La PAZ. 28046 Madrid, Spain; (Á.G.-G.); (I.I.-d.-C.)
- Experimental Therapies and Novel Biomarkers in Cancer, Instituto de Investigación Sanitaria del Hospital La Paz. IdiPAZ, 28046 Madrid, Spain
| | - Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Correspondence:
| | - Inmaculada Ibáñez-de-Caceres
- Epigenetics Laboratory, INGEMM, Hospital La PAZ. 28046 Madrid, Spain; (Á.G.-G.); (I.I.-d.-C.)
- Experimental Therapies and Novel Biomarkers in Cancer, Instituto de Investigación Sanitaria del Hospital La Paz. IdiPAZ, 28046 Madrid, Spain
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Yang Y, Wu F, Zhang J, Sun R, Li F, Li Y, Chang S, Wang L, Wang X, Liu L, Huang C. EGR1 interacts with DNMT3L to inhibit the transcription of miR-195 and plays an anti-apoptotic role in the development of gastric cancer. J Cell Mol Med 2019; 23:7372-7381. [PMID: 31515938 PMCID: PMC6815817 DOI: 10.1111/jcmm.14597] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/10/2019] [Accepted: 07/23/2019] [Indexed: 12/11/2022] Open
Abstract
EGR1 regulates the expression of its downstream target genes and may exert different biological effects in different tumours. We found that the expression of EGR1 was increased in gastric cancer (GC), and silencing the expression of EGR1 promoted the apoptosis of GC cells. Moreover, overexpression of EGR1 repressed the apoptosis of GC cells. Bioinformatics analysis showed that EGR1 had binding sites at the upstream promoter region of miR‐195; ChIP assays were applied to determine EGR1 occupancy of the miR‐195 promoter. The RT‐PCR results showed that EGR1 suppressed the expression of miR‐195. The mechanism by which EGR1 acts as a transcriptional repressor is still unclear. Bioinformatics analysis showed that EGR1 may interact with DNMT3L. We confirmed that EGR1 and DNMT3L formed a complex, and EGR1 was an important player in the transcriptional control of miR‐195. Overexpression of miR‐195 inhibited proliferation and promoted apoptosis in GC cells. We found a well‐matched miR‐195 binding site at the AKT3 3′‐UTR. Double luciferase reporter assays showed that AKT3 was a target of miR‐195, and silencing AKT3 repressed cell proliferation and promoted apoptosis. Our results indicated EGR1 may interact with DNMT3L to inhibit the miR‐195‐AKT3 axis and regulate the GC cell apoptosis.
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Affiliation(s)
- Yang Yang
- School of Public Health, Xi'anJiaotong University Health Science Center, Xi'an, China
| | - Fei Wu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'anJiaotong University Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jing Zhang
- Department of Clinical Medicine, Medical College of Yan'an University, Yan'an, Shaanxi, China
| | - Ruifang Sun
- Department of Pathology, School of Basic Medical Sciences, Xi'anJiaotong University Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Fang Li
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'anJiaotong University Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yulong Li
- Department of gastroenterology, Shaanxi provincial people's hospital, Xi'an, China
| | - Su'e Chang
- Department of Orthopedics, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lumin Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'anJiaotong University Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiaofei Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'anJiaotong University Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Liying Liu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'anJiaotong University Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'anJiaotong University Health Science Center, Xi'an Jiaotong University, Xi'an, China
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The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol 2019; 20:590-607. [PMID: 31399642 DOI: 10.1038/s41580-019-0159-6] [Citation(s) in RCA: 1115] [Impact Index Per Article: 223.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/22/2022]
Abstract
DNA methylation is of paramount importance for mammalian embryonic development. DNA methylation has numerous functions: it is implicated in the repression of transposons and genes, but is also associated with actively transcribed gene bodies and, in some cases, with gene activation per se. In recent years, sensitive technologies have been developed that allow the interrogation of DNA methylation patterns from a small number of cells. The use of these technologies has greatly improved our knowledge of DNA methylation dynamics and heterogeneity in embryos and in specific tissues. Combined with genetic analyses, it is increasingly apparent that regulation of DNA methylation erasure and (re-)establishment varies considerably between different developmental stages. In this Review, we discuss the mechanisms and functions of DNA methylation and demethylation in both mice and humans at CpG-rich promoters, gene bodies and transposable elements. We highlight the dynamic erasure and re-establishment of DNA methylation in embryonic, germline and somatic cell development. Finally, we provide insights into DNA methylation gained from studying genetic diseases.
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Surace AEA, Hedrich CM. The Role of Epigenetics in Autoimmune/Inflammatory Disease. Front Immunol 2019; 10:1525. [PMID: 31333659 PMCID: PMC6620790 DOI: 10.3389/fimmu.2019.01525] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/18/2019] [Indexed: 12/21/2022] Open
Abstract
Historically, systemic self-inflammatory conditions were classified as either autoinflammatory and caused by the innate immune system or autoimmune and driven by adaptive immune responses. However, it became clear that reality is much more complex and that autoimmune/inflammatory conditions range along an “inflammatory spectrum” with primarily autoinflammatory vs. autoimmune conditions resembling extremes at either end. Epigenetic modifications influence gene expression and alter cellular functions without modifying the genomic sequence. Methylation of CpG DNA dinucleotides and/or their hydroxymethylation, post-translational modifications to amino termini of histone proteins, and non-coding RNA expression are main epigenetic events. The pathophysiology of autoimmune/inflammatory diseases has been closely linked with disease causing gene mutations (rare) or a combination of genetic susceptibility and epigenetic modifications arising from exposure to the environment (more common). Over recent years, progress has been made in understanding molecular mechanisms involved in systemic inflammation and the contribution of innate and adaptive immune responses. Epigenetic events have been identified as (i) central pathophysiological factors in addition to genetic disease predisposition and (ii) as co-factors determining clinical pictures and outcomes in individuals with monogenic disease. Thus, a complete understanding of epigenetic contributors to autoimmune/inflammatory disease will result in approaches to predict individual disease outcomes and the introduction of effective, target-directed, and tolerable therapies. Here, we summarize recent findings that signify the importance of epigenetic modifications in autoimmune/inflammatory disorders along the inflammatory spectrum choosing three examples: the autoinflammatory bone condition chronic nonbacterial osteomyelitis (CNO), the “mixed pattern” disorder psoriasis, and the autoimmune disease systemic lupus erythematosus (SLE).
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Affiliation(s)
- Anna Elisa Andrea Surace
- Department of Women's and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Christian M Hedrich
- Department of Women's and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.,Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, United Kingdom.,Pädiatrische Rheumatologie, Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
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Uysal F, Akkoyunlu G, Ozturk S. Decreased expression of DNA methyltransferases in the testes of patients with non-obstructive azoospermia leads to changes in global DNA methylation levels. Reprod Fertil Dev 2019; 31:1386-1394. [PMID: 31030726 DOI: 10.1071/rd18246] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 02/13/2019] [Indexed: 12/27/2022] Open
Abstract
DNA methylation plays key roles in epigenetic regulation during mammalian spermatogenesis. DNA methyltransferases (DNMTs) function in de novo and maintenance methylation processes by adding a methyl group to the fifth carbon atom of the cytosine residues within cytosine-phosphate-guanine (CpG) and non-CpG dinucleotide sites. Azoospermia is one of the main causes of male infertility, and is classified as obstructive (OA) or non-obstructive (NOA) azoospermia based on histopathological characteristics. The molecular background of NOA is still largely unknown. DNA methylation performed by DNMTs is implicated in the transcriptional regulation of spermatogenesis-related genes. The aim of the present study was to evaluate the cellular localisation and expression levels of the DNMT1, DNMT3A and DNMT3B proteins, as well as global DNA methylation profiles in testicular biopsy samples obtained from men with various types of NOA, including hypospermatogenesis (hyposperm), round spermatid (RS) arrest, spermatocyte (SC) arrest and Sertoli cell-only (SCO) syndrome. In the testicular biopsy samples, DNMT1 expression and global DNA methylation levels decreased gradually from the hyposperm to SCO groups (P P P <0.05). Although both DNMT1 and DNMT3A were localised in the cytoplasm and nucleus of the spermatogenic cells, staining for DNMT3B was more intensive in the nucleus of spermatogenic cells. In conclusion, the findings suggest that significant changes in DNMT expression and global DNA methylation levels in spermatogenic cells may contribute to development of male infertility in the NOA groups. Further studies are needed to determine the molecular biological effects of the altered DNMT expression and DNA methylation levels on development of male infertility.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey; and Department of Histology and Embryology, Ankara University School of Medicine, 06100, Ankara, Turkey
| | - Gokhan Akkoyunlu
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey; and Corresponding author
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Somasundaram S, Forrest ME, Moinova H, Cohen A, Varadan V, LaFramboise T, Markowitz S, Khalil AM. The DNMT1-associated lincRNA DACOR1 reprograms genome-wide DNA methylation in colon cancer. Clin Epigenetics 2018; 10:127. [PMID: 30348202 PMCID: PMC6196572 DOI: 10.1186/s13148-018-0555-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/26/2018] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND DNA methylation is a key epigenetic mark in mammalian organisms that plays key roles in chromatin organization and gene expression. Although DNA methylation in gene promoters is generally associated with gene repression, recent studies demonstrate that DNA methylation in gene bodies and intergenic regions of the genome may result in distinct modes of gene regulation. Furthermore, the molecular mechanisms underlying the establishment and maintenance of DNA methylation in human health and disease remain to be fully elucidated. We recently demonstrated that a subset of long non-coding RNAs (lncRNAs) associates with the major DNA methyltransferase DNMT1 in human colon cancer cells, and the dysregulation of such lncRNAs contribute to aberrant DNA methylation patterns. RESULTS In the current study, we assessed the impact of a key DNMT1-associated lncRNA, DACOR1, on genome-wide DNA methylation using reduced representation bisulfite sequencing (RRBS). Our findings demonstrated that induction of DACOR1 in colon cancer cells restores DNA methylation at thousands of CpG sites throughout the genome including promoters, gene bodies, and intergenic regions. Importantly, these sites overlap with regions of the genome that become hypomethylated in colon tumors. Furthermore, induction of DACOR1 results in repression of FOS and JUN and, consequently, reduced AP-1 transcription factor activity. CONCLUSION Collectively, our results demonstrate a key role of lncRNAs in regulating DNA methylation in human cells, and the dysregulation of such lncRNAs could emerge as a key mechanism by which DNA methylation patterns become altered in human tumors.
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Affiliation(s)
- Saigopal Somasundaram
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Megan E Forrest
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Helen Moinova
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Allison Cohen
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Vinay Varadan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Sanford Markowitz
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ahmad M Khalil
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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Murín R, Abdalla M, Murínová N, Hatok J, Dobrota D. The metabolism of 5-methylcytosine residues in DNA. Physiol Res 2018. [PMID: 29527909 DOI: 10.33549/physiolres.933550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The fundamental biochemical processes of 5-methylcytosine (5-mC) synthesis, maintenance, conversion and removal determine the time and spatial pattern of DNA methylation. This has a strong effect on a plethora of physiological aspects of cellular metabolism. While the presence of 5-mC within the promoter region can silence gene expression, its derivative - 5-hydroxymethylcytosine exerts an opposite effect. Dysregulations in the metabolism of 5-mC lead to an altered DNA methylation pattern which is linked with a disrupted epigenome, and are considered to play a significant part in the etiology of several human diseases. A summary of recent knowledge about the molecular processes participating in DNA methylation pattern shaping is provided here.
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Affiliation(s)
- R Murín
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
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Larsen K, Kristensen KK, Callesen H. DNA methyltransferases and tRNA methyltransferase DNMT2 in developing pig brain - expression and promoter methylation. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Zhong Y, Choi T, Kim M, Jung KH, Chai YG, Binas B. Isolation of primitive mouse extraembryonic endoderm (pXEN) stem cell lines. Stem Cell Res 2018; 30:100-112. [PMID: 29843002 DOI: 10.1016/j.scr.2018.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/16/2018] [Accepted: 05/16/2018] [Indexed: 01/09/2023] Open
Abstract
Mouse blastocysts contain the committed precursors of the extraembryonic endoderm (ExEn), which express the key transcription factor Oct4, depend on LIF/LIF-like factor-driven Jak/Stat signaling, and initially exhibit lineage plasticity. Previously described rat blastocyst-derived ExEn precursor-like cell lines (XENP cells/HypoSCs) also show these features, but equivalent mouse blastocyst-derived cell lines are lacking. We now present mouse blastocyst-derived cell lines, named primitive XEN (pXEN) cells, which share these and additional characteristics with the XENP cells/HypoSCs, but not with previously known mouse blastocyst-derived XEN cell lines. Otherwise, pXEN cells are highly similar to XEN cells by morphology, lineage-intrinsic differentiation potential, and multi-gene expression profile, although the pXEN cell profile correlates better with the blastocyst stage. Finally, we show that pXEN cells easily convert into XEN-like cells but not vice versa. The findings indicate that (i) pXEN cells are more representative than XEN cells of the blastocyst stage; (ii) mouse pXEN, rather than XEN, cells are homologs of rat XENP cells/HypoSCs, which we propose to call rat pXEN cells.
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Affiliation(s)
- Yixiang Zhong
- Department of Molecular & Life Science, College of Science and Technology, Hanyang University (ERICA Campus), 55 Hanyangdaehak-ro, Sangrok-gu, Ansan-si, Gyeonggi-do 15588, Republic of Korea
| | - Taewoong Choi
- Department of Molecular & Life Science, College of Science and Technology, Hanyang University (ERICA Campus), 55 Hanyangdaehak-ro, Sangrok-gu, Ansan-si, Gyeonggi-do 15588, Republic of Korea
| | - Minjae Kim
- Department of Molecular & Life Science, College of Science and Technology, Hanyang University (ERICA Campus), 55 Hanyangdaehak-ro, Sangrok-gu, Ansan-si, Gyeonggi-do 15588, Republic of Korea
| | - Kyoung Hwa Jung
- Department of Molecular & Life Science, College of Science and Technology, Hanyang University (ERICA Campus), 55 Hanyangdaehak-ro, Sangrok-gu, Ansan-si, Gyeonggi-do 15588, Republic of Korea
| | - Young Gyu Chai
- Department of Molecular & Life Science, College of Science and Technology, Hanyang University (ERICA Campus), 55 Hanyangdaehak-ro, Sangrok-gu, Ansan-si, Gyeonggi-do 15588, Republic of Korea
| | - Bert Binas
- Department of Molecular & Life Science, College of Science and Technology, Hanyang University (ERICA Campus), 55 Hanyangdaehak-ro, Sangrok-gu, Ansan-si, Gyeonggi-do 15588, Republic of Korea..
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Prolonged Growth Hormone/Insulin/Insulin-like Growth Factor Nutrient Response Signaling Pathway as a Silent Killer of Stem Cells and a Culprit in Aging. Stem Cell Rev Rep 2018; 13:443-453. [PMID: 28229284 PMCID: PMC5493720 DOI: 10.1007/s12015-017-9728-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The dream of slowing down the aging process has always inspired mankind. Since stem cells are responsible for tissue and organ rejuvenation, it is logical that we should search for encoded mechanisms affecting life span in these cells. However, in adult life the hierarchy within the stem cell compartment is still not very well defined, and evidence has accumulated that adult tissues contain rare stem cells that possess a broad trans-germ layer differentiation potential. These most-primitive stem cells-those endowed with pluripotent or multipotent differentiation ability and that give rise to other cells more restricted in differentiation, known as tissue-committed stem cells (TCSCs) - are of particular interest. In this review we present the concept supported by accumulating evidence that a population of so-called very small embryonic-like stem cells (VSELs) residing in adult tissues positively impacts the overall survival of mammals, including humans. These unique cells are prevented in vertebrates from premature depletion by decreased sensitivity to growth hormone (GH), insulin (INS), and insulin-like growth factor (IGF) signaling, due to epigenetic changes in paternally imprinted genes that regulate their resistance to these factors. In this context, we can envision nutrient response GH/INS/IGF signaling pathway as a lethal factor for these most primitive stem cells and an important culprit in aging.
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Uysal F, Ozturk S, Akkoyunlu G. Superovulation alters DNA methyltransferase protein expression in mouse oocytes and early embryos. J Assist Reprod Genet 2018; 35:503-513. [PMID: 29164502 PMCID: PMC5904060 DOI: 10.1007/s10815-017-1087-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/08/2017] [Indexed: 12/22/2022] Open
Abstract
PURPOSE DNA methylation is an epigenetic mechanism that plays critical roles during mammalian oocyte and preimplantation embryo development. It is achieved by adding a methyl group to the fifth carbon atom of cytosine residues within cytosine-phosphate-guanine (CpG) and non-CpG dinucleotide sites using DNA methyltransferase (DNMT) enzymes for de novo and maintenance methylation processes. DNMT1, DNMT3A, and DNMT3B play important roles in establishing methylation of developmentally related genes in oocytes and early embryos. The purpose of this study is to identify the effect of superovulation on the expression and subcellular localizations of these three DNMT enzymes in the mouse oocytes and early embryos. METHODS Three groups composed of control, normal dose [5 IU pregnant mare serum gonadotropin (PMSG) and 5 IU human chorionic gonadotropin (hCG)], and high dose [7.5 IU PMSG and 7.5 IU hCG] were created from 4-5-week-old female BALB/c mice. The relative expression and subcellular localizations of the DNMT proteins in the control and experiment groups have been characterized by using immunofluorescence staining subsequently analyzed in detailed. RESULTS DNMT1, DNMT3A, and DNMT3B protein expression in the germinal vesicle and metaphase II oocytes and in one-cell and two-cell embryos differed significantly when some of the normal- and high-dose groups were compared with the control counterparts. CONCLUSION This study has demonstrated for the first time that superovulation alters expression levels of the DNMT proteins, a finding that indicates that certain developmental defects in superovulated oocytes and early embryos may result from impaired DNA methylation processes.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, School of Medicine, Akdeniz University, Campus, 07070, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, School of Medicine, Akdeniz University, Campus, 07070, Antalya, Turkey
| | - Gokhan Akkoyunlu
- Department of Histology and Embryology, School of Medicine, Akdeniz University, Campus, 07070, Antalya, Turkey.
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Hervouet E, Peixoto P, Delage-Mourroux R, Boyer-Guittaut M, Cartron PF. Specific or not specific recruitment of DNMTs for DNA methylation, an epigenetic dilemma. Clin Epigenetics 2018; 10:17. [PMID: 29449903 PMCID: PMC5807744 DOI: 10.1186/s13148-018-0450-y] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/30/2018] [Indexed: 11/28/2022] Open
Abstract
Our current view of DNA methylation processes is strongly moving: First, even if it was generally admitted that DNMT3A and DNMT3B are associated with de novo methylation and DNMT1 is associated with inheritance DNA methylation, these distinctions are now not so clear. Secondly, since one decade, many partners of DNMTs have been involved in both the regulation of DNA methylation activity and DNMT recruitment on DNA. The high diversity of interactions and the combination of these interactions let us to subclass the different DNMT-including complexes. For example, the DNMT3L/DNMT3A complex is mainly related to de novo DNA methylation in embryonic states, whereas the DNMT1/PCNA/UHRF1 complex is required for maintaining global DNA methylation following DNA replication. On the opposite to these unspecific DNA methylation machineries (no preferential DNA sequence), some recently identified DNMT-including complexes are recruited on specific DNA sequences. The coexistence of both types of DNA methylation (un/specific) suggests a close cooperation and an orchestration between these systems to maintain genome and epigenome integrities. Deregulation of these systems can lead to pathologic disorders.
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Affiliation(s)
- Eric Hervouet
- INSERM unit 1098, University of Bourgogne Franche-Comté, Besançon, France.,EPIGENExp (EPIgenetics and GENe EXPression Technical Platform), Besançon, France
| | - Paul Peixoto
- INSERM unit 1098, University of Bourgogne Franche-Comté, Besançon, France.,EPIGENExp (EPIgenetics and GENe EXPression Technical Platform), Besançon, France
| | | | | | - Pierre-François Cartron
- 3INSERM unit S1232, University of Nantes, Nantes, France.,4Institut de cancérologie de l'Ouest, Nantes, France.,REpiCGO (Cancéropole Grand-Ouest), Nantes, France.,EpiSAVMEN Networks, Nantes, Région Pays de la Loire France
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41
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Bolund ACS, Starnawska A, Miller MR, Schlünssen V, Backer V, Børglum AD, Christensen K, Tan Q, Christiansen L, Sigsgaard T. Lung function discordance in monozygotic twins and associated differences in blood DNA methylation. Clin Epigenetics 2017; 9:132. [PMID: 29299071 PMCID: PMC5740718 DOI: 10.1186/s13148-017-0427-2] [Citation(s) in RCA: 16] [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: 07/28/2017] [Accepted: 11/23/2017] [Indexed: 01/16/2023] Open
Abstract
Background Lung function is an important predictor of morbidity and mortality, with accelerated lung function decline reported to have immense consequences for the world's healthcare systems. The lung function decline across individual's lifetime is a consequence of age-related changes in lung anatomical structure and combination of various environmental factors; however, the exact molecular mechanisms contributing to this decline are not fully understood. DNA methylation is an epigenetic modification that changes across individual's lifetime, as well as allows for interplay between environmental and genetic factors. DNA methylation plays a crucial role in regulation of gene expression, with increasing evidence linking aberrant DNA methylation levels with a number of common human diseases. In this study, we investigated possible associations between genome-wide DNA methylation levels and lung function in 169 pairs of middle-aged monozygotic twins (86 male pairs: mean age (min-max) = 66 years (57-79); 83 female pairs: mean age (min-max) = 66 years (56-78)). The twins were collected from the Danish Twin Registry and were examined at baseline (1998-1999) and follow-up (2008-2011) visits. Using the twin design, we correlated intra-pair differences in cross-sectional and longitudinal lung function with intra-pair blood DNA methylation differences at follow-up by linear regression analyses adjusted for sex, age, BMI, smoking, and blood cell composition measured for each individual with the use of flow cytometry. Results We identified several differentially methylated CpG sites associated with forced expiratory volume the first second (FEV1) and forced vital capacity (FVC). Three probes identified for level of FVC were located in GLIPR1L2 gene (lowest p value = 7.14 × 10-8), involved in innate immunity and tumour-suppressor/pro-oncogenic mechanisms. Change in FEV1 during the 11-year follow-up period was associated with blood DNA methylation level in TRIM27 gene (p value = 1.55 × 10-6), a negative regulator of CD4 T cells, and also involved in cancer development. Several enriched pathways were identified, especially for FEV1, with one being "TGFBR" (Benjamini-Hochbergadjp value = 0.045), the receptor for TGFβ, a growth factor involved in normal lung tissue repair through pro-fibrotic effects. Conclusions Our findings suggest that epigenetic regulation of immunological- and cancer-related genes, as well as TGF-β-receptor-related genes, may be involved in the cross-sectional level and longitudinal change in lung function in middle-aged monozygotic twins.
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Affiliation(s)
- Anneli C. S. Bolund
- Department of Public Health, Section for Environment Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Martin R. Miller
- Institute of Occupational and Environmental Medicine, University of Birmingham, Birmingham, UK
| | - Vivi Schlünssen
- Department of Public Health, Section for Environment Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Vibeke Backer
- Department of Respiratory Medicine, Bispebjerg University Hospital, Copenhagen, Denmark
| | - Anders D. Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Kaare Christensen
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, University Hospital, Odense, Denmark
| | - Qihua Tan
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Lene Christiansen
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Torben Sigsgaard
- Department of Public Health, Section for Environment Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
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42
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Uysal F, Ozturk S, Akkoyunlu G. DNMT1, DNMT3A and DNMT3B proteins are differently expressed in mouse oocytes and early embryos. J Mol Histol 2017; 48:417-426. [PMID: 29027601 DOI: 10.1007/s10735-017-9739-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/09/2017] [Indexed: 12/18/2022]
Abstract
DNA methylation is one of the epigenetic mechanisms and plays important roles during oogenesis and early embryo development in mammals. DNA methylation is basically known as adding a methyl group to the fifth carbon atom of cytosine residues within cytosine-phosphate-guanine (CpG) and non-CpG dinucleotide sites. This mechanism is composed of two main processes: de novo methylation and maintenance methylation, both of which are catalyzed by specific DNA methyltransferase (DNMT) enzymes. To date, six different DNMTs have been characterized in mammals defined as DNMT1, DNMT2, DNMT3A, DNMT3B, DNMT3C, and DNMT3L. While DNMT1 primarily functions in maintenance methylation, both DNMT3A and DNMT3B are essentially responsible for de novo methylation. As is known, either maintenance or de novo methylation processes appears during oocyte and early embryo development terms. The aim of the present study is to investigate spatial and temporal expression levels and subcellular localizations of the DNMT1, DNMT3A, and DNMT3B proteins in the mouse germinal vesicle (GV) and metaphase II (MII) oocytes, and early embryos from 1-cell to blastocyst stages. We found that there are remarkable differences in the expressional levels and subcellular localizations of the DNMT1, DNMT3A and DNMT3B proteins in the GV and MII oocytes, and 1-cell, 2-cell, 4-cell, 8-cell, morula, and blastocyst stage embryos. The fluctuations in the expression of DNMT proteins in the analyzed oocytes and early embryos are largely compatible with DNA methylation changes and genomic imprintestablishment appearing during oogenesis and early embryo development. To understand precisemolecular biological meaning of differently expressing DNMTs in the early developmental periods, further studies are required.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Gokhan Akkoyunlu
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey.
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Mostowska A, Szczepańska M, Wirstlein P, Skrzypczak J, Jagodziński PP. Association between DNMT3L polymorphic variants and the risk of endometriosis-associated infertility. Mol Med Rep 2015; 13:1040-6. [PMID: 26647998 DOI: 10.3892/mmr.2015.4626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 11/06/2015] [Indexed: 11/05/2022] Open
Abstract
Endometriosis is considered to be an epigenetic disease. It has previously been reported that the DNA methyltransferase 3-like (DNMT3L) rs8129776 single nucleotide polymorphism (SNP) contributes to endometrioma. In the present study, high‑resolution melting curve analysis was used to investigate the risks associated with the DNMT3L c.910‑635A/G (rs8129776), c.832C/T (rs7354779), c.812C/T (rs113593938) and c.344+62C/T (rs2276248) SNPs on stage I‑II endometriosis‑associated infertility. Included in the present study were patients presenting with stage I‑II endometriosis‑associated infertility (n=154) and a control cohort of healthy patients with confirmed fertility (n=383). No significant association between the above‑listed DNMT3L SNPs and the development of endometriosis‑associated infertility was identified. The lowest P‑values generated from trend analysis were observed in the DNMT3L c.832C/T (rs7354779) SNP (Ptrend=0.114). Furthermore, haplotype analyses of the DNMT3L SNPs failed to reveal any risk association between the development of endometriosis‑associated infertility and the above‑listed polymorphisms, even when the SNPs were present in combinations. Finally, a meta‑analysis was performed to examine the association between the DNMT3L rs8129776 SNP and the development of endometrioma, from which no association between the two was identified. On the basis of these results, the present study has demonstrated that variations in the DNMT3L gene do not contribute to stage I-II endometriosis-associated infertility.
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Affiliation(s)
- Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poznań 60‑781, Poland
| | - Malgorzata Szczepańska
- Department of Obstetrics, Gynecology and Gynecological Oncology, Division of Reproduction, Poznań University of Medical Sciences, Poznań 60‑781, Poland
| | - Przemyslaw Wirstlein
- Department of Obstetrics, Gynecology and Gynecological Oncology, Division of Reproduction, Poznań University of Medical Sciences, Poznań 60‑781, Poland
| | - Jana Skrzypczak
- Department of Obstetrics, Gynecology and Gynecological Oncology, Division of Reproduction, Poznań University of Medical Sciences, Poznań 60‑781, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poznań 60‑781, Poland
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Uysal F, Akkoyunlu G, Ozturk S. Dynamic expression of DNA methyltransferases (DNMTs) in oocytes and early embryos. Biochimie 2015; 116:103-13. [PMID: 26143007 DOI: 10.1016/j.biochi.2015.06.019] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/26/2015] [Indexed: 11/26/2022]
Abstract
Epigenetic mechanisms play critical roles in oogenesis and early embryo development in mammals. One of these epigenetic mechanisms, DNA methylation is accomplished through the activities of DNA methyltransferases (DNMTs), which are responsible for adding a methyl group to the fifth carbon atom of the cytosine residues within cytosine-phosphate-guanine (CpG) and non-CpG dinuclotide sites. Five DNMT enzymes have been identified in mammals including DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L. They function in two different methylation processes: maintenance and de novo. For maintenance methylation, DNMT1 preferentially transfers methyl groups to the hemi-methylated DNA strands following DNA replication. However, for de novo methylation activities both DNMT3A and DNMT3B function in the methylation of the unmodified cytosine residues. Although DNMT3L indirectly contributes to de novo methylation process, DNMT2 enables the methylation of the cytosine 38 in the anticodon loop of aspartic acid transfer RNA and does not methylate DNA. In this review article, we have evaluated and discussed the existing published studies to characterize the spatial and temporal expression patterns of the DNMTs in mouse, bovine and human oocytes and early embryos. We have also reviewed the effects of in vitro culture conditions (serum abundance and glucose concentration), aging, superovulation, vitrification, and somatic cell nuclear transfer technology on the dynamics of DNMTs.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey
| | - Gokhan Akkoyunlu
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Antalya, Turkey.
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Liao HF, Mo CF, Wu SC, Cheng DH, Yu CY, Chang KW, Kao TH, Lu CW, Pinskaya M, Morillon A, Lin SS, Cheng WTK, Bourc'his D, Bestor T, Sung LY, Lin SP. Dnmt3l-knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency. Reproduction 2015; 150:245-56. [PMID: 26159833 DOI: 10.1530/rep-15-0031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 07/09/2015] [Indexed: 12/18/2022]
Abstract
Nuclear transfer (NT) is a technique used to investigate the development and reprogramming potential of a single cell. DNA methyltransferase-3-like, which has been characterized as a repressive transcriptional regulator, is expressed in naturally fertilized egg and morula/blastocyst at pre-implantation stages. In this study, we demonstrate that the use of Dnmt3l-knockout (Dnmt3l-KO) donor cells in combination with Trichostatin A treatment improved the developmental efficiency and quality of the cloned embryos. Compared with the WT group, Dnmt3l-KO donor cell-derived cloned embryos exhibited increased cell numbers as well as restricted OCT4 expression in the inner cell mass (ICM) and silencing of transposable elements at the blastocyst stage. In addition, our results indicate that zygotic Dnmt3l is dispensable for cloned embryo development at pre-implantation stages. In Dnmt3l-KO mouse embryonic fibroblasts, we observed reduced nuclear localization of HDAC1, increased levels of the active histone mark H3K27ac and decreased accumulation of the repressive histone marks H3K27me3 and H3K9me3, suggesting that Dnmt3l-KO donor cells may offer a more permissive epigenetic state that is beneficial for NT reprogramming.
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Affiliation(s)
- Hung-Fu Liao
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Chu-Fan Mo
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Shinn-Chih Wu
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Dai-Han Cheng
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Chih-Yun Yu
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Kai-Wei Chang
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Tzu-Hao Kao
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Chia-Wei Lu
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Marina Pinskaya
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Antonin Morillon
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Shih-Shun Lin
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, T
| | - Winston T K Cheng
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Déborah Bourc'his
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Timothy Bestor
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Li-Ying Sung
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Shau-Ping Lin
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, T
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Yi JM, Kim TO. Epigenetic alterations in inflammatory bowel disease and cancer. Intest Res 2015; 13:112-21. [PMID: 25931995 PMCID: PMC4414752 DOI: 10.5217/ir.2015.13.2.112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 12/15/2022] Open
Abstract
Overwhelming evidences supports the idea that inflammatory bowel disease (IBD) is caused by a complex interplay between genetic alterations of multiple genes and an aberrant interaction with environmental factors. There is growing evidence that epigenetic factors can play a significant part in the pathogenesis of IBD. Significant effort has been invested in uncovering genetic and epigenetic factors, which may increase the risk of IBD, but progress has been slow, and few IBD-specific factors have been detected so far. It has been known for decades that DNA methylation is the most well studied epigenetic modification, and analysis of DNA methylation is leading to a new generation of cancer biomarkers. Therefore, in this review, we summarize the role of DNA methylation alteration in IBD pathogenesis, and discuss specific genes or genetic loci using recent molecular technology advances. Here, we suggest that DNA methylation should be studied in depth to understand the molecular pathways of IBD pathogenesis, and discuss epigenetic studies of IBD that may have a significant impact on the field of IBD research.
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Affiliation(s)
- Joo Mi Yi
- Research Institute, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan, Korea
| | - Tae Oh Kim
- Department of Internal Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea
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Perotti A, Rossi V, Mutti A, Buschini A. Methy-sens Comet assay and DNMTs transcriptional analysis as a combined approach in epigenotoxicology. Biomarkers 2014; 20:64-70. [DOI: 10.3109/1354750x.2014.992813] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Medina-Franco JL, Méndez-Lucio O, Dueñas-González A, Yoo J. Discovery and development of DNA methyltransferase inhibitors using in silico approaches. Drug Discov Today 2014; 20:569-77. [PMID: 25526932 DOI: 10.1016/j.drudis.2014.12.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/19/2014] [Accepted: 12/10/2014] [Indexed: 01/08/2023]
Abstract
Multiple strategies have evolved during the past few years to advance epigenetic compounds targeting DNA methyltransferases (DNMTs). Significant progress has been made in HTS, lead optimization and determination of 3D structures of DNMTs. In light of the emerging concept of epi-informatics, computational approaches are employed to accelerate the development of DNMT inhibitors helping to screen chemical databases, mine the DNMT-relevant chemical space, uncover SAR and design focused libraries. Computational methods also synergize with natural-product-based drug discovery and drug repurposing. Herein, we survey the latest developments of in silico approaches to advance epigenetic drug and probe discovery targeting DNMTs.
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Affiliation(s)
- José L Medina-Franco
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico.
| | - Oscar Méndez-Lucio
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Alfonso Dueñas-González
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México and Instituto Nacional de Cancerología, Av. San Fernando 22, Mexico City 14080, Mexico
| | - Jakyung Yoo
- Life Science Research Institute, Daewoong Pharmaceutical Co. Ltd., 72 Dugye-Ro, Pogok-Eup, Gyeonggi-do 449-814, Republic of Korea
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Dekker AD, De Deyn PP, Rots MG. Epigenetics: The neglected key to minimize learning and memory deficits in Down syndrome. Neurosci Biobehav Rev 2014; 45:72-84. [DOI: 10.1016/j.neubiorev.2014.05.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/04/2014] [Accepted: 05/13/2014] [Indexed: 10/25/2022]
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Li M, Cleves MA, Mallick H, Erickson SW, Tang X, Nick TG, Macleod SL, Hobbs CA. A genetic association study detects haplotypes associated with obstructive heart defects. Hum Genet 2014; 133:1127-38. [PMID: 24894164 PMCID: PMC4313870 DOI: 10.1007/s00439-014-1453-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/20/2014] [Indexed: 10/25/2022]
Abstract
The development of congenital heart defects (CHDs) involves a complex interplay between genetic variants, epigenetic variants, and environmental exposures. Previous studies have suggested that susceptibility to CHDs is associated with maternal genotypes, fetal genotypes, and maternal-fetal genotype (MFG) interactions. We conducted a haplotype-based genetic association study of obstructive heart defects (OHDs), aiming to detect the genetic effects of 877 SNPs involved in the homocysteine, folate, and transsulfuration pathways. Genotypes were available for 285 mother-offspring pairs with OHD-affected pregnancies and 868 mother-offspring pairs with unaffected pregnancies. A penalized logistic regression model was applied with an adaptive least absolute shrinkage and selection operator (lasso), which dissects the maternal effect, fetal effect, and MFG interaction effects associated with OHDs. By examining the association between 140 haplotype blocks, we identified 9 blocks that are potentially associated with OHD occurrence. Four haplotype blocks, located in genes MGMT, MTHFS, CBS, and DNMT3L, were statistically significant using a Bayesian false-discovery probability threshold of 0.8. Two blocks in MGMT and MTHFS appear to have significant fetal effects, while the CBS and DNMT3L genes may have significant MFG interaction effects.
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Affiliation(s)
- Ming Li
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, 13 Children’s Way Mail Slot 512-40, Little Rock, AR 72202, USA
| | - Mario A. Cleves
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, 13 Children’s Way Mail Slot 512-40, Little Rock, AR 72202, USA
| | - Himel Mallick
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stephen W. Erickson
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Xinyu Tang
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, 13 Children’s Way Mail Slot 512-40, Little Rock, AR 72202, USA
| | - Todd G. Nick
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, 13 Children’s Way Mail Slot 512-40, Little Rock, AR 72202, USA
| | - Stewart L. Macleod
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, 13 Children’s Way Mail Slot 512-40, Little Rock, AR 72202, USA
| | - Charlotte A. Hobbs
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, 13 Children’s Way Mail Slot 512-40, Little Rock, AR 72202, USA
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