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Vasileva F, Hristovski R, Font-Lladó R, Georgiev G, Sacot A, López-Ros V, Calleja-González J, Barretina-Ginesta J, López-Bermejo A, Prats-Puig A. Physical Exercise-Induced DNA Methylation in Disease-Related Genes in Healthy Adults-A Systematic Review With Bioinformatic Analysis. J Strength Cond Res 2024; 38:384-393. [PMID: 38088908 DOI: 10.1519/jsc.0000000000004686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
ABSTRACT Vasileva, F, Hristovski, R, Font-Lladó, R, Georgiev, G, Sacot, A, López-Ros, V, Calleja-González, J, Barretina-Ginesta, J, López-Bermejo, A, and Prats-Puig, A. Physical exercise-induced DNA methylation in disease-related genes in healthy adults-A systematic review with bioinformatic analysis. J Strength Cond Res 38(2): 384-393, 2024-This study aimed to systematically review the existing literature regarding physical exercise (PE) and DNA methylation (DNAm) in healthy adults. Specific goals were to (a) identify differently methylated genes (DMGs) after PE intervention, their imprinting status, chromosome and genomic location, function, and related diseases; and (b) to screen for core genes and identify methylation changes of the core genes that can be modified by PE intervention. Our search identified 2,869 articles from which 8 were finally included. We identified 1851 DMGs ( p < 0.05) after PE intervention, although 45 of them were imprinted. Aerobic exercise (AE) seems to induce more DNA hypermethylation rather than hypomethylation, whereas anaerobic exercise (AN) seems to induce more DNA hypomethylation rather than hypermethylation. Aerobic exercise induced highest % of methylation changes on chromosome 6, whereas AN and mixed type (MT) on chromosome 1. Mixed type induced higher % of methylation changes close to transcription start site in comparison to AE and AN. After PE intervention, DMGs were mainly involved in fat metabolism, cell growth, and neuronal differentiation, whereas diseases regulated by those genes were mainly chronic diseases (metabolic, cardiovascular, neurodegenerative). Finally, 19 core genes were identified among DMGs, all related to protein metabolism. In conclusion, our findings may shed some light on the mechanisms explaining PE-induced health benefits such as the potential role that PE-induced DNAm may have in disease prevention and disease treatment.
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Affiliation(s)
- Fidanka Vasileva
- University School of Health and Sport, University of Girona, Girona, Spain
- Pediatric Endocrinology Research Group, Girona Institute for Biomedical Research, Girona, Spain
| | - Robert Hristovski
- Faculty of Physical Education, Sport and Health, University Ss. Cyril and Methodius, Skopje, Republic of North Macedonia
| | - Raquel Font-Lladó
- University School of Health and Sport, University of Girona, Girona, Spain
- Research Group of Culture and Education, Institute of Educational Research, University of Girona, Girona, Spain
| | - Georgi Georgiev
- Faculty of Physical Education, Sport and Health, University Ss. Cyril and Methodius, Skopje, Republic of North Macedonia
| | - Arnau Sacot
- University School of Health and Sport, University of Girona, Girona, Spain
- Basquet Girona, Girona, Spain
| | - Víctor López-Ros
- University School of Health and Sport, University of Girona, Girona, Spain
- Chair of Sport and Physical Education-Centre of Olympic Studies, University of Girona, Girona, Spain
| | - Julio Calleja-González
- Department of Physical Education and Sport, Faculty of Education and Sport, University of the Basque Country, Vitoria, Spain
| | | | - Abel López-Bermejo
- Pediatric Endocrinology Research Group, Girona Institute for Biomedical Research, Girona, Spain
- Pediatric Endocrinology, Dr. Josep Girona Hospital, Girona, Spain
- Department of Medical Sciences, University of Girona, Girona, Spain; and
| | - Anna Prats-Puig
- University School of Health and Sport, University of Girona, Girona, Spain
- Research Group of Clinical Anatomy, Embryology and Neuroscience, Department of Medical Sciences, University of Girona, Girona, Spain
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2
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Hassan A, Rijo P, Abuamara TMM, Ali Lashin LS, Kamar SA, Bangay G, Al-Sawahli MM, Fouad MK, Zoair MA, Abdalrhman TI, Elebeedy D, Ibrahim IA, Mohamed AF, Abd El Maksoud AI. Synergistic Differential DNA Demethylation Activity of Danshensu ( Salvia miltiorrhiza) Associated with Different Probiotics in Nonalcoholic Fatty Liver Disease. Biomedicines 2024; 12:279. [PMID: 38397881 PMCID: PMC10886676 DOI: 10.3390/biomedicines12020279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/25/2024] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a major hepatic disorder occurring in non-alcohol-drinking individuals. Salvianic acid A or Danshensu (DSS, 3-(3, 4-dihydroxyphenyl)-(2R)-lactic acid), derived from the root of Danshen (Salvia miltiorrhiza), has demonstrated heart and liver protective properties. In this work, we investigated the antioxidant activity and hepatoprotective activity of Danshensu alone and in combination with different agents, such as probiotic bacteria (Lactobacillus casei and Lactobacillus acidophilus), against several assays. The inhibition mechanism of the methylation gene biomarkers, such as DNMT-1, MS, STAT-3, and TET-1, against DSS was evaluated by molecular docking and RT-PCR techniques. The physicochemical and pharmacokinetic ADMET properties of DSS were determined by SwissADME and pkCSM. The results indicated that all lipid blood test profiles, including cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C), were reduced after the oral administration of Danshensu combined with probiotics (L. casei and L. acidophilus) that demonstrated good, efficient free radical scavenging activity, measured using anti-oxidant assays. ADMET and drug-likeness properties certify that the DSS could be utilized as a feasible drug since DSS showed satisfactory physicochemical and pharmacokinetic ADMET properties.
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Affiliation(s)
- Amr Hassan
- Department of Bioinformatics, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat 32897, Egypt
| | - Patrícia Rijo
- CBIOS—Lusófona University’s Research Center for Biosciences and Health Technologies, 1749-024 Lisbon, Portugal;
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Tamer M. M. Abuamara
- Department of Basic Medical Science, Faculty of Dentistry, Al-Ahliyya Amman University, Amman 19111, Jordan; (T.M.M.A.); (L.S.A.L.); (S.A.K.)
- Department of Histology, Faculty of Medicine, Al-Azhar University, Cairo 11884, Egypt
| | - Lashin Saad Ali Lashin
- Department of Basic Medical Science, Faculty of Dentistry, Al-Ahliyya Amman University, Amman 19111, Jordan; (T.M.M.A.); (L.S.A.L.); (S.A.K.)
- Department of Medical Physiology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Sherif A. Kamar
- Department of Basic Medical Science, Faculty of Dentistry, Al-Ahliyya Amman University, Amman 19111, Jordan; (T.M.M.A.); (L.S.A.L.); (S.A.K.)
- Department of Anatomy and Embryology, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt
| | - Gabrielle Bangay
- CBIOS—Lusófona University’s Research Center for Biosciences and Health Technologies, 1749-024 Lisbon, Portugal;
- Universidad de Alcalá de Henares. Facultad de Farmacia, Departamento de Ciencias Biomédicas (Área de Farmacología; Nuevos agentes antitumorales, Acción tóxica sobre células leucémicas), Ctra. Madrid-Barcelona km. 33,600, 28805 Alcalá de Henares, Madrid, España
| | - Majid Mohammed Al-Sawahli
- Department of Pharmaceutics, College of Pharmacy, The Islamic University, Najaf 54001, Iraq;
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Kafr Elsheikh University, Kafr Elsheikh 33516, Egypt
| | - Marina K. Fouad
- College of Biotechnology, Misr University of Science and Technology, Giza 12573, Egypt; (M.K.F.); (D.E.); (A.I.A.E.M.)
| | - Mohammad A. Zoair
- Department of Physiology, Faculty of Medicine, Al-Azhar University, Cairo 11884, Egypt;
| | - Tamer I. Abdalrhman
- Department of Histology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt;
| | - Dalia Elebeedy
- College of Biotechnology, Misr University of Science and Technology, Giza 12573, Egypt; (M.K.F.); (D.E.); (A.I.A.E.M.)
| | - Ibrahim A. Ibrahim
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat 32897, Egypt;
| | - Aly F. Mohamed
- Holding Company for Vaccine and Sera Production (VACSERA), Giza 22311, Egypt;
| | - Ahmed I. Abd El Maksoud
- College of Biotechnology, Misr University of Science and Technology, Giza 12573, Egypt; (M.K.F.); (D.E.); (A.I.A.E.M.)
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat 32897, Egypt
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3
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Sato H, Hara T, Meng S, Tsuji Y, Arao Y, Sasaki K, Miyoshi N, Kobayashi S, Doki Y, Eguchi H, Ishii H. Drug Discovery and Development of miRNA-Based Nucleotide Drugs for Gastrointestinal Cancer. Biomedicines 2023; 11:2235. [PMID: 37626731 PMCID: PMC10452413 DOI: 10.3390/biomedicines11082235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/29/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Short non-coding RNAs, miRNAs, play roles in the control of cell growth and differentiation in cancer. Reportedly, the introduction of miRNAs could reduce the biologically malignant behavior of cancer cells, suggesting a possible use as therapeutic reagents. Given that the forced expression of several miRNAs, including miR-302, results in the cellular reprograming of human and mouse cells, which is similar to the effects of the transcription factors Oct4, Sox2, Klf4, and c-Myc, this suggests that the selective introduction of several miRNAs will be able to achieve anti-cancer effects at the epigenetic and metabolic levels. In this review article, we bring together the recent advances made in studies of microRNA-based therapeutic approaches to therapy-resistant cancers, especially in gastrointestinal organs.
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Affiliation(s)
- Hiromichi Sato
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan; (H.S.)
- Department of Gastrointestinal Surgery, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan
| | - Tomoaki Hara
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan; (H.S.)
| | - Sikun Meng
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan; (H.S.)
| | - Yoshiko Tsuji
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan; (H.S.)
| | - Yasuko Arao
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan; (H.S.)
| | - Kazuki Sasaki
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan; (H.S.)
- Department of Gastrointestinal Surgery, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan
| | - Norikatsu Miyoshi
- Department of Gastrointestinal Surgery, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan
| | - Shogo Kobayashi
- Department of Gastrointestinal Surgery, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastrointestinal Surgery, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastrointestinal Surgery, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan
| | - Hideshi Ishii
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita 565-0871, Osaka, Japan; (H.S.)
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Garrido N, Boitrelle F, Saleh R, Durairajanayagam D, Colpi G, Agarwal A. Sperm epigenetics landscape: correlation with embryo quality, reproductive outcomes and offspring's health. Panminerva Med 2023; 65:166-178. [PMID: 37335245 DOI: 10.23736/s0031-0808.23.04871-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Epigenetics refers to how gene expression and function are modulated without modifying the DNA sequence but through subtle molecular changes or interactions with it. As spermatogenesis progresses, male germ cells suffer plenty of epigenetic modifications, resulting in the definitive epigenome of spermatozoa conditioning its functionality, and this process can be altered by several internal and external factors. The paternal epigenome is crucial for sperm function, fertilization, embryo development, and offspring's health, and altered epigenetic states are associated with male infertility with or without altered semen parameters, embryo quality impairment, and worse ART outcomes together with the future offspring's health risks mainly through intergenerational transmission of epigenetic marks. Identifying epigenetic biomarkers may improve male factor diagnosis and the development of targeted therapies, not only to improve fertility but also to allow an early detection of risk and disease prevention in the progeny. While still there is much research to be done, hopefully in the near future, improvements in high-throughput technologies applied to epigenomes will permit our understanding of the underlying epigenetic mechanisms and the development of diagnostics and therapies leading to improved reproductive outcomes. In this review, we discuss the mechanisms of epigenetics in sperm and how epigenetics behave during spermatogenesis. Additionally, we elaborate on the relationship of sperm epigenetics with sperm parameters and male infertility, and highlight the impact of sperm epigenetic alterations on sperm parameters, embryo quality, ART outcomes, miscarriage rates and offspring's health. Furthermore, we provide insights into the future research of epigenetic alterations in male infertility.
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Affiliation(s)
- Nicolás Garrido
- Global Andrology Forum, Moreland Hills, OH, USA
- IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Florence Boitrelle
- Global Andrology Forum, Moreland Hills, OH, USA
- Reproductive Biology, Fertility Preservation, Andrology, CECOS, Poissy Hospital, Poissy, France
- Paris Saclay University, UVSQ, INRAE, BREED, Jouy-en-Josas, France
| | - Ramadan Saleh
- Global Andrology Forum, Moreland Hills, OH, USA
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Damayanthi Durairajanayagam
- Global Andrology Forum, Moreland Hills, OH, USA
- Department of Physiology, Faculty of Medicine, Universiti Teknologi MARA, Selangor, Malaysia
| | - Giovanni Colpi
- Global Andrology Forum, Moreland Hills, OH, USA
- Next Fertility Procrea, Lugano, Switzerland
| | - Ashok Agarwal
- Global Andrology Forum, Moreland Hills, OH, USA -
- American Center for Reproductive Medicine, Cleveland, OH, USA
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5
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Hao J, Liu Y. Epigenetics of methylation modifications in diabetic cardiomyopathy. Front Endocrinol (Lausanne) 2023; 14:1119765. [PMID: 37008904 PMCID: PMC10050754 DOI: 10.3389/fendo.2023.1119765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/01/2023] [Indexed: 03/17/2023] Open
Abstract
Type 2 diabetes is one of the most common metabolic diseases with complications including diabetic cardiomyopathy and atherosclerotic cardiovascular disease. Recently, a growing body of research has revealed that the complex interplay between epigenetic changes and the environmental factors may significantly contribute to the pathogenesis of cardiovascular complications secondary to diabetes. Methylation modifications, including DNA methylation and histone methylation among others, are important in developing diabetic cardiomyopathy. Here we summarized the literatures of studies focusing on the role of DNA methylation, and histone modifications in microvascular complications of diabetes and discussed the mechanism underlying these disorders, to provide the guidance for future research toward an integrated pathophysiology and novel therapeutic strategies to treat or prevent this frequent pathological condition.
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Affiliation(s)
- Jing Hao
- Department of Emergency, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Liu
- Department of Pharmacy, Children’s Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Yao Liu,
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6
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Arcanjo RB, Vieira MC, Sivaguru M, Nowak RA. Impact of mono(2-ethylhexyl) phthalate (MEHP) on the development of mouse embryo in vitro. Reprod Toxicol 2023; 115:111-123. [PMID: 36535558 PMCID: PMC10195034 DOI: 10.1016/j.reprotox.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/19/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Mono(2-ethylhexyl) phthalate (MEHP) is the most studied metabolite of di(2-ethylhexyl) phthalate (DEHP), a phthalate found in cosmetics, flooring, paints, and plastics products, including toys and medical tubing. Humans are frequently exposed to this compound due to its ubiquitous presence in our environment. DEHP and MEHP are known to be endocrine-disrupting chemicals and exposure levels have been associated to decreased reproductive success. However, few studies have focused on the direct effects of MEHP on embryos. The present study investigated effects of MEHP (0.1, 1, 10, 100 and 1000 µM) on mice preimplantation embryonic development, evaluating percentage of blastocyst formation, hatching from zona pellucida, methylation-related genes, cell lineage commitment, micronucleation, and adherens junction marker at different stages of development during in vitro culture for 6 days. We show MEHP negatively impacts embryo competence by reducing blastocyst formation and hatching at 100 and 1000 µM. In addition, 100 µM MEHP increases the expression of Tet3 gene in blastocysts, which is related to a reduction of DNA methylation, an important mechanism regulating gene expression. Exposed embryos that completed the hatching process in groups 0.1, 1 and 10 µM MEHP had similar number of inner cell mass and trophectoderm cells compared to the control, while micronucleation occurrence and E-cadherin expression was not affected in exposed morulae by MEHP at 10 or 100 µM. Our results showed that high concentrations of MEHP can negatively impact embryo development. New studies unveiling the mechanism of toxicity involved and encompassing further developmental stages are warranted for further understanding.
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Affiliation(s)
- Rachel Braz Arcanjo
- Department of Animal Sciences, University of Illinois Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL 61801, United States.
| | - Marcos Costa Vieira
- Department of Ecology and Evolution, University of Chicago, 1107 East 57th street, Chicago, IL 60637, United States.
| | - Mayandi Sivaguru
- Cytometry and Microscopy to Omics Facility, 231 Edward R. Madigan Laboratory, Roy. J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, 1201 West Gregory Drive, Urbana, IL 61801, United States.
| | - Romana A Nowak
- Department of Animal Sciences, University of Illinois Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL 61801, United States.
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Vachher M, Bansal S, Kumar B, Yadav S, Burman A. Deciphering the role of aberrant DNA methylation in NAFLD and NASH. Heliyon 2022; 8:e11119. [PMID: 36299516 PMCID: PMC9589178 DOI: 10.1016/j.heliyon.2022.e11119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/30/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2022] Open
Abstract
The global incidence of nonalcoholic fatty liver disease (NAFLD) is mounting incessantly, and it is emerging as the most frequent cause of chronic and end stage liver disorders. It is the starting point for a range of conditions from simple steatosis to more progressive nonalcoholic steatohepatitis (NASH) and associated hepatocellular carcinoma (HCC). Dysregulation of insulin secretion and dyslipidemia due to obesity and other lifestyle variables are the primary contributors to establishment of NAFLD. Onset and progression of NAFLD is orchestrated by an interplay of metabolic environment with genetic and epigenetic factors. An incompletely understood mechanism of NAFLD progression has greatly hampered the progress in identification of novel prognostic and therapeutic strategies. Emerging evidence suggests altered DNA methylation pattern as a key determinant of NAFLD pathogenesis. Environmental and lifestyle factors can manipulate DNA methylation patterns in a reversible manner, which manifests as changes in gene expression. In this review we attempt to highlight the importance of DNA methylation in establishment and progression of NAFLD. Development of novel diagnostic, prognostic and therapeutic strategies centered around DNA methylation signatures and modifiers has also been explored.
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8
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Yu JJ, Non AL, Heinrich EC, Gu W, Alcock J, Moya EA, Lawrence ES, Tift MS, O'Brien KA, Storz JF, Signore AV, Khudyakov JI, Milsom WK, Wilson SM, Beall CM, Villafuerte FC, Stobdan T, Julian CG, Moore LG, Fuster MM, Stokes JA, Milner R, West JB, Zhang J, Shyy JY, Childebayeva A, Vázquez-Medina JP, Pham LV, Mesarwi OA, Hall JE, Cheviron ZA, Sieker J, Blood AB, Yuan JX, Scott GR, Rana BK, Ponganis PJ, Malhotra A, Powell FL, Simonson TS. Time Domains of Hypoxia Responses and -Omics Insights. Front Physiol 2022; 13:885295. [PMID: 36035495 PMCID: PMC9400701 DOI: 10.3389/fphys.2022.885295] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
The ability to respond rapidly to changes in oxygen tension is critical for many forms of life. Challenges to oxygen homeostasis, specifically in the contexts of evolutionary biology and biomedicine, provide important insights into mechanisms of hypoxia adaptation and tolerance. Here we synthesize findings across varying time domains of hypoxia in terms of oxygen delivery, ranging from early animal to modern human evolution and examine the potential impacts of environmental and clinical challenges through emerging multi-omics approaches. We discuss how diverse animal species have adapted to hypoxic environments, how humans vary in their responses to hypoxia (i.e., in the context of high-altitude exposure, cardiopulmonary disease, and sleep apnea), and how findings from each of these fields inform the other and lead to promising new directions in basic and clinical hypoxia research.
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Affiliation(s)
- James J. Yu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Amy L. Non
- Department of Anthropology, Division of Social Sciences, University of California, San Diego, La Jolla, CA, United States,*Correspondence: Amy L. Non, Tatum S. Simonson,
| | - Erica C. Heinrich
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, United States
| | - Wanjun Gu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Joe Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, MX, United States
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Elijah S. Lawrence
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Michael S. Tift
- Department of Biology and Marine Biology, College of Arts and Sciences, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Katie A. O'Brien
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,Department of Physiology, Development and Neuroscience, Faculty of Biology, School of Biological Sciences, University of Cambridge, Cambridge, ENG, United Kingdom
| | - Jay F. Storz
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Anthony V. Signore
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Jane I. Khudyakov
- Department of Biological Sciences, University of the Pacific, Stockton, CA, United States
| | | | - Sean M. Wilson
- Lawrence D. Longo, MD Center for Perinatal Biology, Loma Linda, CA, United States
| | | | | | | | - Colleen G. Julian
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lorna G. Moore
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Aurora, CO, United States
| | - Mark M. Fuster
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jennifer A. Stokes
- Department of Kinesiology, Southwestern University, Georgetown, TX, United States
| | - Richard Milner
- San Diego Biomedical Research Institute, San Diego, CA, United States
| | - John B. West
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jiao Zhang
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - John Y. Shyy
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - José Pablo Vázquez-Medina
- Department of Integrative Biology, College of Letters and Science, University of California, Berkeley, Berkeley, CA, United States
| | - Luu V. Pham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine, Johns Hopkins Medicine, Baltimore, MD, United States
| | - Omar A. Mesarwi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - James E. Hall
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Zachary A. Cheviron
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT, United States
| | - Jeremy Sieker
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Arlin B. Blood
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Jason X. Yuan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Graham R. Scott
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Brinda K. Rana
- Moores Cancer Center, UC San Diego, La Jolla, CA, United States,Department of Psychiatry, UC San Diego, La Jolla, CA, United States
| | - Paul J. Ponganis
- Center for Marine Biotechnology and Biomedicine, La Jolla, CA, United States
| | - Atul Malhotra
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Frank L. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,*Correspondence: Amy L. Non, Tatum S. Simonson,
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9
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New advances of DNA/RNA methylation modification in liver fibrosis. Cell Signal 2021; 92:110224. [PMID: 34954394 DOI: 10.1016/j.cellsig.2021.110224] [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: 11/29/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 11/23/2022]
Abstract
Liver fibrosis is a complex pathological process caused by multiple pathogenic factors,such as ethanol, viruses, toxins, drugs or cholestasis, and it can eventually develop into liver cirrhosis without effective treatment. Activation of hepatic stellate cells (HSCs) is a pivotal cellular event in the pathogenesis of liver fibrosis. However, the pathogenesis of liver fibrosis has not been fully elucidated. DNA/RNA methylation can regulate gene expression without alteration in its sequence, and numerous studies have shown the involvement of DNA methylation in the activation of HSCs and then promote the progression of liver fibrosis. In addition, RNA methylation has recently been reported to play a regulatory role in this process. In this review, we focus on the aberrant DNA/RNA methylation of selected genes and explore their functional mechanism in regulating HSCs activation and liver fibrogenesis. All of these findings will enhance our understanding of DNA/RNA methylation and their roles in liver fibrosis and provide the basis to identify effective therapeutic targets.
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10
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Embryo culture media differentially alter DNA methylating enzymes and global DNA methylation in embryos and oocytes. J Mol Histol 2021; 53:63-74. [PMID: 34741214 PMCID: PMC8570397 DOI: 10.1007/s10735-021-10038-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/28/2021] [Indexed: 11/06/2022]
Abstract
The effects of culture media on DNA methylation process, which is one of the epigenetic mechanisms, have not been clearly elucidated although it is known that in vitro culture conditions alter epigenetic mechanisms. This study was designed to address the question: does embryo culture media approach, sequential or single step, differentially affect DNA methylating enzymes and global DNA methylation. Mouse zygotes were cultured either in single step or sequential culture media until the blastocyst stage and in vivo developed blastocyst were utilized as control. Similarly, GV stage oocytes were in vitro matured either in single step or first step of sequential culture media. In vivo matured MII oocytes were used as control. The expression levels and cellular localization of Dnmt1 and 3a enzymes were analyzed by immunofluorescence and western blot analysis while global DNA methylation was evaluated by immunofluorescence. We found that signal intensities of Dnmt1 and Dnmt3a enzymes were significantly low in embryos or oocytes cultured in sequential media compared to single step media and control, which were comparable amongst themself. Similarly, global DNA methylation level in single step media and control groups was comparable but both was higher than the sequential media. This study demonstrated that composition of culture media may differentially affect DNA methylation levels in mouse embryos and oocytes. Since abnormal DNA methylation may cause aberrant oocyte or embryo development, we think that further studies are needed to test human embryos and oocyte, and to explain molecular mechanisms.
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11
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Hallamaa M, Seikkula J, Willman S, Ollila H, Jokimaa V. Pregnancy potential and perinatal outcomes of embryos cryopreserved twice: a case-control study. Reprod Biomed Online 2021; 43:607-613. [PMID: 34412972 DOI: 10.1016/j.rbmo.2021.06.028] [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: 03/24/2021] [Revised: 05/27/2021] [Accepted: 06/29/2021] [Indexed: 10/20/2022]
Abstract
RESEARCH QUESTION What are the pregnancy and perinatal outcomes of twice-cryopreserved embryos compared with embryos cryopreserved once? DESIGN Retrospective register-based case-control study. The case group consisted of transfers of twice-cryopreserved embryos (n = 89), and the control group of transfers of embryos cryopreserved once (n = 304). Matching criteria were embryonic age at transfer and female age category of less than 35 years or 35 and greater. RESULTS The survival rate of twice-cryopreserved embryos was 92.2%, and 93.7% of the planned frozen embryo transfers (FET) could be completed. FET was performed with cleavage-stage embryos in 17 cases and 68 controls and with blastocysts in 72 cases and 238 controls. The rates of live birth (27.0% versus 31.9%, adjusted odds ratio [OR] 0.70, 95% CI 0.40-1.22, P = 0.21), clinical pregnancy (31.5% versus 36.8%, adjusted OR 0.71, 95% CI 0.42-1.21, P = 0.21) and miscarriage (4.5% versus 3.9%, adjusted OR 1.10, 95% CI 0.33-3.60, P = 0.88) in the case and the control groups were comparable. No difference was seen in the preterm delivery rate (cases 4.2% versus controls 10.3%, P = 0.69). Twenty-five children were born in the case group and 100 in the control group. No difference in birthweight was detected between the groups and there were no large for gestational age fetuses or congenital malformations in the case group. CONCLUSIONS Uncompromised live birth rates and neonatal outcomes may be expected after the transfer of twice-cryopreserved embryos. To avoid embryo wastage and transfer of multiple embryos, good quality surplus embryos from FET cycles may be cryopreserved again by vitrification.
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Affiliation(s)
- Marianne Hallamaa
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku 20520, Finland.
| | - Jaana Seikkula
- Department of Obstetrics and Gynecology, Central Hospital of Central Finland, Jyväskylä 40620, Finland
| | - Sami Willman
- Ovumia Fertinova Jyväskylä, Jyväskylä 40100, Finland
| | - Helena Ollila
- Turku Clinical Research Centre, Turku University Hospital, Turku 20521, Finland
| | - Varpu Jokimaa
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku 20520, Finland
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12
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Campbell CR, Tiley GP, Poelstra JW, Hunnicutt KE, Larsen PA, Lee HJ, Thorne JL, Dos Reis M, Yoder AD. Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur. Heredity (Edinb) 2021; 127:233-244. [PMID: 34272504 PMCID: PMC8322134 DOI: 10.1038/s41437-021-00446-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation-rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprises nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (Microcebus murinus), we estimated the mutation rate to be among the highest calculated for a mammal at 1.52 × 10-8 (95% credible interval: 1.28 × 10-8-1.78 × 10-8) mutations/site/generation. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG sites. Despite the surprising nature of these results, we found both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria. We also sequenced a technical replicate to estimate a false-negative and false-positive rate for our data and show that any point estimate of a de novo mutation rate should be considered with a large degree of uncertainty. For validation, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species for which de novo mutation rates have also been estimated. These comparisons revealed general consistency of the mutation spectrum between the pedigree-based and the substitution-rate analyses for all species compared.
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Affiliation(s)
- C Ryan Campbell
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | | | - Kelsie E Hunnicutt
- Department of Biology, Duke University, Durham, NC, USA
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Peter A Larsen
- Department of Biology, Duke University, Durham, NC, USA
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA
| | - Hui-Jie Lee
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA.
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13
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Yadav P, Bandyopadhayaya S, Ford BM, Mandal C. Interplay between DNA Methyltransferase 1 and microRNAs During Tumorigenesis. Curr Drug Targets 2021; 22:1129-1148. [PMID: 33494674 DOI: 10.2174/1389450122666210120141546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/16/2020] [Accepted: 10/18/2020] [Indexed: 01/18/2023]
Abstract
Cancer is a genetic disease resulting from genomic changes; however, epigenetic alterations act synergistically with these changes during tumorigenesis and cancer progression. Epigenetic variations are gaining more attention as an important regulator in tumor progression, metastasis and therapy resistance. Aberrant DNA methylation at CpG islands is a central event in epigeneticmediated gene silencing of various tumor suppressor genes. DNA methyltransferase 1 (DNMT1) predominately methylates at CpG islands on hemimethylated DNA substrates in proliferation of cells. DNMT1 has been shown to be overexpressed in various cancer types and exhibits tumor-promoting potential. The major drawbacks to DNMT1-targeted cancer therapy are the adverse effects arising from nucleoside and non-nucleoside based DNMT1 inhibitors. This paper focuses on the regulation of DNMT1 by various microRNAs (miRNAs), which may be assigned as future DNMT1 modulators, and highlights how DNMT1 regulates various miRNAs involved in tumor suppression. Importantly, the role of reciprocal inhibition between DNMT1 and certain miRNAs in tumorigenic potential is approached in this review. Hence, this review seeks to project an efficient and strategic approach using certain miRNAs in conjunction with conventional DNMT1 inhibitors as a novel cancer therapy. It has also been pinpointed to select miRNA candidates associated with DNMT1 regulation that may not only serve as potential biomarkers for cancer diagnosis and prognosis, but may also predict the existence of aberrant methylation activity in cancer cells.
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Affiliation(s)
- Pooja Yadav
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh- 305817, Ajmer, Rajasthan, India
| | - Shreetama Bandyopadhayaya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh- 305817, Ajmer, Rajasthan, India
| | - Bridget M Ford
- Department of Biology, University of the Incarnate Word, San Antonio, TX 78209, United States
| | - Chandi Mandal
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh- 305817, Ajmer, Rajasthan, India
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14
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Thorsen M, Bilenberg N, Thorsen L, Michel TM. Oxidative Stress in Adults with Autism Spectrum Disorder: A Case Control Study. J Autism Dev Disord 2021; 52:275-282. [PMID: 33677727 DOI: 10.1007/s10803-021-04897-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 12/27/2022]
Abstract
Oxidative stress has been proposed as being important in the pathophysiology of autism spectrum disorders (ASD), and heightened levels of oxidative stress has found in children with ASD. Our aim was to investigate, whether this change is temporary or persist into adulthood. We included 89 adult patients with ASD and sex and age matched controls. Plasma levels of antioxidants superoxide dismutase 1 (SOD1) and superoxide dismutase 2 (SOD2) and pro-oxidant xanthine oxidase (XO) were measured. Individuals with ASD had higher levels of SOD1, which furthermore correlated with autism severity as measured by autism quotient-score. We found no difference regarding SOD2 and XO between ASD group and controls. However, SOD1 and SOD2 were elevated in males compared to females.
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Affiliation(s)
- Morten Thorsen
- Research Unit of the Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark. .,Department of Psychiatry, Psychiatry in the Region of Southern Denmark, Odense, Denmark. .,Center for applied Neuroscience Odense, BRIDGE, Odense, Denmark. .,Department of Child and Adolescent Psychiatry, Aalborg University Hospital, Aalborg, Denmark.
| | - Niels Bilenberg
- Research Unit of Child- and Adolescent Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Center for applied Neuroscience Odense, BRIDGE, Odense, Denmark
| | - Lena Thorsen
- Research Unit of the Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Psychiatry, Aalborg University Hospital, Aalborg, Denmark
| | - Tanja Maria Michel
- Research Unit of the Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Psychiatry, Psychiatry in the Region of Southern Denmark, Odense, Denmark.,Center for applied Neuroscience Odense, BRIDGE, Odense, Denmark
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15
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Arumugam T, Ghazi T, Chuturgoon AA. Molecular and epigenetic modes of Fumonisin B 1 mediated toxicity and carcinogenesis and detoxification strategies. Crit Rev Toxicol 2021; 51:76-94. [PMID: 33605189 DOI: 10.1080/10408444.2021.1881040] [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] [Indexed: 02/06/2023]
Abstract
Fumonisin B1 (FB1) is a natural contaminant of agricultural commodities that has displayed a myriad of toxicities in animals. Moreover, it is known to be a hepatorenal carcinogen in rodents and may be associated with oesophageal and hepatocellular carcinomas in humans. The most well elucidated mode of FB1-mediated toxicity is its disruption of sphingolipid metabolism; however, enhanced oxidative stress, endoplasmic reticulum stress, autophagy, and alterations in immune response may also play a role in its toxicity and carcinogenicity. Alterations to the host epigenome may impact on the toxic and carcinogenic response to FB1. Seeing that the contamination of FB1 in food poses a considerable risk to human and animal health, a great deal of research has focused on new methods to prevent and attenuate FB1-induced toxic consequences. The focus of the present review is on the molecular and epigenetic interactions of FB1 as well as recent research involving FB1 detoxification.
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Affiliation(s)
- Thilona Arumugam
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Terisha Ghazi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anil A Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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16
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Gross N, Taylor T, Crenshaw T, Khatib H. The Intergenerational Impacts of Paternal Diet on DNA Methylation and Offspring Phenotypes in Sheep. Front Genet 2020; 11:597943. [PMID: 33250925 PMCID: PMC7674940 DOI: 10.3389/fgene.2020.597943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/14/2020] [Indexed: 11/13/2022] Open
Abstract
Knowledge of non-genomic inheritance of traits is currently limited. Although it is well established that maternal diet influences offspring inheritance of traits through DNA methylation, studies on the impact of prepubertal paternal diet on DNA methylation are rare. This study aimed to evaluate the impact of prepubertal diet in Polypay rams on complex traits, DNA methylation, and transmission of traits to offspring. A total of 10 littermate pairs of F0 rams were divided so that one ram was fed a control diet, and the other was fed the control diet with supplemental methionine. Diet was associated with earlier age at puberty in treatment vs. control F0 rams. F0 treatment rams tended to show decreased pubertal weight compared to control rams; however, no differences were detected in overall growth. A total of ten F0 rams were bred, and the entire F1 generation was fed a control diet. Diet of F0 rams had a significant association with scrotal circumference (SC) and weight at puberty of F1 offspring. The paternal diet was not significantly associated with F1 ram growth or age at puberty. The DNA methylation of F0 ram sperm was assessed, and genes related to both sexual development (e.g., DAZAP1, CHD7, TAB1, MTMR2, CELSR1, MGAT1) and body weight (e.g., DUOX2, DUOXA2) were prevalent in the data. These results provide novel information about the mechanisms through which the prepubertal paternal diet may alter body weight at puberty and sexual development.
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Affiliation(s)
- Nicole Gross
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Todd Taylor
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas Crenshaw
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
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17
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Hyun J, Jung Y. DNA Methylation in Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2020; 21:ijms21218138. [PMID: 33143364 PMCID: PMC7662478 DOI: 10.3390/ijms21218138] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a widespread hepatic disorder in the United States and other Westernized countries. Nonalcoholic steatohepatitis (NASH), an advanced stage of NAFLD, can progress to end-stage liver disease, including cirrhosis and liver cancer. Poor understanding of mechanisms underlying NAFLD progression from simple steatosis to NASH has limited the development of effective therapies and biomarkers. An accumulating body of studies has suggested the importance of DNA methylation, which plays pivotal roles in NAFLD pathogenesis. DNA methylation signatures that can affect gene expression are influenced by environmental and lifestyle experiences such as diet, obesity, and physical activity and are reversible. Hence, DNA methylation signatures and modifiers in NAFLD may provide the basis for developing biomarkers indicating the onset and progression of NAFLD and therapeutics for NAFLD. Herein, we review an update on the recent findings in DNA methylation signatures and their roles in the pathogenesis of NAFLD and broaden people’s perspectives on potential DNA methylation-related treatments and biomarkers for NAFLD.
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Affiliation(s)
- Jeongeun Hyun
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea;
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
- Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Korea
- Cell and Matter Institute, Dankook University, Cheonan 31116, Korea
| | - Youngmi Jung
- Department of Integrated Biological Science, Pusan National University, Pusan 46241, Korea
- Department of Biological Sciences, Pusan National University, Pusan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2262
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18
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Zhou X, Yan B, Xu X, Yu XL, Fu XF, Cai YF, Xu YY, Tang YG, Zhang XZ, Wang HY. Risk and mechanism of glucose metabolism disorder in the offspring conceived by female fertility maintenance technology. Cryobiology 2020; 96:68-75. [PMID: 32771331 DOI: 10.1016/j.cryobiol.2020.08.001] [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: 03/03/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 10/23/2022]
Abstract
Although female fertility maintenance technology (FFMT) provides an effective option for preserving fertility in patients with cancer suffering from fertility loss due to cancer treatment, previous studies have shown that the technique has certain potential risks and requires an assessment of the health status of the offspring since FFMT may lead to glucose metabolism disorder in offspring mice. The present animal study examined the glucose metabolism of adult mice offspring born from ovarian tissue cryopreservation and orthotopic allotransplantation. The mice were divided into three groups: normal, fresh ovary transplantation, and cryopreserved ovary transplantation. We recorded fasting blood glucose, glucose tolerance, and fasting serum insulin level for six months. Liver DNA, RNA, and proteins were extracted to detect the interaction between DNA methylation and Grb10 expression and insulin signaling pathway factors such as P-IGF1R, P-IRS2, P-AKT, and Grb10. Female recipient mice that received FFMT could successfully give birth after mating. The average litter size and total litter size of the cryopreserved and fresh groups showed marked differences compared with the normal group. Compared with the normal group, the fasting blood glucose and fasting serum insulin levels were higher in the cryopreserved and fresh groups. The mRNA and protein expressions of Grb10 were higher in the fresh and cryopreserved groups. Compared with the normal group, the DNA methylation status of four of the 11 sites of the Grb10 promoter was lower in the cryopreserved group. Grb10 overexpression inhibited the downstream phosphorylation protein factor expression (p-IGF-1R, p-IRS2, and p-Akt) of the IGF-1R signaling pathway. Female fertility maintenance technology (FFMT), including ovarian tissue cryopreservation (OTC), and orthotopic allotransplantation techniques might lead to glucose metabolism disorders in offspring mice.
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Affiliation(s)
- Xue Zhou
- Ningxia Human Sperm Bank, General Hospital of Ningxia Medical University, Yinchuan, 750001, China; Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, PR China
| | - Bei Yan
- Ningxia Human Sperm Bank, General Hospital of Ningxia Medical University, Yinchuan, 750001, China; Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China
| | - Xian Xu
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China
| | - Xiao-Li Yu
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China
| | - Xu-Feng Fu
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China
| | - Yu-Fang Cai
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China
| | - Yan-Yan Xu
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China
| | - Yun-Ge Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, 510600, China
| | - Xin-Zong Zhang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, 510600, China.
| | - Hong-Yan Wang
- Ningxia Human Sperm Bank, General Hospital of Ningxia Medical University, Yinchuan, 750001, China; Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China.
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19
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Rygiel CA, Dolinoy DC, Perng W, Jones TR, Solano M, Hu H, Téllez-Rojo MM, Peterson KE, Goodrich JM. Trimester-Specific Associations of Prenatal Lead Exposure With Infant Cord Blood DNA Methylation at Birth. Epigenet Insights 2020; 13:2516865720938669. [PMID: 32734142 PMCID: PMC7372614 DOI: 10.1177/2516865720938669] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/03/2020] [Indexed: 12/23/2022] Open
Abstract
Gestational exposure to lead (Pb) adversely impacts offspring health through
multiple mechanisms, one of which is the alteration of the epigenome including
DNA methylation. This study aims to identify differentially methylated CpG sites
associated with trimester-specific maternal Pb exposure in umbilical cord blood
(UCB) leukocytes. Eighty-nine mother-child dyads from the Early Life Exposure in
Mexico to Environmental Toxicants (ELEMENT) longitudinal birth cohorts with
available UCB samples were selected for DNA methylation analysis via the
Infinium Methylation EPIC BeadChip, which quantifies methylation at >850 000
CpG sites. Maternal blood lead levels (BLLs) during each trimester (T1:
6.56 ± 5.35 µg/dL; T2: 5.93 ± 5.00 µg/dL; T3: 6.09 ± 4.51 µg/dL), bone Pb
(patella: 11.8 ± 9.25 µg/g; tibia: 11.8 ± 6.73 µg/g), a measure of cumulative Pb
exposure, and UCB Pb (4.86 ± 3.74 µg/dL) were measured. After quality control
screening, data from 786 024 CpG sites were used to identify differentially
methylated positions (DMPs) and differentially methylated regions (DMRs) by Pb
biomarkers using separate linear regression models, controlling for sex and
estimated UCB cell-type proportions. We identified 3 DMPs associated with
maternal T1 BLL, 2 with T3 BLL, and 2 with tibia bone Pb. We identified one DMR
within PDGFRL associated with T1 BLL, one located at
chr6:30095136-30095295 with T3 BLL, and one within TRHR with
tibia bone Pb (adjusted P-value < .05). Pathway analysis
identified 15 overrepresented gene pathways for differential methylation that
overlapped among all 3 trimesters with the largest overlap between T1 and T2
(adjusted P-value < .05). Pathways of interest include nodal
signaling pathway and neurological system processes. These data provide evidence
for differential methylation by prenatal Pb exposure that may be
trimester-specific.
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Affiliation(s)
- Christine A Rygiel
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Wei Perng
- Department of Epidemiology, University of Colorado School of Public Health, Denver, CO, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | - Howard Hu
- Department of Environmental and Occupational Health Sciences, University of Washington School of Public Health, Seattle, WA, USA
| | | | - Karen E Peterson
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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20
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Thorsen M. Oxidative stress, metabolic and mitochondrial abnormalities associated with autism spectrum disorder. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 173:331-354. [PMID: 32711815 DOI: 10.1016/bs.pmbts.2020.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Autism spectrum disorder is a neurodevelopmental disorder characterized by impaired development and by abnormal function in regards to social interaction, communication and restricted, repetitive behavior. It affects approximately 1% of the worldwide population. Like other psychiatric disorders the diagnosis is based on observation of, and interview with the patient and next of kin, and diagnostic tests. Many genes have been associated with autism, but only few highly penetrant. Some researchers have instead focused on oxidative stress, metabolic abnormalities and mitochondrial dysfunction as an explanation of the disorder. Currently no cure exists for the disorder, making these abnormalities interesting as they are possibly correctable with supplements or treatment. These various processes cannot be seen independently as they are influencing and interacting with each other. Furthermore many of the metabolic changes seen in autism have also been shown in other psychiatric disorders such as attention deficit hyperactivity disorder, schizophrenia and bipolar disorder along with often comorbid disorders like epilepsy and intellectual disability. As such some of these abnormalities are not specific, however, could indicate a similar mechanism for the development of these disorders, with symptomatology and severity varying according to the location and the amount of damage done to proteins, cells and DNA. Clinical studies trying to treat these abnormalities, have widely been successful in correcting the metabolic abnormalities seen, but only some studies have also shown bettering of autistic symptoms. Hopefully with increased knowledge of the pathophysiology of the disorder, future preventive measures or treatment can be developed.
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Affiliation(s)
- Morten Thorsen
- Department of Child and Adolescent Psychiatry, Aalborg, Denmark.
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21
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Wang Y, Liu Q, Kang J, Zhang Y, Quan F. Overexpression of PGC7 in donor cells maintains the DNA methylation status of imprinted genes in goat embryos derived from somatic cell nuclear transfer technology. Theriogenology 2020; 151:86-94. [PMID: 32344274 DOI: 10.1016/j.theriogenology.2020.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/26/2020] [Accepted: 04/11/2020] [Indexed: 11/27/2022]
Abstract
Abnormal methylation of imprinted genes is commonly observed in the embryos cloned by somatic cell nuclear transfer (SCNT) procedure and is one of the primary reasons for their abnormal development and high mortality. Primordial germ cell 7 (PGC7), a developmentally regulated gene highly expressed in primordial germ cells, maintains the methylation level of imprinted genes by reducing the levels of 5-hydroxy-methylcytosine(5hmC) and increasing the levels of 5-methylcytosine(5 mC) during embryonic development. In this study, we explored the methylation status of H19 differentially methylated regions (DMRs) in the organs of SCNT-cloned goat fetuses. Our results showed abnormal methylation patterns of the imprinted genes in the lungs and placenta of dead cloned goat fetuses than those in normal goat fetuses. The Igf2r DMRs were hypomethylated in the heart, liver, spleen, lungs, kidneys, and placenta of dead cloned goat fetuses compared with normal goat fetuses (P < 0.05). In addition, imprinted gene Igf2r DMRs were hypomethylated in the early-stage SCNT embryos than the IVF embryos. In contrast, imprinted gene Xist DMRs were hypermethylated in SCNT embryos than the IVF embryos. Significantly, the use of PGC7 overexpressing donor cells corrected the abnormal methylation of imprinted genes Igf2r and Xist in SCNT embryos (P < 0.05). Our results suggested that PGC7 plays a vital role in maintaining the methylation of imprinted genes during goat early embryonic development. Moreover, PGC7 overexpression in donor cells may reduce the developmental abnormalities associated with the SCNT embryos, while significantly enhancing both the pregnancy and kids born rates (P < 0.05) thereby increasing SCNT efficiency in livestock.
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Affiliation(s)
- Yufei Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qingqing Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jian Kang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Fusheng Quan
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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22
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Integrative Analysis of Methylome and Transcriptome Reveals the Regulatory Mechanisms of Hair Follicle Morphogenesis in Cashmere Goat. Cells 2020; 9:cells9040969. [PMID: 32295263 PMCID: PMC7226977 DOI: 10.3390/cells9040969] [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: 02/10/2020] [Revised: 03/22/2020] [Accepted: 04/05/2020] [Indexed: 12/31/2022] Open
Abstract
Studies in humans and mice have revealed that hair follicle morphogenesis relies on tightly coordinated ectodermal–mesodermal interactions, involving multiple signals and regulatory factors. DNA methylation and long non-coding RNA (lncRNA) play a critical role in early embryonic skin development by controlling gene expression. Acting as an indirect regulator, lncRNA could recruit DNA methyltransferases to specific genomic sites to methylate DNA. However, the molecular regulation mechanisms underlying hair follicle morphogenesis is unclear in cashmere goat. In this study, RNA-seq and whole-genome bisulfite sequencing (WGBS) in embryonic day 65 (E 65) and E 120 skin tissues of cashmere goat were used to reveal this complex regulatory process. The RNA-seq, qRT-PCR, and immunohistochemistry results showed that Wnt signaling played an important role in both hair follicle induction and differentiation stage; transcriptional factors (TFs), including HOXC13, SOX9, SOX21, JUNB, LHX2, VDR, and GATA3, participated in hair follicle differentiation via specific expression at E 120. Subsequently, the combination of WGBS and RNA-seq analysis showed that the expression of some hair follicle differentiation genes and TF genes were negatively correlated with the DNA methylation level generally. A portion of hair follicle differentiation genes were methylated and repressed in the hair follicle induction stage but were subsequently demethylated and expressed during the hair follicle differentiation stage, suggesting that DNA methylation plays an important role in hair morphogenesis by regulating associated gene expression. Furthermore, 45 upregulated and 147 downregulated lncRNAs in E 120 compared with E 65 were identified by lncRNA mapping, and then the potential differentially expressed lncRNAs associated with DNA methylation on the target gene were revealed. In conclusion, critical signals and genes were revealed during hair follicle morphogenesis in the cashmere goat. In this process, DNA methylation was lower in the hair follicle differentiation compared with the hair follicle induction stage and may play an important role in hair morphogenesis by regulating associated gene expression. Furthermore, potential lncRNAs associated with DNA methylation on target genes were delineated. This study enriches the regulatory network and molecular mechanisms on hair morphogenesis.
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23
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Mohana Devi S, Mahalaxmi I, Kaavya J, Chinnkulandhai V, Balachandar V. Does epigenetics have a role in age related macular degeneration and diabetic retinopathy? Genes Dis 2020; 8:279-286. [PMID: 33997175 PMCID: PMC8093576 DOI: 10.1016/j.gendis.2020.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/06/2020] [Indexed: 02/08/2023] Open
Abstract
Epigenetic mechanisms play an important part in the regulation of gene expression and these alterations may induce long-term changes in gene function and metabolism. They have received extensive attention in bridging the gap between environmental exposures and disease development via their influence on gene expression. DNA methylation is the earliest discovered epigenetic alteration. In this review, we try to examine the role of DNA methylation and histone modification in Age related macular degeneration (AMD) and Diabetic Retinopathy (DR), its vascular complications and recent progress. Given the complex nature of AMD and DR, it is crucial to improve therapeutics which will greatly enhance the quality of life and reduce the burden for millions of patients living with these potentially blinding conditions.
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Affiliation(s)
- S Mohana Devi
- SN ONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, 41/18, College Road, Chennai, 600006, India
| | - I Mahalaxmi
- Department of Zoology, Avinashilingam Institute for Home Science and Higher Education for Women, Avinashilingam University for Women, Coimbatore, Tamil Nadu, 641046, India
| | - J Kaavya
- Department of Zoology, Avinashilingam Institute for Home Science and Higher Education for Women, Avinashilingam University for Women, Coimbatore, Tamil Nadu, 641046, India
| | - V Chinnkulandhai
- Department of Biochemistry, Dr.N.G.P Arts and Science College, Coimbatore, Tamil Nadu, 641046, India
| | - V Balachandar
- Human Molecular Genetics and Stem Cells Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, Tamil Nadu, 641046, India
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24
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Schumann NAB, Mendonça AS, Silveira MM, Vargas LN, Leme LO, de Sousa RV, Franco MM. Procaine and S-Adenosyl-l-Homocysteine Affect the Expression of Genes Related to the Epigenetic Machinery and Change the DNA Methylation Status of In Vitro Cultured Bovine Skin Fibroblasts. DNA Cell Biol 2019; 39:37-49. [PMID: 31750745 DOI: 10.1089/dna.2019.4934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cloning using somatic cell nuclear transfer (SCNT) has many potential applications such as in transgenic and genomic-edited animal production. Abnormal epigenetic reprogramming of somatic cell nuclei is probably the major cause of the low efficiency associated with SCNT. Strategies to alter DNA reprogramming in donor cell nuclei may help improve the cloning efficiency. In the present study, we aimed to characterize the effects of procaine and S-adenosyl-l-homocysteine (SAH) as demethylating agents during the cell culture of bovine skin fibroblasts. We characterized the effects of procaine and SAH on the expression of genes related to the epigenetic machinery, including the DNA methyltransferase 1 (DNMT1), DNA methyltransferase 3 alpha (DNMT3A), DNA methyltransferase 3 beta (DNMT3B), TET1, TET2, TET3, and OCT4 genes, and on DNA methylation levels of bovine skin fibroblasts. We found that DNA methylation levels of satellite I were reduced by SAH (p = 0.0495) and by the combination of SAH and procaine (p = 0.0479) compared with that in the control group. Global DNA methylation levels were lower in cells that were cultivated with both compounds than in control cells (procaine [p = 0.0116], SAH [p = 0.0408], and both [p = 0.0163]). Regarding gene expression, there was a decrease in the DNMT1 transcript levels in cells cultivated with SAH (p = 0.0151) and SAH/procaine (0.0001); a decrease in the DNMT3A transcript levels in cells cultivated with SAH/procaine (p = 0.016); and finally, a decrease in the DNMT3B transcript levels in cells cultivated with procaine (p = 0.0007), SAH (p = 0.0060), and SAH/procaine (p = 0.0021) was found. Higher levels of TET3 transcripts in cells cultivated with procaine (p = 0.0291), SAH (p = 0.0373), and procaine/SAH (p = 0.0013) compared with the control were also found. Regarding the OCT4 gene, no differences were found. Our results showed that the use of procaine and SAH during bovine cell culture was able to alter the epigenetic profile of the cells. This approach may be a useful alternative strategy to improve the efficiency of reprogramming the somatic nuclei after fusion, which in turn will improve the SCNT efficiency.
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Affiliation(s)
- Naiara A B Schumann
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Brazil
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Anelise S Mendonça
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Brazil
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Márcia M Silveira
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Brazil
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Luna N Vargas
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Brazil
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Ligiane O Leme
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Regivaldo V de Sousa
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Maurício M Franco
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Brazil
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- School of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
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25
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Zhang Q, Zheng S, Wang S, Jiang Z, Xu S. The Effects of Low Selenium on DNA Methylation in the Tissues of Chickens. Biol Trace Elem Res 2019; 191:474-484. [PMID: 30737629 DOI: 10.1007/s12011-019-1630-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/01/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation is involved in epigenetic mechanisms associated with gene suppression, and its abnormalities lead to gene instability and disease development. As an essential trace element in humans and animals, selenium (Se) is also associated with abnormal changes in DNA methylation. However, the effect of low Se on DNA methylation in avian tissues has not been reported. In the current study, chickens were fed a low-Se diet (0.033 mg Se/kg) or supplemented with 0.15 mg Se/kg as selenite for up to 55 days. DNA methylation levels were examined by high-performance liquid chromatography (HPLC). DNA methyltransferases (DNMTs) and methyl-DpG-binding domain protein 2 (MBD2) mRNA levels were examined through the applications of RT-PCR. The experiment aims to explore the relationship between low Se and DNA methylation. The results showed that total DNA methylation levels in the muscle tissues, brain, immune tissues, and liver of the low-selenium diet group were decreased compared with the control group. The degree of DNA methylation reduction in different tissues from largest to smallest was liver > cerebellum > thymus > brain > spleen ≥ leg muscles > pectoral muscles > bursa of Fabricius > thalamus > wing muscles. DNMT1, DNMT3A, and DNMT3B mRNA expression levels of the low-selenium diet group were decreased compared with those in the control group. The mRNA expression of the MBD2 gene was increased. The results indicate that low Se can reduce the DNA methylation levels of tissues, especially within the liver. These conclusions provide a basis for exploring the pathogenesis of selenium deficiency from the perspective of DNA methylation and create a new basis for comparative medicine.
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Affiliation(s)
- Qiaojian Zhang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Shufang Zheng
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Shengchen Wang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Zhihui Jiang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China.
| | - Shiwen Xu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China.
- Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
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26
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Yuan T, Zhao W, Niu Y, Fu Y, Lu L, Niu D. Exploration of the temporal-spatial expression pattern and DNA methylation-related regulation of the duck telomerase reverse transcriptase gene. Poult Sci 2019; 98:3257-3267. [PMID: 31064004 DOI: 10.3382/ps/pez240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 04/09/2019] [Indexed: 12/14/2022] Open
Abstract
Telomerase reverse transcriptase (TERT) is a catalytic subunit of telomerase that adds TTAGGG repeats to the 3'-overhang of telomeres. In the present study, we detected that the duck TERT (dTERT) gene was highly expressed in small intestine and kidney, followed by heart, leg muscle, spleen, pancreas, gonad, and liver at neonatal stage. From embryonic to neonatal stage, the highest dTERT mRNA in liver appeared at stage E19 (19 days at embryonic stage), while for the leg muscle the maximum expression occurred at E26. We also measured the relative telomerase activity (RTA) and relative telomere length (RTL) in the examined tissues and found that the changed tendency of RTA and RTL was not very consistent with that of TERT. In silico analysis revealed that there were three CpG islands (S1, S2, and S3) within the 5' regulatory region of the dTERT gene. Bisulfite sequencing PCR (BSP) assay showed that liver (D7, 7 days after birth) which expressed significantly lower dTERT mRNA had an obviously higher methylation level of S1 compared with small intestine (D7) or liver (E19). Quantitative real-time PCR analysis revealed that the expression of DNA methyltransferase DNMT1 in liver (D7) was significantly higher than that in small intestine (D7) or in liver (E19). In vitro, dTERT expression was upregulated and the methylation status of S1 decreased in both duck embryonic fibroblasts and small intestinal epithelial cells following treatment with the demethylation reagent, 5-aza-2'-deoxycytidine (5-aza-dC), further suggesting that dTERT is epigenetically regulated by DNA methylation. This work lays a solid foundation for further study of TERT function and regulation in avian species.
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Affiliation(s)
- Taoyan Yuan
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.,Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, 145 Shiqiao Road, Hangzhou 310021, China
| | - Wanqiu Zhao
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.,Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, 145 Shiqiao Road, Hangzhou 310021, China
| | - Yifan Niu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China
| | - Yan Fu
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, 145 Shiqiao Road, Hangzhou 310021, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou 310021, Zhejiang, China
| | - Dong Niu
- College of Animal Science and Technology, Zhejiang A&F University
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27
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Zheng J, Xu H, Cao H. A Long Polymorphic GT Microsatellite within a Gene Promoter Mediates Non-Imprinted Allele-Specific DNA Methylation of a CpG Island in a Goldfish Inter-Strain Hybrid. Int J Mol Sci 2019; 20:ijms20163923. [PMID: 31409051 PMCID: PMC6721770 DOI: 10.3390/ijms20163923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 11/26/2022] Open
Abstract
It is now widely accepted that allele-specific DNA methylation (ASM) commonly occurs at non-imprinted loci. Most of the non-imprinted ASM regions observed both within and outside of the CpG island show a strong correlation with DNA polymorphisms. However, what polymorphic cis-acting elements mediate non-imprinted ASM of the CpG island remains unclear. In this study, we investigated the impact of polymorphic GT microsatellites within the gene promoter on non-imprinted ASM of the local CpG island in goldfish. We generated various goldfish heterozygotes, in which the length of GT microsatellites or some non-repetitive sequences in the promoter of no tail alleles was different. By examining the methylation status of the downstream CpG island in these heterozygotes, we found that polymorphisms of a long GT microsatellite can lead to the ASM of the downstream CpG island during oogenesis and embryogenesis, polymorphisms of short GT microsatellites and non-repetitive sequences in the promoter exhibited no significant effect on the methylation of the CpG island. We also observed that the ASM of the CpG island was associated with allele-specific expression in heterozygous embryos. These results suggest that a long polymorphic GT microsatellite within a gene promoter mediates non-imprinted ASM of the local CpG island in a goldfish inter-strain hybrid.
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Affiliation(s)
- Jianbo Zheng
- Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China.
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Haomang Xu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huiwen Cao
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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28
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Braga TF, Silva TCF, Marques MG, de Souza AP, Albring D, Silva LP, Caetano AR, Dode MAN, Franco MM. The dynamics of gene expression, lipid composition and DNA methylation reprogramming are different during in vitro maturation of pig oocytes obtained from prepubertal gilts and cycling sows. Reprod Domest Anim 2019; 54:1217-1229. [PMID: 31269288 DOI: 10.1111/rda.13501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/20/2019] [Indexed: 01/21/2023]
Abstract
This study aimed to characterize the gene expression, lipid composition and DNA methylation reprogramming during in vitro maturation (IVM) of pig oocytes with different developmental competencies. We used prepubertal gilts and cycling sows as a model to obtain oocytes with different levels of competency. We found that genes involved in lipid metabolism, SLC27A4, CPT2 and PLIN2, and DNA methylation, DNMT3A, TET1 and TET3, possessed altered transcript expression levels during IVM. Specifically, SLC27A4 mRNA (p = 0.05) increased in oocytes from cycling females, whereas CPT2 (p = 0.05), PLIN2 (p = 0.02) and DNMT3A (p = 0.02) increased in oocytes from prepubertal females during IVM. Additionally, TET3 mRNA increased during IVM in oocytes from prepubertal (p = 0.0005) and cycling females (p = 0.02). The TET1 transcript decreased (p = 0.05) during IVM in oocytes from cycling sows. Regarding lipid composition, mass spectrometry revealed a cluster of ions, with molecular masses higher than m/z 700, which comprises a group of complex phospholipids, was identified in all groups of oocytes, except in those from prepubertal gilts. With respect to DNA methylation reprogramming, it was noted that the less competent oocytes were not able to reprogramme the XIST gene during IVM. We conclude that the maternal mRNA store, lipid composition and epigenetic reprogramming are still being established during maturation and are related to oocyte competence. In addition, we propose that the methylation pattern of the XIST may be used as molecular marker for oocyte competence in pigs.
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Affiliation(s)
- Thiago Felipe Braga
- Universidade de Brasília - UnB, Brasília, Brazil.,Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Thainara Christie Ferreira Silva
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil.,Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | | | | | | | | | | | | | - Maurício Machaim Franco
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil.,Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, Brazil.,Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Uberlândia, Brazil
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29
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Chamani IJ, Keefe DL. Epigenetics and Female Reproductive Aging. Front Endocrinol (Lausanne) 2019; 10:473. [PMID: 31551923 PMCID: PMC6736555 DOI: 10.3389/fendo.2019.00473] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 06/28/2019] [Indexed: 12/12/2022] Open
Abstract
With more women than ever waiting until a more advanced age to have children, there exists a newfound urgency to identify the various implications aging has on human reproduction, and understand the disrupted biological processes that result in these changes. In this review, we focus on one recent area of study: the age related epigenetic changes that have been found in female reproductive organs, and the effect these changes may contribute to reproductive outcomes.
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Affiliation(s)
| | - David L. Keefe
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY, United States
- *Correspondence: David L. Keefe
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30
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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: 22] [Impact Index Per Article: 3.7] [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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Khatib H, Gross N. Symposium review: Embryo survival-A genomic perspective of the other side of fertility. J Dairy Sci 2018; 102:3744-3753. [PMID: 30293848 DOI: 10.3168/jds.2018-15252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/31/2018] [Indexed: 01/13/2023]
Abstract
The majority of embryonic loss in cattle occurs within the first 3 to 4 wk of pregnancy, and there are currently no accurate predictors of pregnancy outcome. Existing embryo quality assessment methods include morphological evaluation and embryo biopsy. These methods are not accurate and carry some health risks to the developing embryo, respectively. Therefore, there is need to identify noninvasive biomarkers such as microRNA that can predict embryo quality and pregnancy outcome. Furthermore, researchers need a better understanding of the dynamic interaction between the mother and the embryo. The transcriptome of the uterus shows plasticity that depends on the embryo type so that the expression level of some genes for in vivo embryos would be different from that of in vitro-produced embryos. Similarly, the embryonic transcriptome and epigenome change in response to different environmental factors such as stress, diet, disease, and physiological status of the mother. This embryo-mother crosstalk could be better understood by investigating the molecular signaling that occurs at different stages of embryonic development. Although transcriptomics is a useful tool to assess the roles of genes and pathways in embryo quality and maternal receptivity, it does not provide the exact functions of these genes, and it shows correlation rather than causality. Therefore, an in-depth functional genomic analysis is needed for better understanding of the molecular mechanisms controlling embryo development. In this review, we discuss recent genomic technologies such as RNA interference, gapmer technology, and genome editing techniques used in humans and livestock to elucidate the molecular mechanisms of genes affecting embryo development.
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Affiliation(s)
- H Khatib
- Department of Animal Sciences, University of Wisconsin, Madison 53706.
| | - N Gross
- Department of Animal Sciences, University of Wisconsin, Madison 53706
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Li F, Xue Z, Yuan Y, Huang S, Fan Y, Zhu X, Wei L. Upregulation of CXCR4 through promoter demethylation contributes to inflammatory hyperalgesia in rats. CNS Neurosci Ther 2018; 24:947-956. [PMID: 29577638 PMCID: PMC6489799 DOI: 10.1111/cns.12845] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 02/13/2018] [Accepted: 02/20/2018] [Indexed: 01/27/2023] Open
Abstract
AIM AND METHODS Chronic pain associated with inflammation is a common clinical problem, and the underlying mechanisms yet are incompletely defined. DNA methylation has been implicated in the pathogenesis of chronic pain. However, the specific genes regulated by DNA methylation under inflammatory pain condition remain largely unknown. Here, we investigated how chemokine receptor CXCR4 expression is regulated by DNA methylation and how it contributes to inflammatory pain induced by complete Freund's adjuvant (CFA) in rats. RESULTS Intraplantar injection of CFA could not only induce significant hyperalgesia in rats, but also significantly increase the expression of CXCR4 mRNA and protein in the dorsal root ganglion (DRG). Intrathecal injection of CXCR4 antagonist AMD3100 significantly relieved hyperalgesia in inflammatory rats in a time- and dose-dependent manner. Bisulfite sequencing and methylation-specific PCR demonstrate that CFA injection led to a significant demethylation of CpG island at CXCR4 gene promoter. Consistently, the expression of DNMT3b was significantly downregulated after CFA injection. Online software prediction reveals three binding sites of p65 in the CpG island of CXCR4 gene promoter, which has confirmed by the chromatin immunoprecipitation assay, CFA treatment significantly increases the recruitment of p65 to CXCR4 gene promoter. Inhibition of NF-kB signaling using p65 inhibitor pyrrolidine dithiocarbamate significantly prevented the increases of the CXCR4 expression. CONCLUSION Upregulation of CXCR4 expression due to promoter demethylation followed by increased recruitment of p65 to promoter of CXCR4 gene contributes to inflammatory hyperalgesia. These findings provide a theoretical basis for the treatment of chronic pain from an epigenetic perspective.
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Affiliation(s)
- Feng Li
- Department of AnesthesiologyThe First People's Hospital of YanchengYanchengJiangsuChina
| | - Zhou‐Ya Xue
- Department of AnesthesiologyThe First People's Hospital of YanchengYanchengJiangsuChina
| | - Yuan Yuan
- Department of OtolaryngologyThe First People's Hospital of YanchengYanchengJiangsuChina
| | - Sai‐Sai Huang
- Department of AnesthesiologyAffiliated Hospital of Nantong UniversityNantonChina
| | - Yi‐Hui Fan
- Department of ImmunologySchool of MedicineNantong UniversityNantongChina
| | - Xiang Zhu
- Department of AnesthesiologyAffiliated Hospital of Nantong UniversityNantonChina
| | - Lei Wei
- Department of AnesthesiologySuzhou Municipal Hospital Affiliated to Nanjing Medical UniversitySuzhouJiangsuChina
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Wang FL, Yan LX, Shi HJ, Liu XY, Zheng QY, Sun LN, Wang DS. Genome-wide identification, evolution of DNA methyltransferases and their expression during gonadal development in Nile tilapia. Comp Biochem Physiol B Biochem Mol Biol 2018; 226:73-84. [PMID: 30170023 DOI: 10.1016/j.cbpb.2018.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022]
Abstract
DNA methyltransferases (dnmts) are responsible for DNA methylation and play important roles in organism development. In this study, seven dnmts genes (dnmt1, dnmt2, dnmt3aa, dnmt3ab, dnmt3ba, dnmt3bb.1, dnmt3bb.2) were identified in Nile tilapia. Comprehensive analyses of dnmts were performed using available genome databases from representative animal species. Phylogenetic analysis revealed that the dnmts family were highly conserved in teleosts. Based on transcriptome data from eight adult tilapia tissues, the dnmts were found to be dominantly expressed in the head kidney, testis and ovary. Analyses of the gonadal transcriptome data in different developmental stages revealed that all dnmts were expressed in both ovary and testis, and four de novo dnmts (dnmt3aa, dnmt3ab, dnmt3bb.1, dnmt3bb.2) showed higher expression in the testis than in the ovary. Furthermore, during sex reversal induced by Fadrozole, the expression of these four de novo dnmts increased significantly in treated group compared to female control group. By in situ hybridization, the seven dnmts were found to be expressed mainly in phase I and II oocytes of the ovary and spermatocytes of the testis. When gonads were incubated with a methyltransferase inhibitor (5-AzaCdR) in vitro, the expression of dnmts genes were down-regulated significantly, while the expression of cyp19a1a (a key gene in female pathway) and dmrt1 (a key gene in male pathway) increased significantly. Our results revealed the conservation of dnmts during evolution and indicated a potential role of dnmts in epigenetic regulation of gonadal development.
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Affiliation(s)
- Fei-Long Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Long-Xia Yan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Hong-Juan Shi
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Xing-Yong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Qiao-Yuan Zheng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Li-Na Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China.
| | - De-Shou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China.
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Han C, Deng R, Mao T, Luo Y, Wei B, Meng P, Zhao L, Zhang Q, Quan F, Liu J, Zhang Y. Overexpression of Tet3 in donor cells enhances goat somatic cell nuclear transfer efficiency. FEBS J 2018; 285:2708-2723. [PMID: 29791079 DOI: 10.1111/febs.14515] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 12/14/2022]
Abstract
Ten-eleven translocation 3 (TET3) mediates active DNA demethylation of paternal genomes during mouse embryonic development. However, the mechanism of DNA demethylation in goat embryos remains unknown. In addition, aberrant DNA methylation reprogramming prevalently occurs in embryos cloned by somatic cell nuclear transfer (SCNT). In this study, we reported that TET3 is a key factor in DNA demethylation in goat pre-implantation embryos. Knockdown of Tet3 hindered DNA demethylation at the two- to four-cell stage in goat embryos and decreased Nanog expression in blastocysts. Overexpression of Tet3 in somatic cells can initiate DNA demethylation, reduce 5-methylcytosine level, increase 5-hydroxymethylcytosine level and promote the expression of key pluripotency genes. After SCNT, overexpression of Tet3 in donor cells corrected abnormal DNA hypermethylation of cloned embryos and significantly enhanced in vitro and in vivo developmental rate (P < 0.05). We conclude that overexpression of Tet3 in donor cells significantly improves goat SCNT efficiency.
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Affiliation(s)
- Chengquan Han
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Ruizhi Deng
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Tingchao Mao
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Yan Luo
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Biao Wei
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Peng Meng
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Lu Zhao
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Qing Zhang
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Fusheng Quan
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology, College of Veterinary Medicine, Ministry of Agriculture, Northwest A&F University, Yangling, China
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Wasson JA, Birol O, Katz DJ. A Resource for the Allele-Specific Analysis of DNA Methylation at Multiple Genomically Imprinted Loci in Mice. G3 (BETHESDA, MD.) 2018; 8:91-103. [PMID: 29138238 PMCID: PMC5765370 DOI: 10.1534/g3.117.300417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/30/2017] [Indexed: 01/15/2023]
Abstract
Genomically imprinted loci are expressed mono-allelically, dependent upon the parent of origin. Their regulation not only illuminates how chromatin regulates gene expression but also how chromatin can be reprogrammed every generation. Because of their distinct parent-of-origin regulation, analysis of imprinted loci can be difficult. Single nucleotide polymorphisms (SNPs) are required to accurately assess these elements allele specifically. However, publicly available SNP databases lack robust verification, making analysis of imprinting difficult. In addition, the allele-specific imprinting assays that have been developed employ different mouse strains, making it difficult to systemically analyze these loci. Here, we have generated a resource that will allow the allele-specific analysis of many significant imprinted loci in a single hybrid strain of Mus musculus This resource includes verification of SNPs present within 10 of the most widely used imprinting control regions and allele-specific DNA methylation assays for each gene in a C57BL/6J and CAST/EiJ hybrid strain background.
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Affiliation(s)
- Jadiel A Wasson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Onur Birol
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - David J Katz
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322
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Thomson JP, Ottaviano R, Buesen R, Moggs JG, Schwarz M, Meehan RR. Defining baseline epigenetic landscapes in the rat liver. Epigenomics 2017; 9:1503-1527. [PMID: 29130343 PMCID: PMC5957268 DOI: 10.2217/epi-2017-0029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Aim Characterization of the hepatic epigenome following exposure to chemicals and therapeutic drugs provides novel insights into toxicological and pharmacological mechanisms, however appreciation of genome-wide inter- and intra-strain baseline epigenetic variation, particularly in under-characterized species such as the rat is limited. Material & methods To enhance the utility of epigenomic endpoints safety assessment, we map both DNA modifications (5-methyl-cytosine and 5-hydroxymethyl-cytosine) and enhancer related chromatin marks (H3K4me1 and H3K27ac) across multiple male and female rat livers for two important outbred laboratory rat strains (Sprague–Dawley and Wistar). Results & conclusion Integration of DNA modification, enhancer chromatin marks and gene expression profiles reveals clear gender-specific chromatin states at genes which exhibit gender-specific transcription. Taken together this work provides a valuable baseline liver epigenome resource for rat strains that are commonly used in chemical and pharmaceutical safety assessment.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit, Genome Regulation, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Raffaele Ottaviano
- MRC Human Genetics Unit, Genome Regulation, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Roland Buesen
- BASF SE, Experimental Toxicology & Ecology, 67056 Ludwigshafen, Germany
| | - Jonathan G Moggs
- Preclinical Safety, Translational Medicine, Novartis Institutes for BioMedical Research, CH-4057 Basel, Switzerland
| | - Michael Schwarz
- Department of Toxicology, Institute of Experimental & Clinical Pharmacology & Toxicology, University of Tübingen, 72074 Tübingen, Germany
| | - Richard R Meehan
- MRC Human Genetics Unit, Genome Regulation, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
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Burlina S, Dalfrà MG, Lapolla A. Short- and long-term consequences for offspring exposed to maternal diabetes: a review. J Matern Fetal Neonatal Med 2017; 32:687-694. [PMID: 28969466 DOI: 10.1080/14767058.2017.1387893] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The prevalence of gestational diabetes mellitus is increasing, as is the worldwide prevalence of type 2 diabetes and obesity, even in children and adolescents. Exposure in utero to maternal diabetes carries several short-term consequences due mainly to maternal hyperglycemia, and consequent fetal hyperinsulinemia. Current evidence also supports the hypothesis that adult health and disease have developmental origins, and that disorders in early-life environments prompt metabolic imprinting that results in a greater risk of negative metabolic outcomes later in life. In particular, exposure in utero to maternal diabetes seems to influence long-term metabolic outcomes, carrying a higher risk of obesity and type 2 diabetes, and thus creating a vicious cycle for future generations. In this paper, the short- and long-term consequences of exposure in utero to hyperglycemia are reviewed, focusing particularly on the long-term metabolic consequences, and investigating the possible pathogenic mechanisms involved.
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Affiliation(s)
- S Burlina
- a Department of Medicine , University of Padua , Padua , Italy
| | - M G Dalfrà
- a Department of Medicine , University of Padua , Padua , Italy
| | - A Lapolla
- a Department of Medicine , University of Padua , Padua , Italy
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Zubidat AE, Haim A. Artificial light-at-night - a novel lifestyle risk factor for metabolic disorder and cancer morbidity. J Basic Clin Physiol Pharmacol 2017; 28:295-313. [PMID: 28682785 DOI: 10.1515/jbcpp-2016-0116] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 03/02/2017] [Indexed: 06/07/2023]
Abstract
Both obesity and breast cancer are already recognized worldwide as the most common syndromes in our modern society. Currently, there is accumulating evidence from epidemiological and experimental studies suggesting that these syndromes are closely associated with circadian disruption. It has been suggested that melatonin (MLT) and the circadian clock genes both play an important role in the development of these syndromes. However, we still poorly understand the molecular mechanism underlying the association between circadian disruption and the modern health syndromes. One promising candidate is epigenetic modifications of various genes, including clock genes, circadian-related genes, oncogenes, and metabolic genes. DNA methylation is the most prominent epigenetic signaling tool for gene expression regulation induced by environmental exposures, such as artificial light-at-night (ALAN). In this review, we first provide an overview on the molecular feedback loops that generate the circadian regulation and how circadian disruption by ALAN can impose adverse impacts on public health, particularly metabolic disorders and breast cancer development. We then focus on the relation between ALAN-induced circadian disruption and both global DNA methylation and specific loci methylation in relation to obesity and breast cancer morbidities. DNA hypo-methylation and DNA hyper-methylation, are suggested as the most studied epigenetic tools for the activation and silencing of genes that regulate metabolic and monostatic responses. Finally, we discuss the potential clinical and therapeutic roles of MLT suppression and DNA methylation patterns as novel biomarkers for the early detection of metabolic disorders and breast cancer development.
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Tenayuca J, Cousins K, Yang S, Zhang L. Computational Modeling Approach in Probing the Effects of Cytosine Methylation on the Transcription Factor Binding to DNA. Curr Top Med Chem 2017; 17:1778-1787. [PMID: 27848899 DOI: 10.2174/1568026617666161116142031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/28/2016] [Accepted: 09/21/2016] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Cytosine methylation at CpG dinucleotides is a chief mechanism in epigenetic modification of gene expression patterns. Previous studies demonstrated that increased CpG methylation of Sp1 sites at -268 and -346 of protein kinase C ε promoter repressed the gene expression. MATERIALS & METHODS The present study investigated the impact of CpG methylation on the Sp1 binding via molecular modeling and electrophoretic mobility shift assay. Each of the Sp1 sites contain two CpGs. Methylation of either CpG lowered the binding affinity of Sp1, whereas methylation of both CpGs produced a greater decrease in the binding affinity. Computation of van der Waals (VDW) energy of Sp1 in complex with the Sp1 sites demonstrated increased VDW values from one to two sites of CpG methylation. Molecular modeling indicated that single CpG methylation caused underwinding of the DNA fragment, with the phosphate groups at C1, C4 and C5 reoriented from their original positions. Methylation of both CpGs pinched the minor groove and increased the helical twist concomitant with a shallow, hydrophobic major groove. Additionally, double methylation eliminated hydrogen bonds on recognition helix residues located at positions -1 and 1, which were essential for interaction with O6/N7 of G-bases. Bonding from linker residues Arg565, Lys595 and Lys596 were also reduced. Methylation of single or both CpGs significantly affected hydrogen bonding from all three Sp1 DNA binding domains, demonstrating that the consequences of cytosine modification extend beyond the neighboring nucleotides. RESULTS The results indicate that cytosine methylation causes subtle structural alterations in Sp1 binding sites consequently resulting in inhibition of side chain interactions critical for specific base recognition and reduction of the binding affinity of Sp1.
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Affiliation(s)
- John Tenayuca
- Department of Chemistry and Biochemistry, California State University, San Bernardino, California 92407, United States
| | - Kimberley Cousins
- Department of Chemistry and Biochemistry, California State University, San Bernardino, California 92407, United States
| | - Shumei Yang
- Department of Chemistry & Biochemistry, California State University, San Bernardino, CA 92407, China
| | - Lubo Zhang
- Center for Perinatal Biology, Loma Linda University School of Medicine, Loma Linda, California 92350, United States
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Optical biosensing strategies for DNA methylation analysis. Biosens Bioelectron 2017; 92:668-678. [DOI: 10.1016/j.bios.2016.10.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/05/2016] [Accepted: 10/18/2016] [Indexed: 11/23/2022]
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Abstract
Liver fibrosis arises because prolonged injury combined with excessive scar deposition within hepatic parenchyma arising from overactive wound healing response mediated by activated myofibroblasts. Fibrosis is the common end point for any type of chronic liver injury including alcoholic liver disease, nonalcoholic fatty liver disease, viral hepatitis, and cholestatic liver diseases. Although genetic influences are important, it is epigenetic mechanisms that have been shown to orchestrate many aspects of fibrogenesis in the liver. New discoveries in the field are leading toward the development of epigenetic biomarkers and targeted therapies. This review considers epigenetic mechanisms as well as recent advances in epigenetic programming in the context of hepatic fibrosis.
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Key Words
- CLD, chronic liver disease
- Chronic Liver Disease
- CpG, cytosine-phospho-guanine
- DNA Methylation
- DNMT, DNA methyltransferase
- Epigenetics
- HDAC, histone deacetylase
- HSC, hepatic stellate cell
- Histone Modifications
- Liver Fibrosis
- NAFLD, nonalcoholic fatty liver disease
- PPAR, peroxisome proliferator activated receptor
- TET, Ten Eleven Translocation
- miRNA, microRNA
- ncRNA, non-coding RNA
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Affiliation(s)
| | - Jelena Mann
- Correspondence Address correspondence to: Jelena Mann, PhD, Institute of Cellular Medicine, Faculty of Medical Sciences, 4th Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH United Kingdom. fax: +44-191-208-0723.Institute of Cellular MedicineFaculty of Medical Sciences4th FloorWilliam Leech BuildingNewcastle UniversityFramlington PlaceNewcastle upon TyneNE2 4HH United Kingdom
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Perera E, Yúfera M. Effects of soybean meal on digestive enzymes activity, expression of inflammation-related genes, and chromatin modifications in marine fish (Sparus aurata L.) larvae. FISH PHYSIOLOGY AND BIOCHEMISTRY 2017; 43:563-578. [PMID: 27807713 DOI: 10.1007/s10695-016-0310-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
The effects of soybean meal (SBM) in early diet of Sparus aurata larvae at two developmental windows were assessed. Prolonged (beyond 14 days post-hatch, dph) feeding with SBM decreased the activity of pancreatic enzymes of larvae. In the absence of SBM these larvae later resumed enzyme activities, but exhibited a significant delay in development. Larvae response to SBM involved up-regulation of extracellular matrix remodeling enzymes and pro-inflammatory cytokines, coupled with a drop in putative intestinal enzymes. Larvae receiving SBM at first feeding appear later to have lower expression of inflammation-related genes, especially those fed SBM until 14 dph. Multivariate analysis confirmed that the duration of the SBM early feeding period drives the physiology of larvae in different directions. Feeding larvae with SBM increased global histone H3 acetylation, whereas upon removal of SBM the process was reverted. A more in deep analysis revealed a dynamic interplay among several reversible histone modifications such as H3K14ac and H3K27m3. Finally, we showed that SBM feeding of larvae results in global hypomethylation that persist after SBM removal. This study is the first demonstrating an effect of diet on marine fish epigenetics. It is concluded that there are limitations for extending SBM feeding of S. aurata larvae beyond 14 dph even under co-feeding with live feed, affecting key physiological processes and normal growth. However, up to 14 dph, SBM does not affect normal development, and produces apparently lasting effects on some key enzymes, genes, and chromatin modifications.
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Affiliation(s)
- Erick Perera
- Departamento de Biología Marina y Acuicultura, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Puerto Real, 11510, Cádiz, Spain.
- Control of Food Intake Group, Department of Fish Physiology and Biotechnology, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain.
| | - Manuel Yúfera
- Departamento de Biología Marina y Acuicultura, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Puerto Real, 11510, Cádiz, Spain
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Novel insights into DNA methylation and its critical implications in diabetic vascular complications. Biosci Rep 2017; 37:BSR20160611. [PMID: 28183874 PMCID: PMC5350598 DOI: 10.1042/bsr20160611] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 12/23/2022] Open
Abstract
Recent epidemiological and clinical studies have shown that type 2 diabetic patients can develop diabetic vascular complications even after intensive glycaemic control. It has been suggested that this phenomenon could be explained by the hypothesis of 'metabolic memory'. The underlying mechanisms between these enduring effects and the prior hyperglycaemic state are still not well understood. Preliminary studies demonstrate that hyperglycaemia can regulate gene expression by epigenetic modifications, such as DNA methylation, which can persistently exist even after glucose normalization. Increasing evidence shows that epigenetic mechanisms may play a substantial role in the pathophysiology of diabetes and its associated vascular complications, including atherosclerosis, diabetic cardiomyopathy (DCM), nephropathy and retinopathy. In this review, we will examine the growing role of DNA methylation in diabetes and its vascular complications, thus it can provide critical implications for the early prevention of diabetes and its vascular complications.
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Ambrosi C, Manzo M, Baubec T. Dynamics and Context-Dependent Roles of DNA Methylation. J Mol Biol 2017; 429:1459-1475. [PMID: 28214512 DOI: 10.1016/j.jmb.2017.02.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/26/2017] [Accepted: 02/09/2017] [Indexed: 12/22/2022]
Abstract
DNA methylation is one of the most extensively studied epigenetic marks. It is involved in transcriptional gene silencing and plays important roles during mammalian development. Its perturbation is often associated with human diseases. In mammalian genomes, DNA methylation is a prevalent modification that decorates the majority of cytosines. It is found at the promoters and enhancers of inactive genes, at repetitive elements, and within transcribed gene bodies. Its presence at promoters is dynamically linked to gene activity, suggesting that it could directly influence gene expression patterns and cellular identity. The genome-wide distribution and dynamic behaviour of this mark have been studied in great detail in a variety of tissues and cell lines, including early embryonic development and in embryonic stem cells. In combination with functional studies, these genome-wide maps of DNA methylation revealed interesting features of this mark and provided important insights into its dynamic nature and potential functional role in genome regulation. In this review, we discuss how these recent observations, in combination with insights obtained from biochemical and functional genetics studies, have expanded our current knowledge about the regulation and context-dependent roles of DNA methylation in mammalian genomes.
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Affiliation(s)
- Christina Ambrosi
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program of the Life Sciences Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Massimiliano Manzo
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program of the Life Sciences Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Abstract
Epigenetic mechanisms play important roles in properly occurring mammalian oogenesis. One of these mechanisms is DNA methylation adding a methyl group to the fifth carbon atom of the cytosine residues using S-adenosyl-L-methionine as a methyl donor. DNA methylation generally takes place at cytosine-phosphate-guanine (CpG) dinucleotide sites and rarely occurs at cytosine-phosphate-thymine (CpT), cytosine-phosphate-adenine (CpA), or cytosine-phosphate-cytosine sites, known as non-CpG sites. Basically, two different DNA methylation processes are identified: de novo methylation and maintenance methylation. While the de novo methylation functions in methylation of unmethylated DNA strands, maintenance methylation is capable of methylating hemi-methylated DNA strands following DNA replication. Both DNA methylation processes are catalyzed by special DNA methyltransferase (DNMT) enzymes. To date, five different DNMTs have been identified: DNMT1, DNMT3A, DNMT3B, DNMT3L, and DNMT2. In this chapter, we focus particularly on temporal and spatial expression of DNMTs in mammalian oocytes and granulosa cells.
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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.
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Choi B, Han TS, Min J, Hur K, Lee SM, Lee HJ, Kim YJ, Yang HK. MAL and TMEM220 are novel DNA methylation markers in human gastric cancer. Biomarkers 2016; 22:35-44. [DOI: 10.1080/1354750x.2016.1201542] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Uysal F, Akkoyunlu G, Ozturk S. DNA methyltransferases exhibit dynamic expression during spermatogenesis. Reprod Biomed Online 2016; 33:690-702. [PMID: 27687053 DOI: 10.1016/j.rbmo.2016.08.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/12/2023]
Abstract
DNA methylation is one of the epigenetic marks and plays critically important functions during spermatogenesis in mammals. DNA methylation is catalysed by DNA methyltransferase (DNMT) enzymes, which are responsible for the addition of a methyl group to the fifth carbon atom of the cytosine residues within cytosine-phosphate-guanine (CpG) and non-CpG dinucleotide sites. Structurally and functionally five different DNMT enzymes have been identified in mammals, including DNMT1, DNMT2, DNMT3A, DNMT3B and DNMT3L. These enzymes mainly play roles in two DNA methylation processes: maintenance and de novo. While DNMT1 is primarily responsible for maintenance methylation via transferring methyl groups to the hemi-methylated DNA strands following DNA replication, both DNMT3A and DNMT3B are capable of methylating unmodified cytosine residues, known as de novo methylation. However, DNMT3L indirectly participates in de novo methylation, and DNMT2 carries out methylation of the cytosine 38 in the anticodon loop of aspartic acid transfer RNA. To date, many studies have been performed to determine spatial and temporal expression levels and functional features of the DNMT in the male germ cells. This review article comprehensively discusses dynamic expression of the DNMT during spermatogenesis and their relationship with male infertility development in the light of existing investigations.
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Affiliation(s)
- Fatma Uysal
- 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
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Campus 07070, Antalya, Turkey.
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Aggarwal R, Jha M, Shrivastava A, Jha AK. Natural Compounds: Role in Reversal of Epigenetic Changes. BIOCHEMISTRY (MOSCOW) 2016; 80:972-89. [PMID: 26547065 DOI: 10.1134/s0006297915080027] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The hallmarks of carcinogenesis are characterized by alterations in the expression of multiple genes that occur via genetic and epigenetic alterations, leading to genome rearrangements and instability. The reversible process of epigenetic regulation, which includes changes in DNA methylation, histone modifications, and alteration in microRNA (miRNA) expression that alter phenotype without any change in the DNA sequence, is recognized as a key mechanism in cancer cell metabolism. Recent advancements in the rapidly evolving field of cancer epigenetics have shown the anticarcinogenic potential of natural compounds targeting epigenetic mechanism as a common molecular approach for cancer treatment. This review summarizes the potential of natural chemopreventive agents to reverse cancer-related epigenetic aberrations by regulating the activity of histone deacetylases, histone acetyltransferases, DNA methyltransferase I, and miRNAs. Furthermore, there is impetus for determining novel and effective chemopreventive strategies, either alone or in combination with other anticancer agents that exhibit similar properties, for improving the therapeutic aspects of cancer.
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Affiliation(s)
- Ruchi Aggarwal
- Department of Biotechnology, IMS Engineering College, U. P. 201009, India.
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Morita S, Noguchi H, Horii T, Nakabayashi K, Kimura M, Okamura K, Sakai A, Nakashima H, Hata K, Nakashima K, Hatada I. Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions. Nat Biotechnol 2016; 34:1060-1065. [PMID: 27571369 DOI: 10.1038/nbt.3658] [Citation(s) in RCA: 317] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 07/28/2016] [Indexed: 12/19/2022]
Abstract
Despite the importance of DNA methylation in health and disease, technologies to readily manipulate methylation of specific sequences for functional analysis and therapeutic purposes are lacking. Here we adapt the previously described dCas9-SunTag for efficient, targeted demethylation of specific DNA loci. The original SunTag consists of ten copies of the GCN4 peptide separated by 5-amino-acid linkers. To achieve efficient recruitment of an anti-GCN4 scFv fused to the ten-eleven (TET) 1 hydroxylase, which induces demethylation, we changed the linker length to 22 amino acids. The system attains demethylation efficiencies >50% in seven out of nine loci tested. Four of these seven loci showed demethylation of >90%. We demonstrate targeted demethylation of CpGs in regulatory regions and demethylation-dependent 1.7- to 50-fold upregulation of associated genes both in cell culture (embryonic stem cells, cancer cell lines, primary neural precursor cells) and in vivo in mouse fetuses.
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Affiliation(s)
- Sumiyo Morita
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Hirofumi Noguchi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takuro Horii
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Mika Kimura
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Atsuhiko Sakai
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideyuki Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Izuho Hatada
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
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Gore AV, Athans B, Iben JR, Johnson K, Russanova V, Castranova D, Pham VN, Butler MG, Williams-Simons L, Nichols JT, Bresciani E, Feldman B, Kimmel CB, Liu PP, Weinstein BM. Epigenetic regulation of hematopoiesis by DNA methylation. eLife 2016; 5:e11813. [PMID: 26814702 PMCID: PMC4744183 DOI: 10.7554/elife.11813] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/06/2015] [Indexed: 11/13/2022] Open
Abstract
During embryonic development, cell type-specific transcription factors promote cell identities, while epigenetic modifications are thought to contribute to maintain these cell fates. Our understanding of how genetic and epigenetic modes of regulation work together to establish and maintain cellular identity is still limited, however. Here, we show that DNA methyltransferase 3bb.1 (dnmt3bb.1) is essential for maintenance of hematopoietic stem and progenitor cell (HSPC) fate as part of an early Notch-runx1-cmyb HSPC specification pathway in the zebrafish. Dnmt3bb.1 is expressed in HSPC downstream from Notch1 and runx1, and loss of Dnmt3bb.1 activity leads to reduced cmyb locus methylation, reduced cmyb expression, and gradual reduction in HSPCs. Ectopic overexpression of dnmt3bb.1 in non-hematopoietic cells is sufficient to methylate the cmyb locus, promote cmyb expression, and promote hematopoietic development. Our results reveal an epigenetic mechanism supporting the maintenance of hematopoietic cell fate via DNA methylation-mediated perdurance of a key transcription factor in HSPCs. DOI:http://dx.doi.org/10.7554/eLife.11813.001 The cells in our blood are constantly being replaced with new cells that are produced by stem cells called hematopoietic stem and progenitor cells (or HSPCs for short). The HSPCs form early on in the development of the embryo and continue in the same role throughout the life of the animal. A gene called runx1 is required for HSPCs to form, but is not required for these cells to maintain their role (cell identity) in the long term. In mice, this gene is only expressed for a brief period of time as the HSPCs form, and is switched off in the mature stem cells. Another gene called cmyb – which is switched on by runx1 – is also required for HSPCs to form. However, unlike runx1, cmyb continues to be expressed in mature HSPCs and is required to maintain HSPC identity. It is not known how the temporary activation of runx1 causes the long-term expression of cmyb. One possible explanation is that the cmyb gene may be subject to a process called DNA methylation. This process is carried out by enzymes called DNA methyltransferases and can have long-term effects on the expression of genes by modifying the structure of the DNA that encodes them. Here, Gore et al. investigate the role of a particular DNA methyltransferase in the formation of HSPCs in zebrafish embryos. The experiments show that this enzyme is activated in developing HSPCs in response to an increase in runx1 expression. The loss of this enzyme’s activity reduces both the amount that cmyb is methylated and its level of expression, which results in a gradual decline in the number of HSPCs in zebrafish. Further experiments show that if the DNA methyltransferase is artificially activated in cells that don’t normally form blood cells, these cells change their identity to do so. This switch is accompanied by methylation of cmyb and an increase in its expression. Gore et al.’s findings reveal that the temporary activation of runx1 triggers the production of an enzyme that methylates cmyb to maintain the identity of HSPCs. Future studies should help to reveal exactly how runx1 promotes DNA methylation, and whether this process can be harnessed to promote HSPC formation for research or medical treatments. DOI:http://dx.doi.org/10.7554/eLife.11813.002
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Affiliation(s)
- Aniket V Gore
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Brett Athans
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - James R Iben
- Program in Developmental Endocrinology and Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Kristin Johnson
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Valya Russanova
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Daniel Castranova
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Van N Pham
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Matthew G Butler
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Lisa Williams-Simons
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - James T Nichols
- Institute of Neuroscience, University of Oregon, Eugene, United States
| | - Erica Bresciani
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Bejamin Feldman
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Charles B Kimmel
- Institute of Neuroscience, University of Oregon, Eugene, United States
| | - Paul P Liu
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Brant M Weinstein
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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