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Radwan A, Eccleston J, Sabag O, Marcus H, Sussman J, Ouro A, Rahamim M, Azagury M, Azria B, Stanger BZ, Cedar H, Buganim Y. Transdifferentiation occurs without resetting development-specific DNA methylation, a key determinant of full-function cell identity. Proc Natl Acad Sci U S A 2024; 121:e2411352121. [PMID: 39292740 PMCID: PMC11441492 DOI: 10.1073/pnas.2411352121] [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: 07/02/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024] Open
Abstract
A number of studies have demonstrated that it is possible to directly convert one cell type to another by factor-mediated transdifferentiation, but in the vast majority of cases, the resulting reprogrammed cells are unable to maintain their new cell identity for prolonged culture times and have a phenotype only partially similar to their endogenous counterparts. To better understand this phenomenon, we developed an analytical approach for better characterizing trans-differentiation-associated changes in DNA methylation, a major determinant of long-term cell identity. By examining various models of transdifferentiation both in vitro and in vivo, our studies indicate that despite convincing expression changes, transdifferentiated cells seem unable to alter their original developmentally mandated methylation patterns. We propose that this blockage is due to basic developmental limitations built into the regulatory sequences that govern epigenetic programming of cell identity. These results shed light on the molecular rules necessary to achieve complete somatic cell reprogramming.
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Affiliation(s)
- Ahmed Radwan
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem91120, Israel
| | - Jason Eccleston
- Department of Medicine and Cell, The Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA19104
- Department of Development Biology, The Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA19104
| | - Ofra Sabag
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem91120, Israel
| | - Howard Marcus
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem91120, Israel
| | - Jonathan Sussman
- Department of Medicine and Cell, The Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA19104
- Department of Development Biology, The Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA19104
| | - Alberto Ouro
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem91120, Israel
| | - Moran Rahamim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem91120, Israel
| | - Meir Azagury
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem91120, Israel
| | - Batia Azria
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem91120, Israel
| | - Ben Z. Stanger
- Department of Medicine and Cell, The Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA19104
- Department of Development Biology, The Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA19104
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem91120, Israel
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2
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Hu P, Hao Y, Tang W, Diering GH, Zou F, Kafri T. Analysis of hepatic lentiviral vector transduction; implications for preclinical studies and clinical gene therapy protocols. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.20.608805. [PMID: 39229157 PMCID: PMC11370356 DOI: 10.1101/2024.08.20.608805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Lentiviral vector-transduced T-cells were approved by the FDA as gene therapy anti-cancer medications. Little is known about the host genetic variation effects on the safety and efficacy of the lentiviral vector gene delivery system. To narrow this knowledge-gap, we characterized hepatic gene delivery by lentiviral vectors across the Collaborative Cross (CC) mouse genetic reference population. For 24 weeks, we periodically measured hepatic luciferase expression from lentiviral vectors in 41 CC mouse strains. Hepatic and splenic vector copy numbers were determined. We report that CC mouse strains showed highly diverse outcomes following lentiviral gene delivery. For the first time, moderate correlation between mouse strain-specific sleeping patterns and transduction efficiency was observed. We associated two quantitative trait loci (QTLs) with intra-strain variations in transduction phenotypes, which mechanistically relates to the phenomenon of metastable epialleles. An additional QTL was associated with the kinetics of hepatic transgene expression. Genes comprised in the above QTLs are potential targets to personalize gene therapy protocols. Importantly, we identified two mouse strains that open new directions in characterizing continuous viral vector silencing and HIV latency. Our findings suggest that wide-range patient-specific outcomes of viral vector-based gene therapy should be expected. Thus, novel escalating dose-based clinical protocols should be considered.
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Affiliation(s)
- Peirong Hu
- Gene Therapy Center, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
- These authors contributed equally
| | - Yajing Hao
- Department of Biostatistics, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
- These authors contributed equally
| | - Wei Tang
- Gene Therapy Center, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
| | - Graham H Diering
- Department of Cell Biology and Physiology and UNC Neuroscience Center, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
- Carolina Institute for developmental disabilities, 27510 Carrboro, North Carolina
| | - Fei Zou
- Department of Biostatistics, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
| | - Tal Kafri
- Gene Therapy Center, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, 27599 Chapel Hill, North Carolina
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3
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Deng X, Liang S, Tang Y, Li Y, Xu R, Luo L, Wang Q, Zhang X, Liu Y. Adverse effects of bisphenol A and its analogues on male fertility: An epigenetic perspective. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123393. [PMID: 38266695 DOI: 10.1016/j.envpol.2024.123393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/11/2023] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
In recent years, there has been growing concern about the adverse effects of endocrine disrupting chemicals (EDCs) on male fertility. Epigenetic modification is critical for male germline development, and has been suggested as a potential mechanism for impaired fertility induced by EDCs. Bisphenol A (BPA) has been recognized as a typical EDC. BPA and its analogues, which are still widely used in various consumer products, have garnered increasing attention due to their reproductive toxicity and the potential to induce epigenetic alteration. This literature review provides an overview of studies investigating the adverse effects of bisphenol exposures on epigenetic modifications and male fertility. Existing studies provide evidence that exposure to bisphenols can lead to adverse effects on male fertility, including declined semen quality, altered reproductive hormone levels, and adverse reproductive outcomes. Epigenetic patterns, including DNA methylation, histone modification, and non-coding RNA expression, can be altered by bisphenol exposures. Transgenerational effects, which influence the fertility and epigenetic patterns of unexposed generations, have also been identified. However, the magnitude and direction of certain outcomes varied across different studies. Investigations into the dynamics of histopathological and epigenetic alterations associated with bisphenol exposures during developmental stages can enhance the understanding of the epigenetic effects of bisphenols, the implication of epigenetic alteration on male fertility, and the health of successive generation.
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Affiliation(s)
- Xinyi Deng
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Sihan Liang
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yuqian Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute, Guangdong Provincial Fertility Hospital, Guangzhou, China
| | - Yingxin Li
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ruijun Xu
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Lu Luo
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qiling Wang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute, Guangdong Provincial Fertility Hospital, Guangzhou, China
| | - Xinzong Zhang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute, Guangdong Provincial Fertility Hospital, Guangzhou, China
| | - Yuewei Liu
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China.
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4
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Naro C, Sette C, Geremia R. Purification by STA-PUT Technique of Male Germ Cells from Single Mouse and RNA-Extraction for Transcriptomic Analysis. Methods Mol Biol 2024; 2770:37-52. [PMID: 38351445 DOI: 10.1007/978-1-0716-3698-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Transcriptomic analyses of germ cells at different stages of differentiation have shed light on the transcriptional and post-transcriptional mechanisms regulating gene expression that ensure the correct progression of spermatogenesis and male fertility. In this chapter, we describe a method to isolate meiotic and post-meiotic germ cells, based on gravimetric sedimentation, starting from a testicular germ cell suspension isolated from a single adult mouse. We also describe how to assess the purity and quality of the collected fractions of germ cells and how to optimize the extraction from these samples of RNA for subsequent RNA-sequencing experiment. In our experience, this protocol is suitable for germ cell isolation and transcriptomic analysis for mouse models with spermatogenic defects, overcoming the limits that reduced fertility poses to the obtaining of experimental animals.
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Affiliation(s)
- Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- GSTeP-Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- GSTeP-Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Raffaele Geremia
- Department of Biomedicine and Prevention, Section of Human Anatomy, University of Rome Tor Vergata, Rome, Italy.
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5
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Ansari I, Solé-Boldo L, Ridnik M, Gutekunst J, Gilliam O, Korshko M, Liwinski T, Jickeli B, Weinberg-Corem N, Shoshkes-Carmel M, Pikarsky E, Elinav E, Lyko F, Bergman Y. TET2 and TET3 loss disrupts small intestine differentiation and homeostasis. Nat Commun 2023; 14:4005. [PMID: 37414790 PMCID: PMC10326054 DOI: 10.1038/s41467-023-39512-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
TET2/3 play a well-known role in epigenetic regulation and mouse development. However, their function in cellular differentiation and tissue homeostasis remains poorly understood. Here we show that ablation of TET2/3 in intestinal epithelial cells results in a murine phenotype characterized by a severe homeostasis imbalance in the small intestine. Tet2/3-deleted mice show a pronounced loss of mature Paneth cells as well as fewer Tuft and more Enteroendocrine cells. Further results show major changes in DNA methylation at putative enhancers, which are associated with cell fate-determining transcription factors and functional effector genes. Notably, pharmacological inhibition of DNA methylation partially rescues the methylation and cellular defects. TET2/3 loss also alters the microbiome, predisposing the intestine to inflammation under homeostatic conditions and acute inflammation-induced death. Together, our results uncover previously unrecognized critical roles for DNA demethylation, possibly occurring subsequently to chromatin opening during intestinal development, culminating in the establishment of normal intestinal crypts.
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Affiliation(s)
- Ihab Ansari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Llorenç Solé-Boldo
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Meshi Ridnik
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Gilliam
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Maria Korshko
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Timur Liwinski
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- University Psychiatric Clinics Basel, Clinic for Adults, University of Basel, Basel, Switzerland
| | - Birgit Jickeli
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Noa Weinberg-Corem
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Michal Shoshkes-Carmel
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eli Pikarsky
- The Lautenberg Center for Immunology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eran Elinav
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
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6
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Vargas LN, Nochi ARF, de Castro PS, Cunha ATM, Silva TCF, Togawa RC, Silveira MM, Caetano AR, Franco MM. Differentially methylated regions identified in bovine embryos are not observed in adulthood. Anim Reprod 2023; 20:e20220076. [PMID: 36938311 PMCID: PMC10023072 DOI: 10.1590/1984-3143-ar2022-0076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023] Open
Abstract
The establishment of epigenetic marks during the reprogramming window is susceptible to environmental influences, and stimuli during this critical stage can cause altered DNA methylation in offspring. In a previous study, we found that low levels of sulphur and cobalt (low S/Co) in the diet offered to oocyte donors altered the DNA methylome of bovine embryos. However, due to the extensive epigenetic reprogramming that occurs during embryogenesis, we hypothesized that the different methylation regions (DMRs) identified in the blastocysts may not maintain in adulthood. Here, we aimed to characterize DMRs previously identified in embryos, in the blood and sperm of adult progenies of two groups of heifers (low S/Co and control). We used six bulls and characterized the DNA methylation levels of KDM2A, KDM5A, KMT2D, and DOT1L genes. Our results showed that all DMRs analysed in both groups and tissues were hypermethylated unlike that noticed in the embryonic methylome profiles. These results suggest that embryo DMRs were reprogrammed during the final stages of de novo methylation during embryogenesis or later in development. Therefore, due to the highly dynamic epigenetic state during early embryonic development, we suggest that is essential to validate the DMRs found in embryos in adult individuals.
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Affiliation(s)
- Luna Nascimento Vargas
- Laboratório de Reprodução Animal, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | | | - Paloma Soares de Castro
- Laboratório de Reprodução Animal, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | | | - Thainara Christie Ferreira Silva
- Laboratório de Reprodução Animal, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
| | | | | | | | - Maurício Machaim Franco
- Laboratório de Reprodução Animal, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
- Corresponding author:
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7
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Rabbani M, Zheng X, Manske GL, Vargo A, Shami AN, Li JZ, Hammoud SS. Decoding the Spermatogenesis Program: New Insights from Transcriptomic Analyses. Annu Rev Genet 2022; 56:339-368. [PMID: 36070560 PMCID: PMC10722372 DOI: 10.1146/annurev-genet-080320-040045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Spermatogenesis is a complex differentiation process coordinated spatiotemporally across and along seminiferous tubules. Cellular heterogeneity has made it challenging to obtain stage-specific molecular profiles of germ and somatic cells using bulk transcriptomic analyses. This has limited our ability to understand regulation of spermatogenesis and to integrate knowledge from model organisms to humans. The recent advancement of single-cell RNA-sequencing (scRNA-seq) technologies provides insights into the cell type diversity and molecular signatures in the testis. Fine-grained cell atlases of the testis contain both known and novel cell types and define the functional states along the germ cell developmental trajectory in many species. These atlases provide a reference system for integrated interspecies comparisons to discover mechanistic parallels and to enable future studies. Despite recent advances, we currently lack high-resolution data to probe germ cell-somatic cell interactions in the tissue environment, but the use of highly multiplexed spatial analysis technologies has begun to resolve this problem. Taken together, recent single-cell studies provide an improvedunderstanding of gametogenesis to examine underlying causes of infertility and enable the development of new therapeutic interventions.
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Affiliation(s)
- Mashiat Rabbani
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Xianing Zheng
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Gabe L Manske
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexander Vargo
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Adrienne N Shami
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Urology, University of Michigan, Ann Arbor, Michigan, USA
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
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8
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Farini D, De Felici M. The Beginning of Meiosis in Mammalian Female Germ Cells: A Never-Ending Story of Intrinsic and Extrinsic Factors. Int J Mol Sci 2022; 23:ijms232012571. [PMID: 36293427 PMCID: PMC9604137 DOI: 10.3390/ijms232012571] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/06/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Meiosis is the unique division of germ cells resulting in the recombination of the maternal and paternal genomes and the production of haploid gametes. In mammals, it begins during the fetal life in females and during puberty in males. In both cases, entering meiosis requires a timely switch from the mitotic to the meiotic cell cycle and the transition from a potential pluripotent status to meiotic differentiation. Revealing the molecular mechanisms underlying these interrelated processes represents the essence in understanding the beginning of meiosis. Meiosis facilitates diversity across individuals and acts as a fundamental driver of evolution. Major differences between sexes and among species complicate the understanding of how meiosis begins. Basic meiotic research is further hindered by a current lack of meiotic cell lines. This has been recently partly overcome with the use of primordial-germ-cell-like cells (PGCLCs) generated from pluripotent stem cells. Much of what we know about this process depends on data from model organisms, namely, the mouse; in mice, the process, however, appears to differ in many aspects from that in humans. Identifying the mechanisms and molecules controlling germ cells to enter meiosis has represented and still represents a major challenge for reproductive medicine. In fact, the proper execution of meiosis is essential for fertility, for maintaining the integrity of the genome, and for ensuring the normal development of the offspring. The main clinical consequences of meiotic defects are infertility and, probably, increased susceptibility to some types of germ-cell tumors. In the present work, we report and discuss data mainly concerning the beginning of meiosis in mammalian female germ cells, referring to such process in males only when pertinent. After a brief account of this process in mice and humans and an historical chronicle of the major hypotheses and progress in this topic, the most recent results are reviewed and discussed.
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9
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Svoboda LK, Perera BPU, Morgan RK, Polemi KM, Pan J, Dolinoy DC. Toxicoepigenetics and Environmental Health: Challenges and Opportunities. Chem Res Toxicol 2022; 35:1293-1311. [PMID: 35876266 PMCID: PMC9812000 DOI: 10.1021/acs.chemrestox.1c00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The rapidly growing field of toxicoepigenetics seeks to understand how toxicant exposures interact with the epigenome to influence disease risk. Toxicoepigenetics is a promising field of environmental health research, as integrating epigenetics into the field of toxicology will enable a more thorough evaluation of toxicant-induced disease mechanisms as well as the elucidation of the role of the epigenome as a biomarker of exposure and disease and possible mediator of exposure effects. Likewise, toxicoepigenetics will enhance our knowledge of how environmental exposures, lifestyle factors, and diet interact to influence health. Ultimately, an understanding of how the environment impacts the epigenome to cause disease may inform risk assessment, permit noninvasive biomonitoring, and provide potential opportunities for therapeutic intervention. However, the translation of research from this exciting field into benefits for human and animal health presents several challenges and opportunities. Here, we describe four significant areas in which we see opportunity to transform the field and improve human health by reducing the disease burden caused by environmental exposures. These include (1) research into the mechanistic role for epigenetic change in environment-induced disease, (2) understanding key factors influencing vulnerability to the adverse effects of environmental exposures, (3) identifying appropriate biomarkers of environmental exposures and their associated diseases, and (4) determining whether the adverse effects of environment on the epigenome and human health are reversible through pharmacologic, dietary, or behavioral interventions. We then highlight several initiatives currently underway to address these challenges.
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Affiliation(s)
- Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Katelyn M Polemi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Junru Pan
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
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10
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Erichsen L, Thimm C, Santourlidis S. Methyl Group Metabolism in Differentiation, Aging, and Cancer. Int J Mol Sci 2022; 23:8378. [PMID: 35955511 PMCID: PMC9369357 DOI: 10.3390/ijms23158378] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
Methyl group metabolism belongs to a relatively understudied field of research. Its importance lies in the fact that methyl group metabolic pathways are crucial for the successful conversion of dietary nutrients into the basic building blocks to carry out any cellular methylation reaction. Methyl groups play essential roles in numerous cellular functions such as DNA methylation, nucleotide- and protein biosynthesis. Especially, DNA methylation is responsible for organizing the genome into transcriptionally silent and active regions. Ultimately, it is this proper annotation that determines the quality of expression patterns required to ensure and shape the phenotypic integrity and function of a highly specialized cell type. Life is characterized by constantly changing environmental conditions, which are addressed by changes in DNA methylation. This relationship is increasingly coming into focus as it is of fundamental importance for differentiation, aging, and cancer. The stability and permanence of these metabolic processes, fueling the supplementation of methyl groups, seem to be important criteria to prevent deficiencies and erosion of the methylome. Alterations in the metabolic processes can lead to epigenetic and genetic perturbations, causative for diverse disorders, accelerated aging, and various age-related diseases. In recent decades, the intake of methyl group compounds has changed significantly due to, e.g., environmental pollution and food additives. Based on the current knowledge, this review provides a brief overview of the highly interconnected relationship between nutrition, metabolism, changes in epigenetic modifications, cancer, and aging. One goal is to provide an impetus to additionally investigate changes in DNA methylation as a possible consequence of an impaired methyl group metabolism.
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Affiliation(s)
- Lars Erichsen
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Chantelle Thimm
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Simeon Santourlidis
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany;
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11
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Tachibana K, Kawazoe S, Onoda A, Umezawa M, Takeda K. Effects of Prenatal Exposure to Titanium Dioxide Nanoparticles on DNA Methylation and Gene Expression Profile in the Mouse Brain. FRONTIERS IN TOXICOLOGY 2022; 3:705910. [PMID: 35295148 PMCID: PMC8915839 DOI: 10.3389/ftox.2021.705910] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Background and Objectives: Titanium dioxide nanoparticles (TiO2-NP) are important materials used in commercial practice. Reportedly, TiO2-NP exposure during pregnancy can affect the development of the central nervous system in mouse offspring; however, the underlying mechanism remains unknown. In the present study, we investigated the impact of prenatal TiO2-NP exposure on global DNA methylation and mRNA expression patterns in the brains of neonatal mice. Materials and Methods: Pregnant C57BL/6J mice were intratracheally administered a TiO2-NP suspension (100 μg/mouse) on gestational day 10.5, and brains were collected from male and female offspring at day 1 postpartum. After extraction of methylated DNA by immunoprecipitation, the DNA methylation profile was analyzed using a mouse CpG island microarray. Total RNA was obtained, and mRNA expression profiles were comprehensively assessed using microarray analysis. Results: Among genes in the CpG island microarray, DNA methylation was increased in 614 and 2,924 genes and decreased in 6,220 and 6,477 genes in male and female offspring, respectively. Combined with mRNA microarray analysis, 88 and 89 genes were upregulated (≥1.5-fold) accompanied by demethylation of CpG islands, whereas 13 and 33 genes were downregulated (≤0.67-fold) accompanied by methylation of CpG islands in male and female offspring mice, respectively. Gene Set Enrichment Analysis (GSEA) revealed that these genes were enriched in gene ontology terms related to the regulation of transcription factors, cell proliferation, and organism development. Additionally, MeSH terms related to stem cells and morphogenesis were enriched. Conclusion: Prenatal TiO2-NP exposure induced genome-wide alterations in DNA methylation and mRNA expression in the brains of male and female offspring. Based on GSEA findings, it can be speculated that prenatal TiO2-NP exposure causes adverse effects on brain functions by altering the DNA methylation state of the fetal brain, especially neural stem cells, resulting in the subsequent abnormal regulation of transcription factors that modulate development and differentiation.
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Affiliation(s)
- Ken Tachibana
- Division of Toxicology and Health Science, Faculty of Pharmaceutical Sciences, Sanyo-onoda City University, Sanyo-onoda, Japan.,The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Shotaro Kawazoe
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Atsuto Onoda
- Division of Toxicology and Health Science, Faculty of Pharmaceutical Sciences, Sanyo-onoda City University, Sanyo-onoda, Japan.,The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Masakazu Umezawa
- The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan.,Department of Materials Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Katsushika, Japan
| | - Ken Takeda
- Division of Toxicology and Health Science, Faculty of Pharmaceutical Sciences, Sanyo-onoda City University, Sanyo-onoda, Japan.,The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
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12
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Zhou S, Sakashita A, Yuan S, Namekawa SH. Retrotransposons in the Mammalian Male Germline. Sex Dev 2022:1-19. [PMID: 35231923 DOI: 10.1159/000520683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/25/2021] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are a subset of DNA sequences that constitute a large part of the mammalian genome. They can translocate autonomously or non-autonomously, potentially jeopardizing the heritable germline genome. Retrotransposons coevolved with the host genome, and the germline is the prominent battlefield between retrotransposons and the host genome to maximize their mutual fitness. Host genomes have developed various mechanisms to suppress and control retrotransposons, including DNA methylation, histone modifications, and Piwi-interacting RNA (piRNA), for their own benefit. Thus, rapidly evolved retrotransposons often acquire positive functions, including gene regulation within the germline, conferring reproductive fitness in a species over the course of evolution. The male germline serves as an ideal model to examine the regulation and evolution of retrotransposons, resulting in genomic co-evolution with the host genome. In this review, we summarize and discuss the regulatory mechanisms of retrotransposons, stage-by-stage, during male germ cell development, with a particular focus on mice as an extensively studied mammalian model, highlighting suppression mechanisms and emerging functions of retrotransposons in the male germline.
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Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA
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13
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Ben Maamar M, Beck D, Nilsson E, McCarrey JR, Skinner MK. Developmental alterations in DNA methylation during gametogenesis from primordial germ cells to sperm. iScience 2022; 25:103786. [PMID: 35146397 PMCID: PMC8819394 DOI: 10.1016/j.isci.2022.103786] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 02/08/2023] Open
Abstract
Because epigenetics is a critical component for gene expression, the hypothesis was tested that DNA methylation alterations are dynamic and continually change throughout gametogenesis to generate the mature sperm. Developmental alterations and stage-specific DNA methylation during gametogenesis from primordial germ cells (PGCs) to mature sperm are investigated. Individual developmental stage germ cells were isolated and analyzed for differential DNA methylation regions (DMRs). The number of DMRs was highest in the first three comparisons with mature PGCs, prospermatogonia, and spermatogonia. The most statistically significant DMRs were present at all stages of development and had variations involving both increases or decreases in DNA methylation. DMR-associated genes were identified and correlated with gene functional categories, pathways, and cellular processes. Observations identified a dynamic cascade of epigenetic changes during development that is dramatic during the early developmental stages. Complex epigenetic alterations are required to regulate genome biology and gene expression during gametogenesis. A dynamic cascade of epigenetic change throughout gametogenesis from PGC to sperm Most dramatic epigenetic alterations in PGC and spermatogenic stem cell stages Different DNA methylation regions between and within stages were identified Complex epigenetic alterations required for gene expression during gametogenesis
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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14
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Pandya RK, Uppangala S, Salian SR, Gupta S, Kalthur G, Schlatt S, Adiga SK. Short-Term Hypothermic Holding of Mouse Immature Testicular Tissue Does Not Alter the Expression of DNA Methyltransferases and Global DNA Methylation Level, Post-Organotypic Culture. Front Endocrinol (Lausanne) 2022; 13:854297. [PMID: 35399926 PMCID: PMC8983811 DOI: 10.3389/fendo.2022.854297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/24/2022] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Cryopreservation of immature-testicular-tissue (ITT) prior to gonadotoxic treatment, while experimental, is the only recommended option for fertility preservation in prepubertal boys. The handling and manipulation of ITT prior to banking could influence the functionality, genetic and epigenetic integrity of cells. OBJECTIVES To investigate the impact of length of hypothermic holding of mouse ITT on the relative mRNA expression of the DNA methyltransferases (DNMTs) and global DNA methylation, post 14-days of organotypic culture. METHODS ITT from 6-day old mice were handled at hypothermic temperature (4 °C) for 6 and 24 h prior to 14-days organotypic culture. Relative mRNA expression of Dnmt1, Dnmt3a, and Dnmt3b along with global DNA methylation was measured from the cultured ITT. RESULTS No significant variation in the expression of Dnmt1, Dnmt3a, and Dnmt3b was observed in relation to varying holding time periods used. Further, global DNA methylation was comparable between 0, 6 and 24 h holding groups. CONCLUSIONS Short-term holding of ITT at 4 °C does not affect the DNA methylation process post organotypic culture. While fully acknowledging the limitations of this approach in the mouse model, the results we presented in this report will be of significant interest to the field.
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Affiliation(s)
- Riddhi K. Pandya
- Division of Clinical Embryology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shubhashree Uppangala
- Division of Reproductive Genetics, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sujith R. Salian
- Division of Clinical Embryology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sanjay Gupta
- KS313, Epigenetics and Chromatin Biology Group, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Guruprasad Kalthur
- Division of Reproductive Biology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stefan Schlatt
- Centre of Reproductive Medicine and Andrology (CeRA), University of Münster, Münster, Germany
- *Correspondence: Stefan Schlatt, ; Satish Kumar Adiga,
| | - Satish Kumar Adiga
- Division of Clinical Embryology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- *Correspondence: Stefan Schlatt, ; Satish Kumar Adiga,
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15
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Svoboda LK, Ishikawa T, Dolinoy DC. Developmental toxicant exposures and sex-specific effects on epigenetic programming and cardiovascular health across generations. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac017. [PMID: 36325489 PMCID: PMC9600458 DOI: 10.1093/eep/dvac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/12/2022] [Accepted: 10/01/2022] [Indexed: 05/15/2023]
Abstract
Despite substantial strides in diagnosis and treatment, cardiovascular diseases (CVDs) continue to represent the leading cause of death in the USA and around the world, resulting in significant morbidity and loss of productive years of life. It is increasingly evident that environmental exposures during early development can influence CVD risk across the life course. CVDs exhibit marked sexual dimorphism, but how sex interacts with environmental exposures to affect cardiovascular health is a critical and understudied area of environmental health. Emerging evidence suggests that developmental exposures may have multi- and transgenerational effects on cardiovascular health, with potential sex differences; however, further research in this important area is urgently needed. Lead (Pb), phthalate plasticizers, and perfluoroalkyl substances (PFAS) are ubiquitous environmental contaminants with numerous adverse human health effects. Notably, recent evidence suggests that developmental exposure to each of these toxicants has sex-specific effects on cardiovascular outcomes, but the underlying mechanisms, and their effects on future generations, require further investigation. This review article will highlight the role for the developmental environment in influencing cardiovascular health across generations, with a particular emphasis on sex differences and epigenetic mechanisms. In particular, we will focus on the current evidence for adverse multi and transgenerational effects of developmental exposures to Pb, phthalates, and PFAS and highlight areas where further research is needed.
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Affiliation(s)
- Laurie K Svoboda
- *Correspondence address. Environmental Health Sciences, University of Michigan, School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA. Tel: +734-764-2032; E-mail:
| | - Tomoko Ishikawa
- Environmental Health Sciences, University of Michigan, School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan, School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan, School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
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16
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Ramakrishna NB, Murison K, Miska EA, Leitch HG. Epigenetic Regulation during Primordial Germ Cell Development and Differentiation. Sex Dev 2021; 15:411-431. [PMID: 34847550 DOI: 10.1159/000520412] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/10/2021] [Indexed: 11/19/2022] Open
Abstract
Germline development varies significantly across metazoans. However, mammalian primordial germ cell (PGC) development has key conserved landmarks, including a critical period of epigenetic reprogramming that precedes sex-specific differentiation and gametogenesis. Epigenetic alterations in the germline are of unique importance due to their potential to impact the next generation. Therefore, regulation of, and by, the non-coding genome is of utmost importance during these epigenomic events. Here, we detail the key chromatin changes that occur during mammalian PGC development and how these interact with the expression of non-coding RNAs alongside broader epitranscriptomic changes. We identify gaps in our current knowledge, in particular regarding epigenetic regulation in the human germline, and we highlight important areas of future research.
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Affiliation(s)
- Navin B Ramakrishna
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Genome Institute of Singapore, A*STAR, Biopolis, Singapore, Singapore
| | - Keir Murison
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Harry G Leitch
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, United Kingdom
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17
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Chen Y, Liu X, Liu X, Cui L, He Z, Gao Z, Liu L, Li Z, Wan Z, Yu Z. Correlation between TGF-β2/3 promoter DNA methylation and Smad signaling during palatal fusion induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin. Exp Biol Med (Maywood) 2021; 246:2019-2028. [PMID: 34053232 PMCID: PMC8474981 DOI: 10.1177/15353702211012288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/28/2021] [Indexed: 01/10/2023] Open
Abstract
2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a persistent organic pollutant that is strongly associated with a number of human diseases and birth defects, including cleft palate. Transforming growth factor (TGF) plays a significant role during mammalian palatogenesis. However, the epigenetic mechanism of transforming growth factors in the process of TCDD-induced cleft palate is unclear. The purpose of this research was to investigate the relationship and potential mechanism between TGF-β2/3 promoter DNA methylation and Smad signaling during TCDD-induced cleft palate. Pregnant C57BL/6N mice were exposed to 64 µg/kg TCDD on gestational day 10 (GD10) to establish the cleft palate model and palatal tissues of embryos were collected on GD13, GD14, and GD15 for subsequent experiments. TGF-β2/3 mRNA expression, TGF-β2/3 promoter methylation, and Smad signaling molecules expression were assessed in the palate of the two groups. The results showed that the incidence of cleft palate was 94.7% in the TCDD-treated group whereas no cleft palate was found in the control group. TCDD-treated group altered specific CpG sites of TGF-β2/3 promoter methylation. Compared to the control group, the proliferation of mouse embryonic palate mesenchymal stromal cells (MEPM), the expressions of TGF-β2/3, p-Smad2, and Smad4 were all reduced, while the expression of Smad7 was significantly increased in the atAR group. Smad signaling was downregulated by TCDD. Therefore, we suggest that TGF-β2/3 promoter methylation and Smad signaling may be involved in TCDD-induced cleft palate formation in fetal mice.
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Affiliation(s)
- Yao Chen
- School of Public Health, Xinxiang Medical University, Xinxiang
453003, China
- School of Public Health, Zhengzhou University, Zhengzhou 450001,
China
| | - Xiaozhuan Liu
- Center for Clinical Single-Cell Biomedicine, Henan Provincial
People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 450003,
China
- Department of Immunology, Medical College of Henan University of
Science and Technology, Luoyang 471003, China
| | - Xinxin Liu
- School of Public Health, Zhengzhou University, Zhengzhou 450001,
China
| | - Lingling Cui
- School of Public Health, Zhengzhou University, Zhengzhou 450001,
China
| | - Zhidong He
- School of Public Health, Zhengzhou University, Zhengzhou 450001,
China
| | - Zhan Gao
- The Fifth Affiliated Hospital, Zhengzhou University, Zhengzhou
450052, China
| | - Limin Liu
- School of Public Health, Zhengzhou University, Zhengzhou 450001,
China
| | - Zhitao Li
- Department of Immunology, Medical College of Henan University of
Science and Technology, Luoyang 471003, China
| | - Zhongxiao Wan
- School of Public Health, Zhengzhou University, Zhengzhou 450001,
China
| | - Zengli Yu
- School of Public Health, Xinxiang Medical University, Xinxiang
453003, China
- School of Public Health, Zhengzhou University, Zhengzhou 450001,
China
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18
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Single-molecule micromanipulation studies of methylated DNA. Biophys J 2021; 120:2148-2155. [PMID: 33838135 DOI: 10.1016/j.bpj.2021.03.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylated at the five-carbon position is the most widely studied reversible DNA modification. Prior findings indicate that methylation can alter mechanical properties. However, those findings were qualitative and sometimes contradictory, leaving many aspects unclear. By applying single-molecule magnetic force spectroscopy techniques allowing for direct manipulation and dynamic observation of DNA mechanics and mechanically driven strand separation, we investigated how CpG and non-CpG cytosine methylation affects DNA micromechanical properties. We quantitatively characterized DNA stiffness using persistence length measurements from force-extension curves in the nanoscale length regime and demonstrated that cytosine methylation results in longer contour length and increased DNA flexibility (i.e., decreased persistence length). In addition, we observed the preferential formation of plectonemes over unwound single-stranded "bubbles" of DNA under physiologically relevant stretching forces and supercoiling densities. The flexibility and high structural stability of methylated DNA is likely to have significant consequences on the recruitment of proteins recognizing cytosine methylation and DNA packaging.
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19
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赵 健, 李 东, 安 阳. [Roles of ten eleven translocation proteins family and 5-hydroxymethylcytosine in epigenetic regulation of stem cells and regenerative medicine]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2021; 53:420-424. [PMID: 33879920 PMCID: PMC8072413 DOI: 10.19723/j.issn.1671-167x.2021.02.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Indexed: 06/12/2023]
Abstract
The methylation of cytosine is one of the most fundamental epigenetic modifications in mammalian genomes, and is involved in multiple crucial processes including gene expression, cell differentiation, embryo development and oncogenesis. In the past, DNA methylation was thought to be an irreversible process, which could only be diluted passively through DNA replication. It is now becoming increa-singly obvious that DNA demethylation can be an active process and plays a crucial role in biological processes. Ten eleven translocation (TET) proteins are the key factors modulating DNA demethylation. This family contains three members: TET1, TET2 and TET3. Although three TET proteins have relatively conserved catalytic domains, their roles in organisms are not repeated, and their expression has significant cell/organ specificity. TET1 is mainly expressed in embryonic stem cells, TET2 is mainly expressed in hematopoietic system, and TET3 is widely expressed in cerebellum, cortex and hippocampus. This family catalyzes 5-methylcytosine to 5-hydroxymethylcytosine and other oxidative products, reactivates silenced-gene expression, in turn maintains stem cell pluripotency and regulates lineage specification. With the development of tissue engineering, organ transplantation, autologous tissue transplantation and artificial prosthesis have been widely used in clinical treatment, but these technologies have limitations. Regenerative medicine, which uses stem cells and stem cell related factors for treatment, may provide alternative therapeutic strategies for multiple diseases. Among all kinds of human stem cells, adipose-derived stem cells (ADSCs) are the most prospective stem cell lineage since they have no ethical issues and can be easily obtained with large quantities. To date, ADSCs have been shown to have strong proli-feration capacity, secrete numerous soluble factors and have multipotent differentiation ability. However, the underlying mechanism of the proliferation, secretion, acquired pluripotency, and lineage specific differentiation of ADSCs are still largely unknown. Some studies have explored the role of epigenetic regulation and TET protein in embryonic stem cells, but little is known about its role in ADSCs. By studying the roles of TET proteins and 5-hydroxymethylcytosine in ADSCs, we could provide new theoretical foundation for the clinical application of ADSCs and the stem cell-based therapy. In the future, combined with bioprinting technology, ADSCs may be used in tissue and organ regeneration, plastic surgery reconstruction and other broader fields.
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Affiliation(s)
- 健芳 赵
- 北京大学第三医院成形外科,北京 100191Department of Plastic Surgery, Peking University Third Hospital, Beijing 100191, China
- 北京大学第一医院整形烧伤外科,北京 100034Department of Plastic Surgery and Burns, Peking University First Hospital, Beijing 100034, China
| | - 东 李
- 北京大学第三医院成形外科,北京 100191Department of Plastic Surgery, Peking University Third Hospital, Beijing 100191, China
| | - 阳 安
- 北京大学第三医院成形外科,北京 100191Department of Plastic Surgery, Peking University Third Hospital, Beijing 100191, China
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20
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Saitou M. Mammalian Germ Cell Development: From Mechanism to In Vitro Reconstitution. Stem Cell Reports 2021; 16:669-680. [PMID: 33577794 PMCID: PMC8072030 DOI: 10.1016/j.stemcr.2021.01.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/09/2021] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
The germ cell lineage gives rise to totipotency and perpetuates and diversifies genetic as well as epigenetic information. Specifically, germ cells undergo epigenetic reprogramming/programming, replicate genetic information with high fidelity, and create genetic diversity through meiotic recombination. Driven by advances in our understanding of the mechanisms underlying germ cell development and stem cell/reproductive technologies, research over the past 2 decades has culminated in the in vitro reconstitution of mammalian germ cell development: mouse pluripotent stem cells (PSCs) can now be induced into primordial germ cell-like cells (PGCLCs) and then differentiated into fully functional oocytes and spermatogonia, and human PSCs can be induced into PGCLCs and into early oocytes and prospermatogonia with epigenetic reprogramming. Here, I provide my perspective on the key investigations that have led to the in vitro reconstitution of mammalian germ cell development, which will be instrumental in exploring salient themes in germ cell biology and, with further refinements/extensions, in developing innovative medical applications.
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Affiliation(s)
- Mitinori Saitou
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
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21
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Liu X, Zhang Y, Shen L, He Z, Chen Y, Li N, Zhang X, Zhang T, Gao S, Yue H, Li Z, Yu Z. LncRNA Meg3-mediated regulation of the Smad pathway in atRA-induced cleft palate. Toxicol Lett 2021; 341:51-58. [PMID: 33493612 DOI: 10.1016/j.toxlet.2021.01.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/05/2021] [Accepted: 01/18/2021] [Indexed: 12/15/2022]
Abstract
Palatal mesenchymal cell proliferation is essential to the process of palatogenesis, and the proliferation of mouse embryonic palate mesenchymal (MEPM) cells is impacted by both all-trans retinoic acid (atRA) and the TGF-β/Smad signaling pathway. The long non-coding RNA (lncRNA) MEG3 has been shown to activate TGF-β/Smad signaling and to thereby regulate cell proliferation, differentiation, and related processes. Herein, we found that atRA treatment (100 mg/kg) promoted Meg3 upregulation in MEPM cells, and that such upregulation was linked to the suppression of MEPM cell proliferation in the context of secondary palate fusion on gestational day (GD) 13 and 14. Moreover, the demethylation of specific CpG sites within the lncRNA Meg3 promoter was detected in atRA-treated MEPM cells, likely explaining the observed upregulation of this lncRNA. Smad signaling was also suppressed by atRA treatment in these cells, and RNA immunoprecipitation analyses revealed that Smad2 can directly interact with Meg3 in MEPM cells following atRA treatment. Therefore, we propose a model wherein Meg3 is involved in the suppression of MEPM cell proliferation, functioning at least in part via interacting with the Smad2 protein and thereby suppressing Smad signaling in the context of atRA-induced cleft palate.
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Affiliation(s)
- Xiaozhuan Liu
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuwei Zhang
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lijun Shen
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhidong He
- School of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yao Chen
- School of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Ning Li
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiuli Zhang
- Division of Blood Vessel Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Tingting Zhang
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Suhua Gao
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haodi Yue
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhitao Li
- Medical College of Henan University of Science and Technology, Luoyang, Henan, China
| | - Zengli Yu
- Center for Clinical Single-Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China; School of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
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22
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Garcia-Outeiral V, de la Parte C, Fidalgo M, Guallar D. The Complexity of TET2 Functions in Pluripotency and Development. Front Cell Dev Biol 2021; 8:630754. [PMID: 33537318 PMCID: PMC7848104 DOI: 10.3389/fcell.2020.630754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Ten-eleven translocation-2 (TET2) is a crucial driver of cell fate outcomes in a myriad of biological processes, including embryonic development and tissue homeostasis. TET2 catalyzes the demethylation of 5-methylcytosine on DNA, affecting transcriptional regulation. New exciting research has provided evidence for TET2 catalytic activity in post-transcriptional regulation through RNA hydroxymethylation. Here we review the current understanding of TET2 functions on both DNA and RNA, and the influence of these chemical modifications in normal development and pluripotency contexts, highlighting TET2 versatility in influencing genome regulation and cellular phenotypes.
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Affiliation(s)
- Vera Garcia-Outeiral
- Stem Cells and Human Diseases Group, Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Cristina de la Parte
- Epitranscriptomics and Ageing Group, Department of Biochemistry and Molecular Biology, Center for Research in Molecular Medicine and Chronic Diseases, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel Fidalgo
- Stem Cells and Human Diseases Group, Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Diana Guallar
- Epitranscriptomics and Ageing Group, Department of Biochemistry and Molecular Biology, Center for Research in Molecular Medicine and Chronic Diseases, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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23
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Wanner E, Thoppil H, Riabowol K. Senescence and Apoptosis: Architects of Mammalian Development. Front Cell Dev Biol 2021; 8:620089. [PMID: 33537310 PMCID: PMC7848110 DOI: 10.3389/fcell.2020.620089] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
Mammalian development involves an exquisite choreography of cell division, differentiation, locomotion, programmed cell death, and senescence that directs the transformation of a single cell zygote to a mature organism containing on the order of 40 trillion cells in humans. How a single totipotent zygote undergoes the rapid stages of embryonic development to form over 200 different cell types is complex in the extreme and remains the focus of active research. Processes such as programmed cell death or apoptosis has long been known to occur during development to help sculpt organs and tissue systems. Other processes such as cellular senescence, long thought to only occur in pathologic states such as aging and tumorigenesis have been recently reported to play a vital role in development. In this review, we focus on apoptosis and senescence; the former as an integral mechanism that plays a critical role not only in mature organisms, but that is also essential in shaping mammalian development. The latter as a well-defined feature of aging for which some reports indicate a function in development. We will dissect the dual roles of major gene families, pathways such as Hox, Rb, p53, and epigenetic regulators such as the ING proteins in both early and the late stages and how they play antagonistic roles by increasing fitness and decreasing mortality early in life but contribute to deleterious effects and pathologies later in life.
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Affiliation(s)
- Emma Wanner
- Department of Biology, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Harikrishnan Thoppil
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Karl Riabowol
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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24
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Singh R, Chandel S, Dey D, Ghosh A, Roy S, Ravichandiran V, Ghosh D. Epigenetic modification and therapeutic targets of diabetes mellitus. Biosci Rep 2020; 40:BSR20202160. [PMID: 32815547 PMCID: PMC7494983 DOI: 10.1042/bsr20202160] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 12/11/2022] Open
Abstract
The prevalence of diabetes and its related complications are increasing significantly globally. Collected evidence suggested that several genetic and environmental factors contribute to diabetes mellitus. Associated complications such as retinopathy, neuropathy, nephropathy and other cardiovascular complications are a direct result of diabetes. Epigenetic factors include deoxyribonucleic acid (DNA) methylation and histone post-translational modifications. These factors are directly related with pathological factors such as oxidative stress, generation of inflammatory mediators and hyperglycemia. These result in altered gene expression and targets cells in the pathology of diabetes mellitus without specific changes in a DNA sequence. Environmental factors and malnutrition are equally responsible for epigenetic states. Accumulated evidence suggested that environmental stimuli alter the gene expression that result in epigenetic changes in chromatin. Recent studies proposed that epigenetics may include the occurrence of 'metabolic memory' found in animal studies. Further study into epigenetic mechanism might give us new vision into the pathogenesis of diabetes mellitus and related complication thus leading to the discovery of new therapeutic targets. In this review, we discuss the possible epigenetic changes and mechanism that happen in diabetes mellitus type 1 and type 2 separately. We highlight the important epigenetic and non-epigenetic therapeutic targets involved in the management of diabetes and associated complications.
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Affiliation(s)
- Rajveer Singh
- National Institute of Pharmaceutical Education and Research, Kolkata 164, Manicktala Main Road, Kolkata 700054, India
| | - Shivani Chandel
- National Institute of Pharmaceutical Education and Research, Kolkata 164, Manicktala Main Road, Kolkata 700054, India
| | - Dhritiman Dey
- National Institute of Pharmaceutical Education and Research, Kolkata 164, Manicktala Main Road, Kolkata 700054, India
| | - Arijit Ghosh
- Department of Chemistry, University of Calcutta, Kolkata 700009, India
| | - Syamal Roy
- National Institute of Pharmaceutical Education and Research, Kolkata 164, Manicktala Main Road, Kolkata 700054, India
| | - Velayutham Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata 164, Manicktala Main Road, Kolkata 700054, India
| | - Dipanjan Ghosh
- National Institute of Pharmaceutical Education and Research, Kolkata 164, Manicktala Main Road, Kolkata 700054, India
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25
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Ben Maamar M, Beck D, Nilsson E, McCarrey JR, Skinner MK. Developmental origins of transgenerational sperm histone retention following ancestral exposures. Dev Biol 2020; 465:31-45. [PMID: 32628935 PMCID: PMC7484192 DOI: 10.1016/j.ydbio.2020.06.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022]
Abstract
Numerous environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. Alterations in the germline epigenome are necessary to transmit transgenerational phenotypes. In previous studies, the pesticide DDT (dichlorodiphenyltrichloroethane) and the agricultural fungicide vinclozolin were shown to promote the transgenerational inheritance of sperm differential DNA methylation regions, non-coding RNAs and histone retention, which are termed epimutations. These epimutations are able to mediate this epigenetic inheritance of disease and phenotypic variation. The current study was designed to investigate the developmental origins of the transgenerational differential histone retention sites (called DHRs) during gametogenesis of the sperm. Vinclozolin and DDT were independently used to promote the epigenetic transgenerational inheritance of these DHRs. Male control lineage, DDT lineage and vinclozolin lineage F3 generation rats were used to isolate round spermatids, caput epididymal spermatozoa, and caudal sperm. The DHRs distinguishing the control versus DDT lineage or vinclozolin lineage samples were determined at these three developmental stages. DHRs and a reproducible core of histone H3 retention sites were observed using an H3 chromatin immunoprecipitation-sequencing (ChIP-Seq) analysis in each of the germ cell populations. The chromosomal locations and genomic features of the DHRs were analyzed. A cascade of epigenetic histone retention site alterations was found to be initiated in the round spermatids and then further modified during epididymal sperm maturation. Observations show that in addition to alterations in sperm DNA methylation and ncRNA expression previously identified, the induction of differential histone retention sites (DHRs) in the later stages of spermatogenesis also occurs. This novel component of epigenetic programming during spermatogenesis can be environmentally altered and transmitted to subsequent generations through epigenetic transgenerational inheritance.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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26
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A Mathematical Model for Inheritance of DNA Methylation Patterns in Somatic Cells. Bull Math Biol 2020; 82:84. [PMID: 32613387 DOI: 10.1007/s11538-020-00765-4] [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: 11/20/2019] [Accepted: 06/10/2020] [Indexed: 12/22/2022]
Abstract
DNA methylation is an essential epigenetic mechanism used by cells to regulate gene expression. Interestingly, DNA replication, a function necessary for cell division, disrupts the methylation pattern. Since perturbed methylation patterns are associated with aberrant gene expression and many diseases, including cancer, restoration of the correct pattern following DNA replication is crucial. However, the exact mechanisms of this restoration remain under investigation. DNA methyltransferases (Dnmts) perform methylation by adding a methyl group to cytosines at CpG sites in the DNA. These CpG sites are found in regions of high density, termed CpG islands (CGIs), and regions of low density in the genome. Nearly, every CpG site in a CGI has the same state, either methylated or unmethylated, and almost all CpG sites in regions of low CpG density are methylated. We propose a stochastic model for the dynamics of the post-replicative restoration of methylation patterns. The model considers the recruitment of Dnmts and demethylating enzymes to regions of hyper- and hypomethylation, respectively. The model also includes the interaction between Dnmt1 and PCNA, an enzyme that localizes Dnmt1 to the replication complex. Using our model, we predict that the methylation of regions of DNA can be bistable. Further, we predict that recruitment mechanisms maintain methylation in CGIs, whereas the Dnmt1-PCNA interaction maintains methylation in low-density regions.
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27
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Huang HT, Su SC, Chiou TJ, Lin YH, Shih YC, Wu YX, Fan TH, Twu YC. DNA methylation-mediated Siglec-7 regulation in natural killer cells via two 5' promoter CpG sites. Immunology 2020; 160:38-51. [PMID: 32027025 DOI: 10.1111/imm.13179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 12/31/2022] Open
Abstract
First discovered on the natural killer (NK) cell, the cell surface inhibitory receptor sialic acid-binding immunoglobulin-like lectin-7 (Siglec-7) is known for regulating many important biological activities. However, the detail regulatory mechanism for Siglec-7 expression in NK cells currently remains unclear. In this study, we aimed to investigate how cell surface Siglec-7 expression is regulated and found that, in both NK cell lines and peripheral NK cells, transcription was the main regulatory step. Furthermore, when NK-92MI and peripheral NK cells were treated with DNA methyltransferase (DNMT) inhibitor, the CpG island, with 9 CpG sites, in 5' Siglec-7 promoter became noticeably hypomethylated, and Siglec-7 expression increased in both RNA transcript and surface protein. Within this CpG island, we identified both CpG 8 and CpG 9 as two key regulators responsible for Siglec-7 expression. Additionally, by using histone deacetylases (HDAC) inhibitor, butyric acid, we showed that Siglec-7 expression was also subjected to the histone modification. And a combined treatment with both 5-azacytidine and butyric acid showed an additive effect on Siglec-7 transcript expression in peripheral NK cells.
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Affiliation(s)
- Hsin-Ting Huang
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Chi Su
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Tzeon-Jye Chiou
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Cancer Center, Taipei Municipal Wanfang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yen-Hsi Lin
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chen Shih
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Xuan Wu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Ting-Hsi Fan
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Yuh-Ching Twu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
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28
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Portela JMD, Heckmann L, Wistuba J, Sansone A, van Pelt AMM, Kliesch S, Schlatt S, Neuhaus N. Development and Disease-Dependent Dynamics of Spermatogonial Subpopulations in Human Testicular Tissues. J Clin Med 2020; 9:jcm9010224. [PMID: 31947706 PMCID: PMC7019285 DOI: 10.3390/jcm9010224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 01/03/2020] [Accepted: 01/10/2020] [Indexed: 12/22/2022] Open
Abstract
Cancer therapy and conditioning treatments of non-malignant diseases affect spermatogonial function and may lead to male infertility. Data on the molecular properties of spermatogonia and the influence of disease and/or treatment on spermatogonial subpopulations remain limited. Here, we assessed if the density and percentage of spermatogonial subpopulation changes during development (n = 13) and due to disease and/or treatment (n = 18) in tissues stored in fertility preservation programs, using markers for spermatogonia (MAGEA4), undifferentiated spermatogonia (UTF1), proliferation (PCNA), and global DNA methylation (5mC). Throughout normal prepubertal testicular development, only the density of 5mC-positive spermatogonia significantly increased with age. In comparison, patients affected by disease and/or treatment showed a reduced density of UTF1-, PCNA- and 5mC-positive spermatogonia, whereas the percentage of spermatogonial subpopulations remained unchanged. As an exception, sickle cell disease patients treated with hydroxyurea displayed a reduction in both density and percentage of 5mC- positive spermatogonia. Our results demonstrate that, in general, a reduction in spermatogonial density does not alter the percentages of undifferentiated and proliferating spermatogonia, nor the establishment of global methylation. However, in sickle cell disease patients’, establishment of spermatogonial DNA methylation is impaired, which may be of importance for the potential use of this tissues in fertility preservation programs.
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Affiliation(s)
- Joana M. D. Portela
- Center of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, Albert-Schweitzer-Campus 1, Building D11, 48149 Münster, Germany; (J.M.D.P.); (L.H.); (J.W.); (A.S.); (S.S.)
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
| | - Laura Heckmann
- Center of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, Albert-Schweitzer-Campus 1, Building D11, 48149 Münster, Germany; (J.M.D.P.); (L.H.); (J.W.); (A.S.); (S.S.)
| | - Joachim Wistuba
- Center of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, Albert-Schweitzer-Campus 1, Building D11, 48149 Münster, Germany; (J.M.D.P.); (L.H.); (J.W.); (A.S.); (S.S.)
| | - Andrea Sansone
- Center of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, Albert-Schweitzer-Campus 1, Building D11, 48149 Münster, Germany; (J.M.D.P.); (L.H.); (J.W.); (A.S.); (S.S.)
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Ans M. M. van Pelt
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
| | - Sabine Kliesch
- Center of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, Albert-Schweitzer-Campus 1, Building D11, 48149 Münster, Germany;
| | - Stefan Schlatt
- Center of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, Albert-Schweitzer-Campus 1, Building D11, 48149 Münster, Germany; (J.M.D.P.); (L.H.); (J.W.); (A.S.); (S.S.)
| | - Nina Neuhaus
- Center of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, Albert-Schweitzer-Campus 1, Building D11, 48149 Münster, Germany; (J.M.D.P.); (L.H.); (J.W.); (A.S.); (S.S.)
- Correspondence:
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29
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Ma F, Zhang Q, Zhang CY. Nanomaterial-based biosensors for DNA methyltransferase assay. J Mater Chem B 2020; 8:3488-3501. [DOI: 10.1039/c9tb02458a] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We review the recent advances in the development of nanomaterial-based biosensors for DNA methyltransferase assay.
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Affiliation(s)
- Fei Ma
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Qian Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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30
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Watson H, Salmón P, Isaksson C. Dynamic changes in DNA methylation during embryonic and postnatal development of an altricial wild bird. Ecol Evol 2019; 9:9580-9585. [PMID: 31534676 PMCID: PMC6745840 DOI: 10.1002/ece3.5480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/18/2019] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
DNA methylation could shape phenotypic responses to environmental cues and underlie developmental plasticity. Environmentally induced changes in DNA methylation during development can give rise to stable phenotypic traits and thus affect fitness. In the laboratory, it has been shown that the vertebrate methylome undergoes dynamic reprogramming during development, creating a critical window for environmentally induced epigenetic modifications. Studies of DNA methylation in the wild are lacking, yet are essential for understanding how genes and the environment interact to affect phenotypic development and ultimately fitness. Furthermore, our knowledge of the establishment of methylation patterns during development in birds is limited. We quantified genome-wide DNA methylation at various stages of embryonic and postnatal development in an altricial passerine bird, the great tit Parus major. While, there was no change in global DNA methylation in embryonic tissue during the second half of embryonic development, a twofold increase in DNA methylation in blood occurred between 6 and 15 days posthatch. Though not directly comparable, DNA methylation levels were higher in the blood of nestlings compared with embryonic tissue at any stage of prenatal development. This provides the first evidence that DNA methylation undergoes global change during development in a wild bird, supporting the hypothesis that methylation mediates phenotypic development. Furthermore, the plasticity of DNA methylation demonstrated during late postnatal development, in the present study, suggests a wide window during which DNA methylation could be sensitive to environmental influences. This is particularly important for our understanding of the mechanisms by which early-life conditions influence later-life performance. While, we found no evidence for differences in genome-wide methylation in relation to habitat of origin, environmental variation is likely to be an important driver of variation in methylation at specific loci.
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Affiliation(s)
- Hannah Watson
- Evolutionary Ecology, Biology DepartmentLund UniversityLundSweden
| | - Pablo Salmón
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
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31
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Potential of epigenetic events in human thyroid cancer. Cancer Genet 2019; 239:13-21. [PMID: 31472323 DOI: 10.1016/j.cancergen.2019.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/27/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022]
Abstract
Thyroid cancer remains the highest prevailing endocrine malignancy, and its incidence rate has progressively increased in the previous years. Above 95% of thyroid tumor are follicular cells types of carcinoma in which are considered invasive type of tumor. The pathogenesis and molecular mechanism of thyroid tumors are yet remains elucidated, in spite of activating RET, RAS and BRAF carcinogenesis have been well introduced. Nemours molecular alterations have been defined and have revealed promise for their diagnostic, prognostic and therapeutic capacity but still need further confirmation. Among different types of mechanisms, the current article reviews the importance of epigenetic modifications in thyroid cancer. Increasing data from previous reports demonstrate that acquired epigenetic abnormalities together with genetic changes plays an important role in alteration of gene expression patterns. Aberrant DNA methylation has been well known in the CpG regions and profile of microRNAs (mi-RNAs) expression also involved in cancer development. In addition, the gene expression through epigenetic control contribution to thyroid cancer is analyzed and it is semi considered in the clinic. However the epigenetic of the thyroid cancer is yet remains in its early stages, and it carries encouraging potential thyroid cancer detections in its early stages, assessment of prognosis and targeted cancer treatment.
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32
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Martín-Del-Campo R, Bárcenas-Ibarra A, Lund G, Rodríguez-Ríos D, Yong-Villalobos L, García-Hernández J, García-Gasca A. Mercury Concentration, DNA Methylation, and Mitochondrial DNA Damage in Olive Ridley Sea Turtle Embryos With Schistosomus Reflexus Syndrome. Vet Pathol 2019; 56:940-949. [PMID: 31434549 DOI: 10.1177/0300985819868649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Schistosomus reflexus syndrome (SR) is a rare and lethal congenital malformation that has been reported in the olive ridley sea turtle (Lepidochelys olivacea) in Mexico. Although the etiology remains unclear, it is presumed to be genetic. Since embryonic development in sea turtles largely depends on environmental conditions, we investigated whether sea turtle total mercury content participates in the etiology of SR. Given that several toxins are known to affect both DNA methylation and/or mitochondrial DNA (mtDNA) copy number, we also probed for associations of these parameters to SR and mercury exposure. We measured the levels of each variable in malformed olive ridley sea turtle embryos (either with SR or other non-SR malformations) and embryos without malformations. Malformed embryos (with or without SR) showed higher mercury concentrations compared to normal embryos, while only embryos with SR showed higher levels of methylation compared to embryos without malformations and those with other malformations. Furthermore, we uncovered a positive correlation between mercury concentrations and DNA methylation in SR embryos. With respect to mtDNA copy number, no differences were detected across experimental groups. Because of sample size limitations, this study is an initial attempt to understand the association of environmental toxins (such as mercury) and epigenetic alterations (DNA methylation) in the etiology of SR in sea turtles.
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Affiliation(s)
- Rodolfo Martín-Del-Campo
- Laboratorio de Biología Molecular y Celular, Centro de Investigación en Alimentación y Desarrollo, Mazatlán, Sinaloa, Mexico
| | - Annelisse Bárcenas-Ibarra
- Laboratorio de Biología Molecular y Celular, Centro de Investigación en Alimentación y Desarrollo, Mazatlán, Sinaloa, Mexico
| | - Gertrud Lund
- Departamento de Ingeniería Genética, CINVESTAV (GL, DRR), Irapuato, Guanajuato, Mexico
| | - Dalia Rodríguez-Ríos
- Departamento de Ingeniería Genética, CINVESTAV (GL, DRR), Irapuato, Guanajuato, Mexico
| | - Lenin Yong-Villalobos
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)/Unidad de Genómica Avanzada, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Jaqueline García-Hernández
- Laboratorio de Ciencias Ambientales, Centro de Investigación en Alimentación y Desarrollo, Guaymas, Sonora, Mexico
| | - Alejandra García-Gasca
- Laboratorio de Biología Molecular y Celular, Centro de Investigación en Alimentación y Desarrollo, Mazatlán, Sinaloa, Mexico
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33
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Li KE, Shu X, Gong H, Cheng L, Dong Z, Shu S. Position-dependent correlation between TBX22 exon 5 methylation and palatal shelf fusion in the development of cleft palate. AN ACAD BRAS CIENC 2019; 91:e20180945. [PMID: 31241704 DOI: 10.1590/0001-3765201920180945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/30/2018] [Indexed: 02/05/2023] Open
Abstract
DNA methylation is essential for spatiotemporally-regulated gene expression in embryonic development. TBX22 (Chr X: 107667964-107688978) functioning as a transcriptional repressor affects DNA binding, sumoylation, and transcriptional repression associated with X-linked cleft palate. This study aimed to explore the relationship and potential mechanism between TBX22 exon 5 methylation and palatal shelf fusion induced by all-trans retinoic acid (ATRA). We performed DNA methylation profiling, using MethylRAD-seq, after high throughput sequencing of mouse embryos from control (n=9) and ATRA-treated (to induce cleft palate, n=9) C57BL/6J mice at embryonic gestation days(E) 13.5, 14.5 and 16.5. TBX22 exon 5 was hyper-methylated at the CpG site at E13.5 (P=0.025, log2FC=1.5) and E14.5 (P=0.011, log2FC:1.5) in ATRA-treated, whereas methylation TBX22 exon 5 at the CpG site was not significantly different at E16.5 (P=0.808, log2FC=-0.2) between control and ATRA-treated. MSP results showed a similar trend consistent with the MethylRAD-seq results. qPCR showed the change in TBX22 exon 5 expression level negatively correlated with its TBX22 exon 5 methylation level. These results indicate that changes in TBX22 exon 5 methylation might play an important regulatory role during palatal shelf fusion, and may enlighten the development of novel epigenetic biomarkers in the treatment of CP in the future.
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Affiliation(s)
- K E Li
- The Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
| | - Xuan Shu
- The Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
| | - Hui Gong
- The Department of Gynaecology, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
| | - Liuhanghang Cheng
- The Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
| | - Zejun Dong
- The Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
| | - Shenyou Shu
- The Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, 69, Dongxia North Road, Jinping District, Shantou, 515041, China
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Daum R, Brauchle EM, Berrio DAC, Jurkowski TP, Schenke-Layland K. Non-invasive detection of DNA methylation states in carcinoma and pluripotent stem cells using Raman microspectroscopy and imaging. Sci Rep 2019; 9:7014. [PMID: 31065074 PMCID: PMC6504883 DOI: 10.1038/s41598-019-43520-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 04/26/2019] [Indexed: 11/09/2022] Open
Abstract
DNA methylation plays a critical role in the regulation of gene expression. Global DNA methylation changes occur in carcinogenesis as well as early embryonic development. However, the current methods for studying global DNA methylation levels are invasive and require sample preparation. The present study was designed to investigate the potential of Raman microspectroscopy and Raman imaging as non-invasive, marker-independent and non-destructive tools for the detection of DNA methylation in living cells. To investigate global DNA methylation changes, human colon carcinoma HCT116 cells, which were hypomorphic for DNA methyltransferase 1, therefore showing a lower global DNA methylation (DNMT1−/− cells), were compared to HCT116 wildtype cells. As a model system for early embryogenesis, murine embryonic stem cells were adapted to serum-free 2i medium, leading to a significant decrease in DNA methylation. Subsequently, 2i medium -adapted cells were compared to cells cultured in serum-containing medium. Raman microspectroscopy and imaging revealed significant differences between high- and low-methylated cell types. Higher methylated cells demonstrated higher relative intensities of Raman peaks, which can be assigned to the nucleobases and 5-methylcytosine. Principal component analysis detected distinguishable populations of high- and low-methylated samples. Based on the provided data we conclude that Raman microspectroscopy and imaging are suitable tools for the real-time, marker-independent and artefact-free investigation of the DNA methylation states in living cells.
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Affiliation(s)
- Ruben Daum
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany.,The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Eva M Brauchle
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany.,The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Daniel Alejandro Carvajal Berrio
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany
| | - Tomasz P Jurkowski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Katja Schenke-Layland
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany. .,The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany. .,Department of Medicine/Cardiology, Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive South, MRL 3645, Los Angeles, CA, USA.
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Kuehner JN, Bruggeman EC, Wen Z, Yao B. Epigenetic Regulations in Neuropsychiatric Disorders. Front Genet 2019; 10:268. [PMID: 31019524 PMCID: PMC6458251 DOI: 10.3389/fgene.2019.00268] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/11/2019] [Indexed: 12/14/2022] Open
Abstract
Precise genetic and epigenetic spatiotemporal regulation of gene expression is critical for proper brain development, function and circuitry formation in the mammalian central nervous system. Neuronal differentiation processes are tightly regulated by epigenetic mechanisms including DNA methylation, histone modifications, chromatin remodelers and non-coding RNAs. Dysregulation of any of these pathways is detrimental to normal neuronal development and functions, which can result in devastating neuropsychiatric disorders, such as depression, schizophrenia and autism spectrum disorders. In this review, we focus on the current understanding of epigenetic regulations in brain development and functions, as well as their implications in neuropsychiatric disorders.
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Affiliation(s)
- Janise N Kuehner
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Emily C Bruggeman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States.,Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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Li Y, Zhang L, Li Y, Li W, Guo Z, Li R, Hu X, Bao Z, Wang S. Dynamics of DNA Methylation and DNMT Expression During Gametogenesis and Early Development of Scallop Patinopecten yessoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:196-205. [PMID: 30680591 DOI: 10.1007/s10126-018-09871-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
DNA methylation reprograms during gametogenesis and embryo development, which is essential for germ cell specification and genomic imprinting in mammals. Corresponding process remains poorly investigated in molluscs. Here, we examined global DNA methylation level in the gonads of scallop Patinopecten yessoensis during gametogenesis and in embryos/larvae at different stages. DNA methylation level fluctuates during gametogenesis and early development, peaking at proliferative stage of ovary, growing stage of testis, and in blastulae. To understand the mechanisms underlying these changes, we conducted genome-wide characterization of DNMT family and investigated their expression profiles based on transcriptomes and in situ hybridization. Three genes were identified, namely PyDNMT1, PyDNMT2, and PyDNMT3. Expression of PyDnmt3 agrees with DNA methylation level during oogenesis and early development, suggesting PyDNMT3 may participate in de novo DNA methylation that occurs mainly at proliferative stage of ovary and testis, and in blastulae and gastrulae. PyDnmt1 expression is positively correlated with DNA methylation level during spermatogenesis, and is higher at maturation stage of ovary and in 2-8 cell embryos than other stages, implying possible involvement of PyDNMT1 in DNA methylation maintenance during meiosis and embryonic development. This study will facilitate better understanding of the developmental epigenetic reprogramming in bivalve molluscs.
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Affiliation(s)
- Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Yajuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Wanru Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Zhenyi Guo
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Ruojiao Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China.
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Kwon J, Li YH, Jo YJ, Oh Y, Namgoong S, Kim NH. Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes. PeerJ 2019; 6:e5840. [PMID: 30643672 PMCID: PMC6327883 DOI: 10.7717/peerj.5840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/28/2018] [Indexed: 02/06/2023] Open
Abstract
Inhibition of both MEK1/2 and glycogen synthase kinase-3 (GSK3; 2i system) facilitates the maintenance of naïve stemness for embryonic stem cells in various mammalian species. However, the effect of the inhibition of the 2i system on porcine early embryogenesis is unknown. We investigated the effect of the 2i system on early embryo development, expression of pluripotency-related genes, and epigenetic modifications. Inhibition of MEK1/2 (by PD0325901) and/or GSK3 (by CHIR99021) did not alter the developmental potential of porcine parthenogenetic embryos, but improved blastocyst quality, as judged by the blastocyst cell number, diameter, and reduction in the number of apoptotic cells. The expression levels of octamer-binding transcription factor 4 and SOX2, the primary transcription factors that maintain embryonic pluripotency, were significantly increased by 2i treatments. Epigenetic modification-related gene expression was altered upon 2i treatment. The collective results indicate that the 2i system in porcine embryos improved embryo developmental potential and blastocyst quality by regulating epigenetic modifications and pluripotency-related gene expression.
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Affiliation(s)
- Jeongwoo Kwon
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungcheongbuk-do, Republic of Korea
| | - Ying-Hua Li
- Department of Animal Sciences, Agricultural College, Yanbian University, Yanji, China
| | - Yu-Jin Jo
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungcheongbuk-do, Republic of Korea
| | - YoungJin Oh
- Genetic Engineering, Cheongchungbuk-do Veterinary Service Laboratory, Cheongju, Cheongchungbuk-do, Republic of Korea
| | - Suk Namgoong
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungcheongbuk-do, Republic of Korea
| | - Nam-Hyung Kim
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungcheongbuk-do, Republic of Korea
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Shu X, Dong Z, Cheng L, Shu S. DNA hypermethylation of Fgf16 and Tbx22 associated with cleft palate during palatal fusion. J Appl Oral Sci 2019; 27:e20180649. [PMID: 31596367 PMCID: PMC6768118 DOI: 10.1590/1678-7757-2018-0649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/17/2019] [Accepted: 03/12/2019] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Cleft palate (CP) is a congenital birth defect caused by the failure of palatal fusion. Little is known about the potential role of DNA methylation in the pathogenesis of CP. This study aimed to explore the potential role of DNA methylation in the mechanism of CP. METHODOLOGY We established an all-trans retinoic acid (ATRA)-induced CP model in C57BL/6J mice and used methylation-dependent restriction enzymes (MethylRAD, FspEI) combined with high-throughput sequencing (HiSeq X Ten) to compare genome-wide DNA methylation profiles of embryonic mouse palatal tissues, between embryos from ATRA-treated vs. untreated mice, at embryonic gestation day 14.5 (E14.5) (n=3 per group). To confirm differentially methylated levels of susceptible genes, real-time quantitative PCR (qPCR) was used to correlate expression of differentially methylated genes related to CP. RESULTS We identified 196 differentially methylated genes, including 17,298 differentially methylated CCGG sites between ATRA-treated vs. untreated embryonic mouse palatal tissues (P<0.05, log2FC>1). The CP-related genes Fgf16 (P=0.008, log2FC=1.13) and Tbx22 (P=0.011, log2FC=1.64,) were hypermethylated. Analysis of Fgf16 and Tbx22, using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), identified 3 GO terms and 1 KEGG pathway functionally related to palatal fusion. The qPCR showed that changes in expression level negatively correlated with methylation levels. CONCLUSIONS Taken together, these results suggest that hypermethylation of Fgf16 and Tbx22 is associated with decreased gene expression, which might be responsible for developmental failure of palatal fusion, eventually resulting in the formation of CP.
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Affiliation(s)
- Xuan Shu
- Second Affiliated Hospital of Shantou University Medical College, Cleft Lip and Palate Treatment Center, Shantou, Guangdong, China
| | - Zejun Dong
- Second Affiliated Hospital of Shantou University Medical College, Cleft Lip and Palate Treatment Center, Shantou, Guangdong, China
| | - Liuhanghang Cheng
- Second Affiliated Hospital of Shantou University Medical College, Cleft Lip and Palate Treatment Center, Shantou, Guangdong, China
| | - Shenyou Shu
- Second Affiliated Hospital of Shantou University Medical College, Cleft Lip and Palate Treatment Center, Shantou, Guangdong, China
- Corresponding address: Shenyou Shu Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College 69 Dongxia North Road, Jinping District, Shantou 515041 - China. Phone: +86-18023235288 - Fax: +86-0754-83141156 e-mail:
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Marshall KL, Wang J, Ji T, Rivera RM. The effects of biological aging on global DNA methylation, histone modification, and epigenetic modifiers in the mouse germinal vesicle stage oocyte. Anim Reprod 2018; 15:1253-1267. [PMID: 34221140 PMCID: PMC8203117 DOI: 10.21451/1984-3143-ar2018-0087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A cultural trend in developed countries is favoring a delay in maternal age at first childbirth.
In mammals fertility and chronological age show an inverse correlation. Oocyte quality is
a contributing factor to this multifactorial phenomenon that may be influenced by age-related
changes in the oocyte epigenome. Based on previous reports, we hypothesized that advanced
maternal age would lead to alterations in the oocyte’s epigenome. We tested our hypothesis
by determining protein levels of various epigenetic modifications and modifiers in fully-grown
(≥70 µm), germinal vesicle (GV) stage oocytes of young (10-13 weeks) and aged
(69-70 weeks) mice. Our results demonstrate a significant increase in protein amounts of
the maintenance DNA methyltransferase DNMT1 (P = 0.003) and a trend toward increased global
DNA methylation (P = 0.09) with advanced age. MeCP2, a methyl DNA binding domain protein, recognizes
methylated DNA and induces chromatin compaction and silencing. We hypothesized that chromatin
associated MeCP2 would be increased similarly to DNA methylation in oocytes of aged female
mice. However, we detected a significant decrease (P = 0.0013) in protein abundance of MeCP2
between GV stage oocytes from young and aged females. Histone posttranslational modifications
can also alter chromatin conformation. Di-methylation of H3K9 (H3K9me2) is associated with
permissive heterochromatin while acetylation of H4K5 (H4K5ac) is associated with euchromatin.
Our results indicate a trend toward decreasing H3K9me2 (P = 0.077) with advanced female age
and no significant differences in levels of H4K5ac. These data demonstrate that physiologic
aging affects the mouse oocyte epigenome and provide a better understanding of the mechanisms
underlying the decrease in oocyte quality and reproductive potential of aged females.
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Affiliation(s)
- Kira Lynn Marshall
- Division of Animal Sciences.,Reproductive Sciences, San Diego Zoo Global Institute for Conservation Research, San Pasqual Valley Rd
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Ben Maamar M, Nilsson E, Sadler-Riggleman I, Beck D, McCarrey JR, Skinner MK. Developmental origins of transgenerational sperm DNA methylation epimutations following ancestral DDT exposure. Dev Biol 2018; 445:280-293. [PMID: 30500333 DOI: 10.1016/j.ydbio.2018.11.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/01/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
Abstract
Epigenetic alterations in the germline can be triggered by a number of different environmental factors from diet to toxicants. These environmentally induced germline changes can promote the epigenetic transgenerational inheritance of disease and phenotypic variation. In previous studies, the pesticide DDT was shown to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs), also called epimutations, which can in part mediate this epigenetic inheritance. In the current study, the developmental origins of the transgenerational DMRs during gametogenesis have been investigated. Male control and DDT lineage F3 generation rats were used to isolate embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, adult pachytene spermatocytes, round spermatids, caput epididymal spermatozoa, and caudal sperm. The DMRs between the control versus DDT lineage samples were determined at each developmental stage. The top 100 statistically significant DMRs at each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed. The chromosomal locations and genomic features of the different stage DMRs were analyzed. Although previous studies have demonstrated alterations in the DMRs of primordial germ cells (PGCs), the majority of the DMRs identified in the caudal sperm originated during the spermatogonia stages in the testis. Interestingly, a cascade of epigenetic alterations initiated in the PGCs is required to alter the epigenetic programming during spermatogenesis to obtain the sperm epigenetics involved in the epigenetic transgenerational inheritance phenomenon.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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Abstract
Epigenetics can be explored at different levels and can be divided into two major areas: epigenetics of nuclear-encoded DNA and epigenetics of mitochondrial-encoded DNA. In epigenetics of nuclear-encoded DNA, the main roles are played by DNA methylation, changes in histone structure and several types of non-coding RNAs. Mitochondrial epigenetics seems to be similar in the aspect of DNA methylation and to some extent in the role of non-coding RNAs but differs significantly in changes in components coiling DNA. Nuclear DNA is coiled around histones, but mitochondrial DNA, together with associated proteins, is located in mitochondrial pseudocompartments called nucleoids. It has been shown that mitochondrial epigenetic mechanisms influence cell fate, transcription regulation, cell division, cell cycle, physiological homeostasis, bioenergetics and even pathologies, but not all of these mechanisms have been explored in stem cells. The main issue is that most of these mechanisms have only recently been discovered in mitochondria, while improvements in methodology, especially next-generation sequencing, have enabled in-depth studies. Because studies exploring mitochondria from other aspects show that mitochondria are crucial for the normal behavior of stem cells, it is suggested that precise mitochondrial epigenetics in stem cells should be studied more intensively.
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de Barros FRO, Paula-Lopes FF. Cellular and epigenetic changes induced by heat stress in bovine preimplantation embryos. Mol Reprod Dev 2018; 85:810-820. [DOI: 10.1002/mrd.23040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 06/26/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Flavia R. O. de Barros
- Department of Biological Sciences; Federal University of São Paulo; São Paulo Brazil
- School of Bioprocess Engineering and Biotechnology, Federal University of Technology; Parana Brazil
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Shu X, Shu S, Zhai Y, Zhu L, Ouyang Z. Genome-Wide DNA Methylation Profile of Gene cis-Acting Element Methylations in All-trans Retinoic Acid-Induced Mouse Cleft Palate. DNA Cell Biol 2018; 37:993-1002. [PMID: 30277813 DOI: 10.1089/dna.2018.4369] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
DNA methylation epigenetically regulates gene expression. This study is aimed to investigate genome-wide DNA methylations involved in the regulation of palatal fusion in the all-trans retinoic acid-induced mouse cleft palate model. There were 4,718,556 differentially CCGG methylated sites and 367,504 CCWGG methylated sites for 1497 genes between case and control embryonic mouse palatal tissues. The enhancers (HDAC4 and SMAD3) and promoter (MID1) of these three genes had cis-acting element methylation. HDAC4 is localized within the CCWGG, while MID1 and SMAD3 are localized within the CCGG of the gene intron. The methylation-specific polymerase chain reaction data confirmed the MethylRAD-seq results, while the quantitative reverse transcriptase-polymerase chain reaction result showed that changes in gene expression inversely were associated with the cis-acting element methylation of the gene during retinoic acid-induced palatal fusion. The GO and KEGG data showed that these three genes could regulate cell proliferation, skeletal muscle fiber development, and development-related gene signaling or activity. The cis-acting element methylation of HDAC4, SMAD3, and MID1 may play a regulatory role during palatal fusion. Further research is needed to verify these novel epigenetic biomarkers for cleft palate.
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Affiliation(s)
- Xuan Shu
- The Cleft Lip and Palate Treatment Center, The Second Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Shenyou Shu
- The Cleft Lip and Palate Treatment Center, The Second Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Yuxia Zhai
- The Cleft Lip and Palate Treatment Center, The Second Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Lin Zhu
- The Cleft Lip and Palate Treatment Center, The Second Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Zhan Ouyang
- The Cleft Lip and Palate Treatment Center, The Second Affiliated Hospital of Shantou University Medical College , Shantou, China
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Umezawa M, Onoda A, Korshunova I, Jensen ACØ, Koponen IK, Jensen KA, Khodosevich K, Vogel U, Hougaard KS. Maternal inhalation of carbon black nanoparticles induces neurodevelopmental changes in mouse offspring. Part Fibre Toxicol 2018; 15:36. [PMID: 30201004 PMCID: PMC6131790 DOI: 10.1186/s12989-018-0272-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/24/2018] [Indexed: 02/07/2023] Open
Abstract
Background Engineered nanoparticles are smaller than 100 nm and designed to improve or creating even new physico-chemical properties. Consequently, toxicological properties of materials may change as size reaches the nm size-range. We examined outcomes related to the central nervous system in the offspring following maternal inhalation exposure to nanosized carbon black particles (Printex 90). Methods Time-mated mice (NMRI) were exposed by inhalation, for 45 min/day to 0, 4.6 or 37 mg/m3 aerosolized carbon black on gestation days 4–18, i.e. for a total of 15 days. Outcomes included maternal lung inflammation (differential cell count in bronchoalveolar lavage fluid and Saa3 mRNA expression in lung tissue), offspring neurohistopathology and behaviour in the open field test. Results Carbon black exposure did not cause lung inflammation in the exposed females, measured 11 or 28–29 days post-exposure. Glial fibrillary acidic protein (GFAP) expression levels were dose-dependently increased in astrocytes around blood vessels in the cerebral cortex and hippocampus in six weeks old offspring, indicative of reactive astrogliosis. Also enlarged lysosomal granules were observed in brain perivascular macrophages (PVMs) in the prenatally exposed offspring. The number of parvalbumin-positive interneurons and the expression levels of parvalbumin were decreased in the motor and prefrontal cortices at weaning and 120 days of age in the prenatally exposed offspring. In the open field test, behaviour was dose-dependently altered following maternal exposure to Printex 90, at 90 days of age. Prenatally exposed female offspring moved a longer total distance, and especially males spent significantly longer time in the central zone of the maze. In the offspring, the described effects were long-lasting as they were present at all time points investigated. Conclusion The present study reports for the first time that maternal inhalation exposure to Printex 90 carbon black induced dose-dependent denaturation of PVM and reactive astrocytes, similarly to the findings observed following maternal exposure to Printex 90 by airway instillation. Of note, some of the observed effects have striking similarities with those observed in mouse models of neurodevelopmental disorders. Electronic supplementary material The online version of this article (10.1186/s12989-018-0272-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Masakazu Umezawa
- Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Chiba, Japan.,Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Katsushika, Tokyo, Japan
| | - Atsuto Onoda
- Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Chiba, Japan.,Department of Hygienic Chemistry, Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, Japan.,Japan Society for the Promotion of Science, Chiyoda, Tokyo, 102-0083, Japan
| | - Irina Korshunova
- Biotech Research and Innovation Centre (BRIC), Faculty of Health, University of Copenhagen, Copenhagen K, Denmark
| | - Alexander C Ø Jensen
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen Ø, Denmark
| | - Ismo K Koponen
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen Ø, Denmark
| | - Keld A Jensen
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen Ø, Denmark
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), Faculty of Health, University of Copenhagen, Copenhagen K, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen Ø, Denmark.,Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - Karin S Hougaard
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen Ø, Denmark. .,Institute of Public Health, University of Copenhagen, Copenhagen K, Denmark.
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Zhu X, Wang Y, Tan L, Fu X. The pivotal role of DNA methylation in the radio-sensitivity of tumor radiotherapy. Cancer Med 2018; 7:3812-3819. [PMID: 29952116 PMCID: PMC6089158 DOI: 10.1002/cam4.1614] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/15/2018] [Accepted: 05/21/2018] [Indexed: 12/23/2022] Open
Abstract
Radiotherapy is an important modality for treatment of carcinomas; however, radio‐resistance is still a difficult problem. Aberrant epigenetic alterations play an important role in cancer development. Among epigenetic parameters, DNA methylation has arguably attracted the most attention in the radio‐resistance process. To determine the role of DNA methylation in radiation resistance, several studies were conducted. We summarized previous studies on the role of DNA methylation in radiotherapy. We observed this significant role of DNA methylation in genes related to DNA repair, cell proliferation, cell cycle process, and re‐oxygenation. Furtherly, we also conclude the predictive effect of DNA methylation on tumor radio‐sensitivity and the using of DNA methyltransferase inhibitors in clinical practice. DNA methylation plays a pivotal role in the radio‐sensitivity of tumor radio‐therapy. While hyper‐methylation or hypo‐methylation of genes is related to gene functions.
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Affiliation(s)
- Xueru Zhu
- Department of Radiation Oncology, Shanghai Jiao Tong University Affiliated Chest Hospital, Shanghai, China
| | - Yiting Wang
- Department of Radiation Oncology, Shanghai Jiao Tong University Affiliated Chest Hospital, Shanghai, China
| | - Li Tan
- Department of Cellular and Genetic Medicine, Fudan University School of Basic Medical Sciences, Shanghai, China
| | - Xiaolong Fu
- Department of Radiation Oncology, Shanghai Jiao Tong University Affiliated Chest Hospital, Shanghai, China
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Johnson JP, Beischel L, Schwanke C, Styren K, Crunk A, Schoof J, Elias AF. Overrepresentation of pregnancies conceived by artificial reproductive technology in prenatally identified fetuses with Beckwith-Wiedemann syndrome. J Assist Reprod Genet 2018; 35:985-992. [PMID: 29936652 DOI: 10.1007/s10815-018-1228-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 05/28/2018] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVES In vitro fertilization (IVF) has been linked to an increased risk for imprinting disorders in offspring. The data so far have predominantly been retrospective, comparing the rate of IVF conceptions in affected patients with controls. We describe a series of fetuses with omphalocele that were tested for Beckwith-Wiedemann syndrome (BWS) and subsequently ascertained as to whether pregnancies were conceived by assisted reproductive technologies (ART). METHODS Fetuses were tested for BWS by Southern blot, PCR based methods, and methylation analysis to identify the imprinting status at primarily the IC2 locus, KCNQ1OT1, as well as IC1, H19/IGF-2. Some fetuses were also tested for uniparental disomy of chromosome 11p. RESULTS We tested 301 fetuses with omphalocele for BWS. Forty samples were positive. Sixteen were from IVF pregnancies, for an overall rate of 40%. Such as high proportion of IVF pregnancies in a series of BWS-positive fetuses has not been described previously. Possible factors such as twinning and ascertainment bias are discussed. CONCLUSION We found about a 20-fold overrepresentation of IVF cases in fetuses with BWS/omphalocele when compared with the rate of ART pregnancies in the USA (p < .0001). Our series provides support for an association of IVF and BWS. Patients should be counseled about these risks and made aware of the availability of prenatal diagnosis for detection.
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Affiliation(s)
- John P Johnson
- Department of Medical Genetics, Shodair Children's Hospital, PO Box 5539, Helena, MT, 59604-5539, USA
| | - Linda Beischel
- Montana Department of Public Health and Human Services, Helena, MT, USA
| | - Corbin Schwanke
- Department of Medical Genetics, Shodair Children's Hospital, PO Box 5539, Helena, MT, 59604-5539, USA
| | - Katie Styren
- Department of Medical Genetics, Shodair Children's Hospital, PO Box 5539, Helena, MT, 59604-5539, USA
| | | | - Jonathan Schoof
- Department of Medical Genetics, Shodair Children's Hospital, PO Box 5539, Helena, MT, 59604-5539, USA
| | - Abdallah F Elias
- Department of Medical Genetics, Shodair Children's Hospital, PO Box 5539, Helena, MT, 59604-5539, USA.
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Joh K, Matsuhisa F, Kitajima S, Nishioka K, Higashimoto K, Yatsuki H, Kono T, Koseki H, Soejima H. Growing oocyte-specific transcription-dependent de novo DNA methylation at the imprinted Zrsr1-DMR. Epigenetics Chromatin 2018; 11:28. [PMID: 29875017 PMCID: PMC5989421 DOI: 10.1186/s13072-018-0200-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/31/2018] [Indexed: 12/21/2022] Open
Abstract
Background Zrsr1 is a paternally expressed imprinted gene located in the first intron of Commd1, and the Zrsr1 promoter resides in a differentially methylated region (DMR) that is maternally methylated in the oocyte. However, a mechanism for the establishment of the methylation has remained obscure. Commd1 is transcribed in the opposite direction to Zrsr1 with predominant maternal expression, especially in the adult brain.
Results We found Commed1 transcribed through the DMR in the growing oocyte. Zrsr1-DMR methylation was abolished by the prevention of Commd1 transcription. Furthermore, methylation did not occur at the artificially unmethylated maternal Zrsr1-DMR during embryonic development when transcription through the DMR was restored in the zygote. Loss of methylation at the maternal Zrsr1-DMR resulted in biallelic Zrsr1 expression and reduced the extent of the predominant maternal expression of Commd1. Conclusions These results indicate that the establishment of methylation at Zrsr1-DMR occurs in a transcription-dependent and oocyte-specific manner and caused Zrsr1 imprinting by repressing maternal expression. The predominant maternal expression of Commd1 is likely caused by transcriptional interference by paternal Zrsr1 expression. Electronic supplementary material The online version of this article (10.1186/s13072-018-0200-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiichiro Joh
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan.
| | - Fumikazu Matsuhisa
- Division of Biological Resources and Development, Analytical Research Center for Experimental Sciences, Saga University, Saga, 849-8501, Japan
| | - Shuji Kitajima
- Division of Biological Resources and Development, Analytical Research Center for Experimental Sciences, Saga University, Saga, 849-8501, Japan
| | - Kenichi Nishioka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Hitomi Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Tomohiro Kono
- Laboratory of Animal Developmental Biology, Department of Bioscience, Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan.
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48
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Shu X, Shu S, Cheng H, Tang S, Yang L, Li H, Zhang M, Zhu Z, Liu D, Li K, Dong Z, Cheng L, Ding J. Genome-Wide DNA Methylation Analysis During Palatal Fusion Reveals the Potential Mechanism of Enhancer Methylation Regulating Epithelial Mesenchyme Transformation. DNA Cell Biol 2018; 37:560-573. [PMID: 29608334 DOI: 10.1089/dna.2018.4141] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Epithelial mesenchyme transformation (EMT) of the medial edge epithelium (MEE) is the crucial process during palatal fusion. This work is aimed to elucidate the enhancer regulatory mechanism by genome-wide DNA methylation analysis of EMT during palatal fusion. Over 800 million clean reads, 325 million enzyme reads, and 234 million mapping reads were generated. The mapping rate was 68.85-74.32%, which included differentially methylated 17299 CCGG sites and 2363 CCWGG sites (p < 0.05, log2FC >1). Methylated sites in intron and intergenic regions were more compared to other regions of all DNA elements. GO and KEGG analysis indicated that differential methylation sites related to embryonic palatal fusion genes (HDAC4, TCF7L2, and PDGFRB) at the enhancer were located on CCWGG region of non-CpG islands. In addition, the results showed that the enhancer for HDAC4 was hypermethylated, whereas the enhancers for TCF7L2 and PDGFRB were hypomethylated. The methylation status of enhancer regions of HDAC4, PDGFRB, and TCF7L2, involved in the regulation of the EMT during palatal fusion, may enlighten the development of novel epigenetic biomarkers in the treatment of cleft palate.
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Affiliation(s)
- Xuan Shu
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Shenyou Shu
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Hongqiu Cheng
- 2 Department of Infectious Diseases, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Shijie Tang
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Lujun Yang
- 3 Department of Translational Medicine Center, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Haihong Li
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Mingjun Zhang
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Zhensen Zhu
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Dan Liu
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Ke Li
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Zejun Dong
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Liuhanghang Cheng
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
| | - Jialong Ding
- 1 Department of Burn and Plastic Surgery, 2nd Affiliated Hospital of Shantou University Medical College , Shantou, China
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Ren J, Cheng Y, Ming ZH, Dong XY, Zhou YZ, Ding GL, Pang HY, Rahman TU, Akbar R, Huang HF, Sheng JZ. Intrauterine hyperglycemia exposure results in intergenerational inheritance via DNA methylation reprogramming on F1 PGCs. Epigenetics Chromatin 2018; 11:20. [PMID: 29801514 PMCID: PMC5968593 DOI: 10.1186/s13072-018-0192-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The existing reports about intergenerational or transgenerational effects of intrauterine hyperglycemia have included both intrauterine and postnatal metabolic exposure factors, while the impact of intrauterine hyperglycemia per se has not been assessed alone. A number of studies suggest DNA methylation reprogramming of gametes plays a crucial role in the metabolic inheritance, but it is unclear when and how DNA methylation patterns are altered when exposed to intrauterine hyperglycemia. In this study, we selected nondiabetic F1- and F2-gestational diabetes mellitus (GDM) male mice as founders to examine metabolic changes in the next generation and performed methylome sequencing of day 13.5 primordial germ cells (PGCs) from F1-GDM to explore the underlying epigenetic mechanism. RESULTS We found that intrauterine hyperglycemia exposure resulted in obesity, insulin resistance, and/or glucose intolerance in F2 male mice, but no metabolic changes in F3 male mice at 8 weeks. Using reduced representation bisulfite sequencing, we found DNA methylome of day 13.5 PGCs from F1-GDM fetuses revealed differently methylated genes enriched in obesity and diabetes. Methylation validation of the insulin resistance and fat accumulation gene Fyn showed a consistent hypomethylation status in F1 PGCs, F1 fetal testes, sperm from F1/C-GDM mice, and somatic cells from F2-GDM male mice. In contrast, no methylation alteration was observed in F2-GDM male germ cells and F3-GDM somatic cells. CONCLUSION We provide evidence that intrauterine hyperglycemia exposure per se contributes to intergenerational metabolic changes in the F2 but not F3 generation. And the aberrant DNA methylation reprogramming occurs as early as day 13.5 in PGCs of the F1 generation. Our findings suggest that intrauterine exposure alone is sufficient to cause the epigenetic inheritance in F2 offspring, and the epigenetic memory carried by DNA methylation pattern could be erased by the second wave of methylation reprogramming in F2 PGCs during fetal development.
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Affiliation(s)
- Jun Ren
- Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China.,The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Yi Cheng
- Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China.,The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Zhen-Hua Ming
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China.,Department of Reproductive Endocrinology, Zhejiang Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xin-Yan Dong
- Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China.,The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Yu-Zhong Zhou
- Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China.,The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Guo-Lian Ding
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Yan Pang
- Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China.,The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Tanzil Ur Rahman
- Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China.,The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Rubab Akbar
- Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China.,The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - He-Feng Huang
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China. .,The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian-Zhong Sheng
- Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China. .,The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China.
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50
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The Vast Complexity of the Epigenetic Landscape during Neurodevelopment: An Open Frame to Understanding Brain Function. Int J Mol Sci 2018; 19:ijms19051333. [PMID: 29723958 PMCID: PMC5983638 DOI: 10.3390/ijms19051333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/16/2018] [Accepted: 04/26/2018] [Indexed: 12/31/2022] Open
Abstract
Development is a well-defined stage-to-stage process that allows the coordination and maintenance of the structure and function of cells and their progenitors, in a complete organism embedded in an environment that, in turn, will shape cellular responses to external stimuli. Epigenetic mechanisms comprise a group of process that regulate genetic expression without changing the DNA sequence, and they contribute to the necessary plasticity of individuals to face a constantly changing medium. These mechanisms act in conjunction with genetic pools and their correct interactions will be crucial to zygote formation, embryo development, and brain tissue organization. In this work, we will summarize the main findings related to DNA methylation and histone modifications in embryonic stem cells and throughout early development phases. Furthermore, we will critically outline some key observations on how epigenetic mechanisms influence the rest of the developmental process and how long its footprint is extended from fecundation to adulthood.
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