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Fangninou FF, Yu Z, Li W, Xue L, Yin D. Metastatic effects of perfluorooctanoic acid (PFOA) on Drosophila melanogaster with metabolic reprogramming and dysrhythmia in a multigenerational exposure scenario. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169305. [PMID: 38103603 DOI: 10.1016/j.scitotenv.2023.169305] [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: 07/31/2023] [Revised: 11/27/2023] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
Perfluorooctanoic acid (PFOA) exposure correlated with various cancers and their mortality. Its persistence in the environment made its long-term multigenerational influences of significant concerns. However, it remained unanswered whether its multigenerational exposure could influence metastasis which contributes ~90 % to cancer mortality. In the present study, long-term effects of PFOA were measured in Drosophila melanogaster over 3 consecutive generations. In the morning-eclosed (AM) adult flies, PFOA significantly promoted tumor invasion rates and distances which increased over generations. Regarding metabolic reprogramming, PFOA disturbed the expressions of Glut1 and Pdk1, activities and contents of FASN1 (fatty acid synthase), ACC (acetyl-CoA carboxylase) and SREBP1 (sterol regulatory element binding protein). Regarding antioxidant responses, PFOA exposure generated provoked oxidative stress via H2O2 and stimulated antioxidants including glutathione (GSH), catalase (CAT), melatonin, serotonin and cortisol, with downregulations on PI3K/AKT pathways and upregulations on MAPK ones. The biochemical and molecular effects altered over generations. In the afternoon-eclosed (PM) adult flies, the metastasis of PFOA was more deteriorated than in AM adults. The significant influences of dysrhythmia were also observed in the multigenerational effects of PFOA on the metabolism reprogramming and antioxidant responses. The effects on rhythm-regulating gene expressions and protein levels explained the dysrhythmia and also indicated close interactions among metabolism reprogramming, antioxidant responses and rhythm regulation. ENVIRONMENTAL IMPLICATION: Numerous emerging per- and polyfluoroalkyl substances (PFASs) are being detected. Meanwhile, the toxicities of the emerging PFASs still depend on the progress of legacy PFASs for the continuity of scientific studies. As one legacy PFAS, perfluorooctanoic acid (PFOA) exposure correlated with various cancers and their mortality. Its persistence in the environment made its long-term multigenerational influences of significant concerns. However, it remained unanswered whether its multigenerational exposure could influence metastasis which contributes ~90 % to cancer mortality. The present study performed PFOA exposure for 3 consecutive generations. Results showed that the metastasis by PFOA increased over generations, and it was further deteriorated by dysrhythmia. Further analysis demonstrated the interactive involvement of metabolism reprogramming, antioxidant responses and rhythm regulation. The findings of the present study would highlight considerate points for studying the toxicities of emerging PFASs.
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Affiliation(s)
- Fangnon Firmin Fangninou
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China; Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou 01 BP 526, Benin
| | - Zhenyang Yu
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
| | - Wenzhe Li
- College of Life Science and Technology, Tongji University, Shanghai 200092, PR China
| | - Lei Xue
- College of Life Science and Technology, Tongji University, Shanghai 200092, PR China
| | - Daqiang Yin
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
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Senaldi L, Smith-Raska M. Evidence for germline non-genetic inheritance of human phenotypes and diseases. Clin Epigenetics 2020; 12:136. [PMID: 32917273 PMCID: PMC7488552 DOI: 10.1186/s13148-020-00929-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022] Open
Abstract
It is becoming increasingly apparent that certain phenotypes are inherited across generations independent of the information contained in the DNA sequence, by factors in germ cells that remain largely uncharacterized. As evidence for germline non-genetic inheritance of phenotypes and diseases continues to grow in model organisms, there are fewer reports of this phenomenon in humans, due to a variety of complications in evaluating this mechanism of inheritance in humans. This review summarizes the evidence for germline-based non-genetic inheritance in humans, as well as the significant challenges and important caveats that must be considered when evaluating this process in human populations. Most reports of this process evaluate the association of a lifetime exposure in ancestors with changes in DNA methylation or small RNA expression in germ cells, as well as the association between ancestral experiences and the inheritance of a phenotype in descendants, down to great-grandchildren in some cases. Collectively, these studies provide evidence that phenotypes can be inherited in a DNA-independent manner; the extent to which this process contributes to disease development, as well as the cellular and molecular regulation of this process, remain largely undefined.
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Affiliation(s)
- Liana Senaldi
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Matthew Smith-Raska
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA. .,Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA.
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3
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Wylde Z, Spagopoulou F, Hooper AK, Maklakov AA, Bonduriansky R. Parental breeding age effects on descendants' longevity interact over 2 generations in matrilines and patrilines. PLoS Biol 2019; 17:e3000556. [PMID: 31765371 PMCID: PMC6901263 DOI: 10.1371/journal.pbio.3000556] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 12/09/2019] [Accepted: 11/07/2019] [Indexed: 01/09/2023] Open
Abstract
Individuals within populations vary enormously in mortality risk and longevity, but the causes of this variation remain poorly understood. A potentially important and phylogenetically widespread source of such variation is maternal age at breeding, which typically has negative effects on offspring longevity. Here, we show that paternal age can affect offspring longevity as strongly as maternal age does and that breeding age effects can interact over 2 generations in both matrilines and patrilines. We manipulated maternal and paternal ages at breeding over 2 generations in the neriid fly Telostylinus angusticollis. To determine whether breeding age effects can be modulated by the environment, we also manipulated larval diet and male competitive environment in the first generation. We found separate and interactive effects of parental and grand-parental ages at breeding on descendants' mortality rate and life span in both matrilines and patrilines. These breeding age effects were not modulated by grand-parental larval diet quality or competitive environment. Our findings suggest that variation in maternal and paternal ages at breeding could contribute substantially to intrapopulation variation in mortality and longevity.
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Affiliation(s)
- Zachariah Wylde
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Foteini Spagopoulou
- Uppsala Centre for Evolution and Genomics, Uppsala University, Uppsala, Sweden
| | - Amy K. Hooper
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Alexei A. Maklakov
- Uppsala Centre for Evolution and Genomics, Uppsala University, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
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Loza-Coll MA, Petrossian CC, Boyle ML, Jones DL. Heterochromatin Protein 1 (HP1) inhibits stem cell proliferation induced by ectopic activation of the Jak/STAT pathway in the Drosophila testis. Exp Cell Res 2019; 377:1-9. [PMID: 30817931 DOI: 10.1016/j.yexcr.2019.02.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/22/2019] [Accepted: 02/24/2019] [Indexed: 11/18/2022]
Abstract
Stem cells can divide asymmetrically with respect to cell fate, producing a copy of themselves (self-renewal), while giving rise to progeny that will differentiate along a specific lineage. Mechanisms that bias the balance towards self-renewal or extend the proliferative capacity of the differentiating progeny can result in tissue overgrowth and, eventually, the formation of tumors. Recent work has explored the role of heterochromatin and heterochromatin-associated proteins in the regulation of stem cell behavior under homeostatic conditions, but less is known about their possible roles in potentiating or suppressing stem cell overproliferation. Here we used ectopic activation of the Jak/STAT pathway in germline and somatic stem cells of the D. melanogaster testis as an in vivo model to probe the function of Heterochromatin Protein 1 (HP1) in stem cell overproliferation. Forced expression of HP1 in either early germ or somatic cells suppressed the overgrowth of testes in response to ectopic Jak/STAT activation. Interestingly, HP1 expression led to distinct phenotypes, depending on whether it was overexpressed in somatic or germ cells, possibly reflecting different cell-autonomous and non-autonomous effects in each cell type. Our results provide a new framework for further in vivo studies aimed at understanding the interactions between heterochromatin and uncontrolled stem cell proliferation, as well as the complex cross-regulatory interactions between the somatic and germline lineages in the Drosophila testis.
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Affiliation(s)
| | | | | | - D Leanne Jones
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
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5
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Bantz A, Camon J, Froger JA, Goven D, Raymond V. Exposure to sublethal doses of insecticide and their effects on insects at cellular and physiological levels. CURRENT OPINION IN INSECT SCIENCE 2018; 30:73-78. [PMID: 30553488 DOI: 10.1016/j.cois.2018.09.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/18/2018] [Accepted: 09/21/2018] [Indexed: 06/09/2023]
Abstract
Insecticides were used as pest management tools for a long time. The appearance of resistant insects has led the scientific community to rethink their use and to study the mechanisms underlying the resistance in order to circumvent it. However, we know now that sublethal doses of insecticide induce many effects which should be taken into account for pest control. In this review, we summarized current knowledge on mechanisms used by insects to deal with exposure to sublethal dose of insecticides. Physiological and cellular changes could contribute to the adaptation of the insect to its environment making the challenge of managing pests difficult.
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Affiliation(s)
- Alexandre Bantz
- Laboratoire « Signalisation Fonctionnelle des Canaux Ioniques et Récepteurs » (SiFCIR), UPRES-EA2647 USC INRA 1330, SFR 4207 QUASAV, UFR Sciences, Université d'Angers, 2 Bld Lavoisier, 49045 Angers Cedex 01, France
| | - Jérémy Camon
- Laboratoire « Signalisation Fonctionnelle des Canaux Ioniques et Récepteurs » (SiFCIR), UPRES-EA2647 USC INRA 1330, SFR 4207 QUASAV, UFR Sciences, Université d'Angers, 2 Bld Lavoisier, 49045 Angers Cedex 01, France
| | - Josy-Anne Froger
- Laboratoire « Signalisation Fonctionnelle des Canaux Ioniques et Récepteurs » (SiFCIR), UPRES-EA2647 USC INRA 1330, SFR 4207 QUASAV, UFR Sciences, Université d'Angers, 2 Bld Lavoisier, 49045 Angers Cedex 01, France
| | - Delphine Goven
- Laboratoire « Signalisation Fonctionnelle des Canaux Ioniques et Récepteurs » (SiFCIR), UPRES-EA2647 USC INRA 1330, SFR 4207 QUASAV, UFR Sciences, Université d'Angers, 2 Bld Lavoisier, 49045 Angers Cedex 01, France
| | - Valérie Raymond
- Laboratoire « Signalisation Fonctionnelle des Canaux Ioniques et Récepteurs » (SiFCIR), UPRES-EA2647 USC INRA 1330, SFR 4207 QUASAV, UFR Sciences, Université d'Angers, 2 Bld Lavoisier, 49045 Angers Cedex 01, France.
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Abstract
Gametogenesis represents the most dramatic cellular differentiation pathways in both female and male flies. At the genome level, meiosis ensures that diploid germ cells become haploid gametes. At the epigenome level, extensive changes are required to turn on and shut off gene expression in a precise spatiotemporally controlled manner. Research applying conventional molecular genetics and cell biology, in combination with rapidly advancing genomic tools have helped us to investigate (1) how germ cells maintain lineage specificity throughout their adult reproductive lifetime; (2) what molecular mechanisms ensure proper oogenesis and spermatogenesis, as well as protect genome integrity of the germline; (3) how signaling pathways contribute to germline-soma communication; and (4) if such communication is important. In this chapter, we highlight recent discoveries that have improved our understanding of these questions. On the other hand, restarting a new life cycle upon fertilization is a unique challenge faced by gametes, raising questions that involve intergenerational and transgenerational epigenetic inheritance. Therefore, we also discuss new developments that link changes during gametogenesis to early embryonic development-a rapidly growing field that promises to bring more understanding to some fundamental questions regarding metazoan development.
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Krüppel homolog 1 represses insect ecdysone biosynthesis by directly inhibiting the transcription of steroidogenic enzymes. Proc Natl Acad Sci U S A 2018; 115:3960-3965. [PMID: 29567866 DOI: 10.1073/pnas.1800435115] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In insects, juvenile hormone (JH) and the steroid hormone ecdysone have opposing effects on regulation of the larval-pupal transition. Although increasing evidence suggests that JH represses ecdysone biosynthesis during larval development, the mechanism underlying this repression is not well understood. Here, we demonstrate that the expression of the Krüppel homolog 1 (Kr-h1), a gene encoding a transcription factor that mediates JH signaling, in ecdysone-producing organ prothoracic gland (PG) represses ecdysone biosynthesis by directly inhibiting the transcription of steroidogenic enzymes in both Drosophila and Bombyx Application of a JH mimic on ex vivo cultured PGs from Drosophila and Bombyx larvae induces Kr-h1 expression and inhibits the transcription of steroidogenic enzymes. In addition, PG-specific knockdown of Drosophila Kr-h1 promotes-while overexpression hampers-ecdysone production and pupariation. We further find that Kr-h1 inhibits the transcription of steroidogenic enzymes by directly binding to their promoters to induce promoter DNA methylation. Finally, we show that Kr-h1 does not affect DNA replication in Drosophila PG cells and that the reduction of PG size mediated by Kr-h1 overexpression can be rescued by feeding ecdysone. Taken together, our data indicate direct and conserved Kr-h1 repression of insect ecdysone biosynthesis in response to JH stimulation, providing insights into mechanisms underlying the antagonistic roles of JH and ecdysone.
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8
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Latchney SE, Fields AM, Susiarjo M. Linking inter-individual variability to endocrine disruptors: insights for epigenetic inheritance. Mamm Genome 2018; 29:141-152. [PMID: 29218402 PMCID: PMC5849504 DOI: 10.1007/s00335-017-9729-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/02/2017] [Indexed: 01/11/2023]
Abstract
Endocrine disrupting chemicals (EDCs) can induce a myriad of adverse health effects. An area of active investigation is the multi- and transgenerational inheritance of EDC-induced adverse health effects referring to the transmission of phenotypes across multiple generations via the germline. The inheritance of EDC-induced adverse health effects across multiple generations can occur independent of genetics, spurring much research into the transmission of underlying epigenetic mechanisms. Epigenetic mechanisms play important roles in the development of an organism and are responsive to environmental exposures. To date, rodent studies have demonstrated that acquired epigenetic marks, particularly DNA methylation, that are inherited following parental EDC exposure can escape embryonic epigenome reprogramming. The acquired epimutations can lead to subsequent adult-onset diseases. Increasing studies have reported inter-individual variations that occur with epigenetic inheritance. Factors that underlie differences among individuals could reveal previously unidentified mechanisms of epigenetic transmission. In this review, we give an overview of DNA methylation and posttranslational histone modification as the potential mechanisms for disease transmission, and define the requirements for multi- and transgenerational epigenetic inheritance. We subsequently evaluate rodent studies investigating how acquired changes in epigenetic marks especially DNA methylation across multiple generations can vary among individuals following parental EDC exposure. We also discuss potential sources of inter-individual variations and the challenges in identifying these variations. We conclude our review discussing the challenges in applying rodent generational studies to humans.
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Affiliation(s)
- Sarah E Latchney
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Ashley M Fields
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Martha Susiarjo
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
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Sarkar S, Roy S. Flubendiamide induces transgenerational compound eye alterations in Drosophila melanogaster. Interdiscip Toxicol 2017; 10:142-147. [PMID: 30147421 PMCID: PMC6102675 DOI: 10.1515/intox-2017-0020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 10/22/2017] [Indexed: 12/12/2022] Open
Abstract
Pesticides are one of the major sources of environmental toxicity and contamination. This study reports potential of lepidopteran insecticide formulation, named Flubendiamide, in altering compound eye architecture and bristle pattern orientation for four consecutive generations (P, F1, F2 and F3) in a non-target diptera, Drosophila melanogaster Meigen (Diptera: Drosophilidae). The concentrations of the insecticide formulation selected for treatment of Drosophila (50 and 100 μg/mL) were in accordance with practiced Indian field doses (50 μg/mL for rice and 100 μg/mL for cotton). This study showed trans-generational insecticide-induced changes in the morphology of the compound eyes of the non-target insect D. melanogaster.
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Affiliation(s)
- Saurabh Sarkar
- Toxicology Research Unit, Cytogenetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, India
| | - Sumedha Roy
- Toxicology Research Unit, Cytogenetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, India
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Sarkar S, Khatun S, Dutta M, Roy S. Trans-generational transmission of altered phenotype resulting from flubendiamide-induced changes in apoptosis in larval imaginal discs of Drosophila melanogaster. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2017; 56:350-360. [PMID: 29121551 DOI: 10.1016/j.etap.2017.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 06/07/2023]
Abstract
The eye and wing morphology of Drosophila melanogaster maintain unique, stable pattern of genesis from larval eye and wing imaginal discs. Increased apoptosis in cells of eye and wing discs was found to be associated with flubendiamide (fluoride containing insecticide) exposure (at the range 0.25-10μg/mL) in D. melanogaster larvae. The chemical fed larvae on attaining adulthood revealed alterations in morphology and symmetry of their compound eyes and wings through scanning electron microscopy. Nearly 40% and 30% of flies (P generation) demonstrated alterations in eyes and wings respectively. Transmission electron microscopic study (at the range 1-20μg/mL) also established variation in the rhabdomere and pigment cell orientation as well as in the shape of the ommatidium. Subsequent SEM study with F1 and F2 generation flies also revealed structural variation in eye and wing. Decrease in percentage of altered eye and wing phenotype was noted in subsequent generations (P> F1>F2). Thus, the diamide insecticide, flubendiamide, expected to be environmentally safe at sub-lethal concentrations was found to increase apoptosis in larvae and thereby cause morphological alteration in the adult D. melanogaster. This study further demonstrated trans-generational transmission of altered phenotype in three subsequent generations of a non-target insect model, D. melanogaster.
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Affiliation(s)
- Saurabh Sarkar
- Toxicology Research Unit, Cytogenetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, 713104, India
| | - Salma Khatun
- Toxicology Research Unit, Cytogenetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, 713104, India
| | - Moumita Dutta
- Toxicology Research Unit, Cytogenetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, 713104, India
| | - Sumedha Roy
- Toxicology Research Unit, Cytogenetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, 713104, India.
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11
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Ciabrelli F, Comoglio F, Fellous S, Bonev B, Ninova M, Szabo Q, Xuéreb A, Klopp C, Aravin A, Paro R, Bantignies F, Cavalli G. Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila. Nat Genet 2017; 49:876-886. [PMID: 28436983 PMCID: PMC5484582 DOI: 10.1038/ng.3848] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/27/2017] [Indexed: 12/15/2022]
Abstract
Transgenerational Epigenetic Inheritance (TEI) studies the transmission of alternative functional states through multiple generations in the presence of the same genomic DNA sequence. Very little is known on the principles and the molecular mechanisms governing this type of inheritance. Here, by transiently enhancing 3D chromatin interactions, we established stable and isogenic Drosophila epilines that carry alternative epialleles, defined by differential levels of the Polycomb-dependent H3K27me3 mark. Once established, epialleles can be dominantly transmitted to naïve flies and induce paramutation. Importantly, epilines can be reset to a naïve state by disrupting chromatin interactions. Finally, we show that environmental changes can modulate the expressivity of the epialleles and we extend our paradigm to naturally occurring phenotypes. Our work sheds light on how nuclear organization and Polycomb group proteins contribute to epigenetically inheritable phenotypic variability.
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Affiliation(s)
- Filippo Ciabrelli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Boyan Bonev
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Maria Ninova
- Division of Biology, California Institute of Technology, Pasadena, California, USA
| | - Quentin Szabo
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | | | - Christophe Klopp
- Unité de Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet Tolosan, France
| | - Alexei Aravin
- Division of Biology, California Institute of Technology, Pasadena, California, USA
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
| | - Frédéric Bantignies
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
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12
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Banlaki Z, Cimarelli G, Viranyi Z, Kubinyi E, Sasvari-Szekely M, Ronai Z. DNA methylation patterns of behavior-related gene promoter regions dissect the gray wolf from domestic dog breeds. Mol Genet Genomics 2017; 292:685-697. [DOI: 10.1007/s00438-017-1305-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 03/02/2017] [Indexed: 12/26/2022]
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13
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McCarrey JR, Lehle JD, Raju SS, Wang Y, Nilsson EE, Skinner MK. Tertiary Epimutations - A Novel Aspect of Epigenetic Transgenerational Inheritance Promoting Genome Instability. PLoS One 2016; 11:e0168038. [PMID: 27992467 PMCID: PMC5167269 DOI: 10.1371/journal.pone.0168038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/23/2016] [Indexed: 11/29/2022] Open
Abstract
Exposure to environmental factors can induce the epigenetic transgenerational inheritance of disease. Alterations to the epigenome termed “epimutations” include “primary epimutations” which are epigenetic alterations in the absence of genetic change and “secondary epimutations” which form following an initial genetic change. To determine if secondary epimutations contribute to transgenerational transmission of disease following in utero exposure to the endocrine disruptor vinclozolin, we exposed pregnant female rats carrying the lacI mutation-reporter transgene to vinclozolin and assessed the frequency of mutations in kidney tissue and sperm recovered from F1 and F3 generation progeny. Our results confirm that vinclozolin induces primary epimutations rather than secondary epimutations, but also suggest that some primary epimutations can predispose a subsequent accelerated accumulation of genetic mutations in F3 generation descendants that have the potential to contribute to transgenerational phenotypes. We therefore propose the existence of “tertiary epimutations” which are initial primary epimutations that promote genome instability leading to an accelerated accumulation of genetic mutations.
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Affiliation(s)
- John R. McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
- * E-mail:
| | - Jake D. Lehle
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
| | - Seetha S. Raju
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
| | - Eric E. Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA United States of America
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14
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Smith TA, Martin MD, Nguyen M, Mendelson TC. Epigenetic divergence as a potential first step in darter speciation. Mol Ecol 2016; 25:1883-94. [PMID: 26837057 DOI: 10.1111/mec.13561] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/28/2015] [Accepted: 01/04/2016] [Indexed: 01/07/2023]
Abstract
Recent studies show that epigenetic variation in the form of DNA methylation may serve as a substrate for selection. Theory suggests that heritable epigenetic marks that increase fitness should increase in frequency in a population, and these changes may result in novel morphology, behaviour, or physiology, and ultimately reproductive isolation. Therefore, epigenetic variation might provide the first substrate for selection during the course of evolutionary divergence. This hypothesis predicts that populations in the earliest stages of divergence will differentiate in their methylome prior to any genetic differentiation. While several studies have investigated natural epigenetic variation, empirical studies that test predictions about its role in speciation are surprisingly scarce. Here, we investigate DNA methylation variation using an isoschizomeric digest method, Methyl-Sensitive Amplified Polymorphism, across multiple stages of evolutionary divergence in natural populations of North American stream fishes. We show that epigenetic differentiation between methylomes is greater than genetic divergence among closely related populations across two river drainages. Additionally, we demonstrate that epigenetic divergence is a stronger predictor of the strength of behavioural reproductive isolation and suggest that changes in the methylome could influence the evolution of reproductive isolation between species. Our findings suggest a role for epigenetics not only in the initiation of divergence, but also in the maintenance of species boundaries over greater evolutionary timescales.
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Affiliation(s)
- Tracy A Smith
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
| | - Michael D Martin
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
| | - Michael Nguyen
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
| | - Tamra C Mendelson
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
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15
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Schaefer S, Nadeau JH. THE GENETICS OF EPIGENETIC INHERITANCE: MODES, MOLECULES, AND MECHANISMS. QUARTERLY REVIEW OF BIOLOGY 2016; 90:381-415. [PMID: 26714351 DOI: 10.1086/683699] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Organisms adapt developmental and physiological features to local and transient conditions in part by modulating transcription, translation, and protein functions, usually without changing DNA sequences. Remarkably, these epigenetic changes sometimes endure through meiosis and gametogenesis, thereby affecting phenotypic variation across generations, long after epigenetic changes were triggered. Transgenerational effects challenge our traditional understanding of inheritance. In this review, we focus on patterns of inheritance, molecular features, mechanisms that lead from environmental and genetic perturbations to phenotypic variation in later generations, and issues about study design and replication.
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16
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DNMT3L enables accumulation and inheritance of epimutations in transgenic Drosophila. Sci Rep 2016; 6:19572. [PMID: 26795243 PMCID: PMC4726149 DOI: 10.1038/srep19572] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/14/2015] [Indexed: 11/25/2022] Open
Abstract
DNMT3L is an important epigenetic regulator in mammals, integrating DNA methylation and histone modification based epigenetic circuits. Here we show DNMT3L to be a part of the machinery that enables inheritance of epigenetic modifications from one generation to the next. Ectopic expression of DNMT3L in Drosophila, which lacks DNMT3L and its normal interacting partners DNMT3A and DNMT3B, lead to nuclear reprogramming that was gradual and progressive, resulting in melanotic tumors that were observed only when these flies were maintained for five generations. This global gene expression misregulation was accompanied by aberrations in the levels of H3K4me3 and H3K36me3, globally as well as at specific gene promoters. The levels of these epigenetic aberrations (epimutations) also increased progressively across successive generations. The accumulation and inheritance of epimutations across multiple generations recapitulates the important role of DNMT3L in intergenerational epigenetic inheritance in mammals.
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17
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Qu LS, Jin F, Guo YM, Liu TT, Xue RY, Huang XW, Xu M, Chen TY, Ni ZP, Shen XZ. Nine susceptibility loci for hepatitis B virus-related hepatocellular carcinoma identified by a pilot two-stage genome-wide association study. Oncol Lett 2015; 11:624-632. [PMID: 26870257 PMCID: PMC4727098 DOI: 10.3892/ol.2015.3958] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 10/26/2015] [Indexed: 12/12/2022] Open
Abstract
Previous studies have indicated that complex interactions among viral, environmental and genetic factors lead to hepatocellular carcinoma (HCC). To identify susceptibility alleles for hepatitis B virus (HBV)-related HCC, the present study conducted a pilot two-phase genome-wide association study (GWAS) in 660 Han Chinese individuals. In phase 1, a total of 500,447 single-nucleotide polymorphisms (SNPs) were genotyped in 50 HCC cases and 50 controls using Affymetrix GeneChip 500k Array Set. In phase 2, 1,152 SNPs were selected from phase 1 and genotyped in 282 cases and 278 controls using the Illumina GoldenGate platform. The prior probability of HCC in control subjects was assigned at 0.01, and false-positive report probability (FPRP) was utilized to evaluate the statistical significance. In phase 1, one SNP (rs2212522) showed a significant association with HCC (Pallele=5.23×10−8; ORallele=4.96; 95% CI, 2.72–9.03). In phase 2, among 27 SNPs with unadjusted Pallele<0.05, 9 SNPs were associated with HCC based on FPRP criteria (FPRP <0.20). The strongest statistical evidence for an association signal was with rs2120243 (combined ORallele=1.76; 95% CI, 1.39–2.22; P=2.00×10−6), which maps within the fourth intron of VEPH1. The second strongest statistical evidence for an association was identified for rs1350171 (combined ORallele=1.66; 95% CI, 1.33–2.07; P=6.48×10−6), which maps to the region downstream of the FZD4 gene. The other potential susceptibility genes included PCDH9, PRMT6, LHX1, KIF2B and L3MBTL4. In conclusion, this pilot two-phase GWAS provides the evidence for the existence of common susceptibility loci for HCC. These genes involved various signaling pathways, including those associated with transforming growth factor β, insulin/phosphoinositide 3 kinase, Wnt and epidermal growth factor receptor. These associations must be replicated and validated in larger studies.
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Affiliation(s)
- Li-Shuai Qu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Fei Jin
- Department of Gastroenterology, Shanghai Xuhui Central Hospital, Shanghai 200032, P.R. China
| | - Yan-Mei Guo
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Tao-Tao Liu
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Ru-Yi Xue
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Xiao-Wu Huang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Min Xu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Tao-Yang Chen
- Department of Liver Surgery, Qidong Liver Cancer Institute, Qidong, Jiangsu 226200, P.R. China
| | - Zheng-Ping Ni
- Department of Liver Surgery, Qidong Liver Cancer Institute, Qidong, Jiangsu 226200, P.R. China
| | - Xi-Zhong Shen
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
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18
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Haque MM, Holder LB, Skinner MK. Genome-Wide Locations of Potential Epimutations Associated with Environmentally Induced Epigenetic Transgenerational Inheritance of Disease Using a Sequential Machine Learning Prediction Approach. PLoS One 2015; 10:e0142274. [PMID: 26571271 PMCID: PMC4646459 DOI: 10.1371/journal.pone.0142274] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/20/2015] [Indexed: 11/18/2022] Open
Abstract
Environmentally induced epigenetic transgenerational inheritance of disease and phenotypic variation involves germline transmitted epimutations. The primary epimutations identified involve altered differential DNA methylation regions (DMRs). Different environmental toxicants have been shown to promote exposure (i.e., toxicant) specific signatures of germline epimutations. Analysis of genomic features associated with these epimutations identified low-density CpG regions (<3 CpG / 100bp) termed CpG deserts and a number of unique DNA sequence motifs. The rat genome was annotated for these and additional relevant features. The objective of the current study was to use a machine learning computational approach to predict all potential epimutations in the genome. A number of previously identified sperm epimutations were used as training sets. A novel machine learning approach using a sequential combination of Active Learning and Imbalance Class Learner analysis was developed. The transgenerational sperm epimutation analysis identified approximately 50K individual sites with a 1 kb mean size and 3,233 regions that had a minimum of three adjacent sites with a mean size of 3.5 kb. A select number of the most relevant genomic features were identified with the low density CpG deserts being a critical genomic feature of the features selected. A similar independent analysis with transgenerational somatic cell epimutation training sets identified a smaller number of 1,503 regions of genome-wide predicted sites and differences in genomic feature contributions. The predicted genome-wide germline (sperm) epimutations were found to be distinct from the predicted somatic cell epimutations. Validation of the genome-wide germline predicted sites used two recently identified transgenerational sperm epimutation signature sets from the pesticides dichlorodiphenyltrichloroethane (DDT) and methoxychlor (MXC) exposure lineage F3 generation. Analysis of this positive validation data set showed a 100% prediction accuracy for all the DDT-MXC sperm epimutations. Observations further elucidate the genomic features associated with transgenerational germline epimutations and identify a genome-wide set of potential epimutations that can be used to facilitate identification of epigenetic diagnostics for ancestral environmental exposures and disease susceptibility.
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Affiliation(s)
- M. Muksitul Haque
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, 99164–4236, United States of America
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, 99164, United States of America
| | - Lawrence B. Holder
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, 99164, United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, 99164–4236, United States of America
- * E-mail:
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19
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The history of Distilbène® (Diethylstilbestrol) told to grandchildren--the transgenerational effect. ANNALES D'ENDOCRINOLOGIE 2015; 76:253-9. [PMID: 25934356 DOI: 10.1016/j.ando.2015.03.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 03/02/2015] [Accepted: 03/11/2015] [Indexed: 11/21/2022]
Abstract
The Distilbène® story is a dramatic episode which belongs to the history of medicine. It provided several useful lessons such as the importance of evidence-based medicine and the hazard to develop treatments during pregnancy without careful animal verifications. However, this experience has also provided unexpected progress by suggesting new pathophysiological concepts: fetal programming of adult diseases and/or transgenerational transmission of environmental effects through epigenetic modifications.
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20
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Paternal diet defines offspring chromatin state and intergenerational obesity. Cell 2015; 159:1352-64. [PMID: 25480298 DOI: 10.1016/j.cell.2014.11.005] [Citation(s) in RCA: 260] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 08/27/2014] [Accepted: 10/31/2014] [Indexed: 11/21/2022]
Abstract
The global rise in obesity has revitalized a search for genetic and epigenetic factors underlying the disease. We present a Drosophila model of paternal-diet-induced intergenerational metabolic reprogramming (IGMR) and identify genes required for its encoding in offspring. Intriguingly, we find that as little as 2 days of dietary intervention in fathers elicits obesity in offspring. Paternal sugar acts as a physiological suppressor of variegation, desilencing chromatin-state-defined domains in both mature sperm and in offspring embryos. We identify requirements for H3K9/K27me3-dependent reprogramming of metabolic genes in two distinct germline and zygotic windows. Critically, we find evidence that a similar system may regulate obesity susceptibility and phenotype variation in mice and humans. The findings provide insight into the mechanisms underlying intergenerational metabolic reprogramming and carry profound implications for our understanding of phenotypic variation and evolution.
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21
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Iovino N. Drosophila epigenome reorganization during oocyte differentiation and early embryogenesis. Brief Funct Genomics 2014; 13:246-53. [PMID: 24665128 DOI: 10.1093/bfgp/elu007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In sexually reproducing organisms, propagation of the species relies on specialized haploid cells (gametes) produced by germ cells. During their development in the adult germline, the female and male gametes undergo a complex differentiation process that requires transcriptional regulation and chromatin reorganization. After fertilization, the gametes then go through extensive epigenetic reprogramming, which resets the cells to a totipotent state essential for the development of the embryo. Several histone modifications characterize distinct developmental stages of gamete formation and early embryonic development, but it is unknown whether these modifications have any physiological role. Furthermore, accumulating evidence suggests that environmentally induced chromatin changes can be inherited, yet the mechanisms underlying zygotic inheritance of the gamete epigenome remain unclear. This review gives a brief overview of the mechanisms of transgenerational epigenetic inheritance and examines the function of epigenetics during oogenesis and early embryogenesis with a focus on histone posttranslational modifications.
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22
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Fridmann-Sirkis Y, Stern S, Elgart M, Galili M, Zeisel A, Shental N, Soen Y. Delayed development induced by toxicity to the host can be inherited by a bacterial-dependent, transgenerational effect. Front Genet 2014; 5:27. [PMID: 24611070 PMCID: PMC3933808 DOI: 10.3389/fgene.2014.00027] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 01/25/2014] [Indexed: 11/20/2022] Open
Abstract
Commensal gut bacteria in many species including flies are integral part of their host, and are known to influence its development and homeostasis within generation. Here we report an unexpected impact of host–microbe interactions, which mediates multi-generational, non-Mendelian inheritance of a stress-induced phenotype. We have previously shown that exposure of fly larvae to G418 antibiotic induces transgenerationally heritable phenotypes, including a delay in larval development, gene induction in the gut and morphological changes. We now show that G418 selectively depletes commensal Acetobacter species and that this depletion explains the heritable delay, but not the inheritance of the other phenotypes. Notably, the inheritance of the delay was mediated by a surprising trans-generational effect. Specifically, bacterial removal from F1 embryos did not induce significant delay in F1 larvae, but nonetheless led to a considerable delay in F2. This effect maintains a delay induced by bacterial-independent G418 toxicity to the host. In line with these findings, reintroduction of isolated Acetobacter species prevented the inheritance of the delay. We further show that this prevention is partly mediated by vitamin B2 (Riboflavin) produced by these bacteria; exogenous Riboflavin led to partial prevention and inhibition of Riboflavin synthesis compromised the ability of the bacteria to prevent the inheritance. These results identify host–microbe interactions as a hitherto unrecognized factor capable of mediating non-Mendelian inheritance of a stress-induced phenotype.
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Affiliation(s)
- Yael Fridmann-Sirkis
- Department of Biological Chemistry, Weizmann Institute of Science Rehovot, Israel
| | - Shay Stern
- Department of Biological Chemistry, Weizmann Institute of Science Rehovot, Israel
| | - Michael Elgart
- Department of Biological Chemistry, Weizmann Institute of Science Rehovot, Israel
| | - Matana Galili
- Department of Biological Chemistry, Weizmann Institute of Science Rehovot, Israel
| | - Amit Zeisel
- Department of Physics of Complex Systems, Weizmann Institute of Science Rehovot, Israel
| | - Noam Shental
- Department of Computer Science, The Open University Raanana, Israel
| | - Yoav Soen
- Department of Biological Chemistry, Weizmann Institute of Science Rehovot, Israel
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23
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Stern S, Snir O, Mizrachi E, Galili M, Zaltsman I, Soen Y. Reduction in maternal Polycomb levels contributes to transgenerational inheritance of a response to toxic stress in flies. J Physiol 2014; 592:2343-55. [PMID: 24535443 DOI: 10.1113/jphysiol.2014.271445] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Transgenerational persistence of parental responses to environmental stimuli has been reported in various organisms, but the underlying mechanisms remain underexplored. In one of these reported examples, we have shown that exposure of fly larvae to G418 antibiotic leads to non-Mendelian inheritance of ectopic induction of certain developmental genes. Here we investigate if this inheritance involves changes in mRNA composition within the early, maternal-stage offspring embryos of exposed flies. Exposure to G418 in F1 modified the maternal RNA levels of many genes in their early (F2) embryos. This includes reduction of maternal Polycomb group genes which persisted in the following generation of embryos (F3). To investigate the functional meaning of this reduction, we compared genetically normal embryos of Polycomb mutant females to normal embryos of normal females. Analysis with two different alleles of Polycomb, Pc1 and Pc3, revealed that maternal reduction in Polycomb gene dosage has a positive influence on the inheritance of induced expression. Together, this shows that exposure to G418 stress reduces the maternal levels of Polycomb in the offspring embryos and this reduction contributes to the inheritance of induced expression.
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Affiliation(s)
- Shay Stern
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Orli Snir
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Eran Mizrachi
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Matana Galili
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Inbal Zaltsman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yoav Soen
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
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24
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Stapel LC, Vastenhouw NL. Message control in developmental transitions; deciphering chromatin's role using zebrafish genomics. Brief Funct Genomics 2013; 13:106-20. [PMID: 24170706 DOI: 10.1093/bfgp/elt045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Now that the sequencing of genomes has become routine, understanding how a given genome is used in different ways to obtain cell type diversity in an organism is the next frontier. How specific transcription programs are established during vertebrate embryogenesis, however, remains poorly understood. Transcription is influenced by chromatin structure, which determines the accessibility of DNA-binding proteins to the genome. Although large-scale genomics approaches have uncovered specific features of chromatin structure that are diagnostic for different cell types and developmental stages, our functional understanding of chromatin in transcriptional regulation during development is very limited. In recent years, zebrafish embryogenesis has emerged as an excellent vertebrate model system to investigate the functional relationship between chromatin organization, gene regulation and development in a dynamic environment. Here, we review how studies in zebrafish have started to improve our understanding of the role of chromatin structure in genome activation and pluripotency and in the potential inheritance of transcriptional states from parent to progeny.
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Affiliation(s)
- L Carine Stapel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.
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25
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Environmentally induced epigenetic transgenerational inheritance of altered Sertoli cell transcriptome and epigenome: molecular etiology of male infertility. PLoS One 2013; 8:e59922. [PMID: 23555832 PMCID: PMC3610698 DOI: 10.1371/journal.pone.0059922] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/19/2013] [Indexed: 11/19/2022] Open
Abstract
Environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of adult onset disease, including testis disease and male infertility. The current study was designed to determine the impact of an altered sperm epigenome on the subsequent development of an adult somatic cell (Sertoli cell) that influences the onset of a specific disease (male infertility). A gestating female rat (F0 generation) was exposed to the agriculture fungicide vinclozolin during gonadal sex determination and then the subsequent F3 generation progeny used for the isolation of Sertoli cells and assessment of testis disease. As previously observed, enhanced spermatogenic cell apoptosis was observed. The Sertoli cells provide the physical and nutritional support for the spermatogenic cells. Over 400 genes were differentially expressed in the F3 generation control versus vinclozolin lineage Sertoli cells. A number of specific cellular pathways were identified to be transgenerationally altered. One of the key metabolic processes affected was pyruvate/lactate production that is directly linked to spermatogenic cell viability. The Sertoli cell epigenome was also altered with over 100 promoter differential DNA methylation regions (DMR) modified. The genomic features and overlap with the sperm DMR were investigated. Observations demonstrate that the transgenerational sperm epigenetic alterations subsequently alters the development of a specific somatic cell (Sertoli cell) epigenome and transcriptome that correlates with adult onset disease (male infertility). The environmentally induced epigenetic transgenerational inheritance of testis disease appears to be a component of the molecular etiology of male infertility.
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26
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Abstract
To what extent can variation in phenotypic traits such as disease risk be accurately predicted in individuals? In this Review, I highlight recent studies in model organisms that are relevant both to the challenge of accurately predicting phenotypic variation from individual genome sequences ('whole-genome reverse genetics') and for understanding why, in many cases, this may be impossible. These studies argue that only by combining genetic knowledge with in vivo measurements of biological states will it be possible to make accurate genetic predictions for individual humans.
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27
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Burga A, Lehner B. Beyond genotype to phenotype: why the phenotype of an individual cannot always be predicted from their genome sequence and the environment that they experience. FEBS J 2012; 279:3765-75. [DOI: 10.1111/j.1742-4658.2012.08810.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/07/2012] [Accepted: 08/24/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Alejandro Burga
- Genetic Systems; EMBL/CRG Systems Biology Research Unit; Centre for Genomic Regulation (CRG) and UPF; Barcelona; Spain
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28
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Meagher RB, Müssar KJ. The influence of DNA sequence on epigenome-induced pathologies. Epigenetics Chromatin 2012; 5:11. [PMID: 22818522 PMCID: PMC3439399 DOI: 10.1186/1756-8935-5-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 07/20/2012] [Indexed: 01/13/2023] Open
Abstract
Clear cause-and-effect relationships are commonly established between genotype and the inherited risk of acquiring human and plant diseases and aberrant phenotypes. By contrast, few such cause-and-effect relationships are established linking a chromatin structure (that is, the epitype) with the transgenerational risk of acquiring a disease or abnormal phenotype. It is not entirely clear how epitypes are inherited from parent to offspring as populations evolve, even though epigenetics is proposed to be fundamental to evolution and the likelihood of acquiring many diseases. This article explores the hypothesis that, for transgenerationally inherited chromatin structures, "genotype predisposes epitype", and that epitype functions as a modifier of gene expression within the classical central dogma of molecular biology. Evidence for the causal contribution of genotype to inherited epitypes and epigenetic risk comes primarily from two different kinds of studies discussed herein. The first and direct method of research proceeds by the examination of the transgenerational inheritance of epitype and the penetrance of phenotype among genetically related individuals. The second approach identifies epitypes that are duplicated (as DNA sequences are duplicated) and evolutionarily conserved among repeated patterns in the DNA sequence. The body of this article summarizes particularly robust examples of these studies from humans, mice, Arabidopsis, and other organisms. The bulk of the data from both areas of research support the hypothesis that genotypes predispose the likelihood of displaying various epitypes, but for only a few classes of epitype. This analysis suggests that renewed efforts are needed in identifying polymorphic DNA sequences that determine variable nucleosome positioning and DNA methylation as the primary cause of inherited epigenome-induced pathologies. By contrast, there is very little evidence that DNA sequence directly determines the inherited positioning of numerous and diverse post-translational modifications of histone side chains within nucleosomes. We discuss the medical and scientific implications of these observations on future research and on the development of solutions to epigenetically induced disorders.
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Affiliation(s)
- Richard B Meagher
- Genetics Department, Davison Life Sciences Building, University of Georgia, Athens, GA, 30605, USA.
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29
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Pang S, Curran SP. Longevity and the long arm of epigenetics: acquired parental marks influence lifespan across several generations. Bioessays 2012; 34:652-4. [PMID: 22674543 DOI: 10.1002/bies.201200046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A recent study reported that longevity in Caenorhabditits elegans can be inherited over several generations. This is probably achieved through the following epigenetic mechanism: inherited demethylated histones at some central loci, such as miRNA, transcription factors or signaling regulators affect the expression of certain genes leading to the longevity phenotype.
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Affiliation(s)
- Shanshan Pang
- University of Southern California, Davis School of Gerontology, Los Angeles, CA, USA
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30
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Guerrero-Bosagna C, Skinner MK. Environmentally induced epigenetic transgenerational inheritance of phenotype and disease. Mol Cell Endocrinol 2012; 354:3-8. [PMID: 22020198 PMCID: PMC3312615 DOI: 10.1016/j.mce.2011.10.004] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 10/03/2011] [Accepted: 10/05/2011] [Indexed: 12/15/2022]
Abstract
Environmental epigenetics has an important role in regulating phenotype formation or disease etiology. The ability of environmental factors and exposures early in life to alter somatic cell epigenomes and subsequent development is a critical factor in how environment affects biology. Environmental epigenetics provides a molecular mechanism to explain long term effects of environment on the development of altered phenotypes and "emergent" properties, which the "genetic determinism" paradigm cannot. When environmental factors permanently alter the germ line epigenome, then epigenetic transgenerational inheritance of these environmentally altered phenotypes and diseases can occur. This environmental epigenetic transgenerational inheritance of phenotype and disease is reviewed with a systems biology perspective.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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31
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Stern S, Fridmann-Sirkis Y, Braun E, Soen Y. Epigenetically Heritable Alteration of Fly Development in Response to Toxic Challenge. Cell Rep 2012; 1:528-42. [DOI: 10.1016/j.celrep.2012.03.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 12/14/2011] [Accepted: 03/30/2012] [Indexed: 01/24/2023] Open
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32
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Abstract
Since Mendel, studies of phenotypic variation and disease risk have emphasized associations between genotype and phenotype among affected individuals in families and populations. Although this paradigm has led to important insights into the molecular basis for many traits and diseases, most of the genetic variants that control the inheritance of these conditions continue to elude detection. Recent studies suggest an alternative mode of inheritance where genetic variants that are present in one generation affect phenotypes in subsequent generations, thereby decoupling the conventional relations between genotype and phenotype, and perhaps, contributing to 'missing heritability'. Under some conditions, these transgenerational genetic effects can be as frequent and strong as conventional inheritance, and can persist for multiple generations. Growing evidence suggests that RNA mediates these heritable epigenetic changes. The primary challenge now is to identify the molecular basis for these effects, characterize mechanisms and determine whether transgenerational genetic effects occur in humans.
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Affiliation(s)
- Vicki R Nelson
- Department of Genetics, BRB731, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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33
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Cowley AW, Nadeau JH, Baccarelli A, Berecek K, Fornage M, Gibbons GH, Harrison DG, Liang M, Nathanielsz PW, O'Connor DT, Ordovas J, Peng W, Soares MB, Szyf M, Tolunay HE, Wood KC, Zhao K, Galis ZS. Report of the National Heart, Lung, and Blood Institute Working Group on epigenetics and hypertension. Hypertension 2012; 59:899-905. [PMID: 22431584 DOI: 10.1161/hypertensionaha.111.190116] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Allen W Cowley
- Department of Physiology, Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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34
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Li L, Le F, Wang LY, Xu XR, Lou HY, Zheng YM, Sheng JZ, Huang HF, Jin F. Normal epigenetic inheritance in mice conceived by in vitro fertilization and embryo transfer. J Zhejiang Univ Sci B 2012; 12:796-804. [PMID: 21960342 DOI: 10.1631/jzus.b1000411] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
An association between assisted reproductive technology (ART) and neurobehavioral imprinting disorders has been reported in many studies, and it seems that ART may interfere with imprint reprogramming. However, it has never been explored whether epigenetic errors or imprinting disease susceptibility induced by ART can be inherited transgenerationally. Hence, the aim of this study was to determine the effect of in vitro fertilization and embryo transfer (IVF-ET) on transgenerational inheritance in an inbred mouse model. Mice derived from IVF-ET were outcrossed to wild-type C57BL/6J to obtain their female and male line F2 and F3 generations. Their behavior, morphology, histology, and DNA methylation status at several important differentially methylated regions (DMRs) were analyzed by Morris water maze, hematoxylin and eosin (H&E) staining, and bisulfite genomic sequencing. No significant differences in spatial learning or phenotypic abnormality were found in adults derived from IVF (F1) and female and male line F2 and F3 generations. A borderline trend of hypomethylation was found in H19 DMR CpG island 3 in the female line-derived F3 generation (0.40±0.118, P=0.086). Methylation status in H19/Igf2 DMR island 1, Igf2 DMR, KvDMR, and Snrpn DMR displayed normal patterns. Methylation percentage did not differ significantly from that of adults conceived naturally, and the expression of the genes they regulated was not disturbed. Transgenerational integrity, such as behavior, morphology, histology, and DNA methylation status, was maintained in these generations, which indicates that exposure of female germ cells to hormonal stimulation and gamete manipulation might not affect the individuals and their descendents.
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Affiliation(s)
- Lei Li
- Centre of Reproductive Medicine, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Daphnia as an emerging epigenetic model organism. GENETICS RESEARCH INTERNATIONAL 2012; 2012:147892. [PMID: 22567376 PMCID: PMC3335723 DOI: 10.1155/2012/147892] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 10/25/2011] [Indexed: 12/11/2022]
Abstract
Daphnia offer a variety of benefits for the study of epigenetics. Daphnia's parthenogenetic life cycle allows the study of epigenetic effects in the absence of confounding genetic differences. Sex determination and sexual reproduction are epigenetically determined as are several other well-studied alternate phenotypes that arise in response to environmental stressors. Additionally, there is a large body of ecological literature available, recently complemented by the genome sequence of one species and transgenic technology. DNA methylation has been shown to be altered in response to toxicants and heavy metals, although investigation of other epigenetic mechanisms is only beginning. More thorough studies on DNA methylation as well as investigation of histone modifications and RNAi in sex determination and predator-induced defenses using this ecologically and evolutionarily important organism will contribute to our understanding of epigenetics.
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36
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Larson K, Yan SJ, Tsurumi A, Liu J, Zhou J, Gaur K, Guo D, Eickbush TH, Li WX. Heterochromatin formation promotes longevity and represses ribosomal RNA synthesis. PLoS Genet 2012; 8:e1002473. [PMID: 22291607 PMCID: PMC3266895 DOI: 10.1371/journal.pgen.1002473] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 11/22/2011] [Indexed: 11/19/2022] Open
Abstract
Organismal aging is influenced by a multitude of intrinsic and extrinsic factors, and heterochromatin loss has been proposed to be one of the causes of aging. However, the role of heterochromatin in animal aging has been controversial. Here we show that heterochromatin formation prolongs lifespan and controls ribosomal RNA synthesis in Drosophila. Animals with decreased heterochromatin levels exhibit a dramatic shortening of lifespan, whereas increasing heterochromatin prolongs lifespan. The changes in lifespan are associated with changes in muscle integrity. Furthermore, we show that heterochromatin levels decrease with normal aging and that heterochromatin formation is essential for silencing rRNA transcription. Loss of epigenetic silencing and loss of stability of the rDNA locus have previously been implicated in aging of yeast. Taken together, these results suggest that epigenetic preservation of genome stability, especially at the rDNA locus, and repression of unnecessary rRNA synthesis, might be an evolutionarily conserved mechanism for prolonging lifespan.
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Affiliation(s)
- Kimberly Larson
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Shian-Jang Yan
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Amy Tsurumi
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Jacqueline Liu
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Jun Zhou
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Kriti Gaur
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Dongdong Guo
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Thomas H. Eickbush
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Willis X. Li
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Abstract
A major weakness of most genome-wide association studies has been their inability to fully explain the heritable component of complex disease. Nearly all such studies consider the two parental alleles to be functionally equivalent. However, the existence of imprinted genes demonstrates that this assumption can be wrong. In this review, we describe a wide variety of different mechanisms that underlie many other parent of origin and trans-generational effects that are known to operate in both humans and model organisms, suggesting that these phenomena are perhaps not uncommon in the genome. We propose that the consideration of alternative models of inheritance will improve our understanding of the heritability and causes of human traits and could have significant impacts on the study of complex disorders.
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Affiliation(s)
- A Guilmatre
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
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38
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Ruden DM, Lu X. Hsp90 affecting chromatin remodeling might explain transgenerational epigenetic inheritance in Drosophila. Curr Genomics 2011; 9:500-8. [PMID: 19506739 PMCID: PMC2691676 DOI: 10.2174/138920208786241207] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 08/08/2008] [Accepted: 08/14/2008] [Indexed: 01/01/2023] Open
Abstract
Transgenerational epigenetic inheritance, while poorly understood, is of great interest because it might help explain the increase in the incidence of diseases with an environmental contribution in humans, such as cancer, diabetes, and heart disease. Here, we review five Drosophila examples of transgenerational epigenetic inheritance and propose a unified mechanism that involves Polycomb Response Element/Trithorax Response Element (PRE/TRE) occupancy by either Polycomb Group (PcG) protein complexes or Trithorax group (TrxG) complexes. Among their other activities, PcG complexes cause histone 3 lysine 27 tri-methylation associated with repressed chromatin, whereas Trithorax group (TrxG) complexes induce histone 3 lysine 4 tri-methylation associated with actively transcribed chromatin. In this model, Hsp90 is an environmentally sensitive chromatin remodeling regulator that causes a switch in the chromatin from a permissive state to a non-permissive state for transcription. Consistent with this model, Hsp90 has recently been shown to be a chaperone for Tah1p (TPR-containing protein associated with Hsp90) and Pih1p (protein interacting with Hsp90), which connect to the chromatin remodelling factor Rvb1p (RuvB-like protein 1)/Rvb2p in yeast [1]. Also, Hsp90 is required for optimal activity of the histone H3 lysine-4 methyltransferase SMYD3 in mammals [2, 3]. Since PcG and TrxG complexes are involved in the post-translational modifications of histones, and since such modifications have been shown to be required to maintain imprinted marks, this unified mechanism might also help to explain transgenerational epigenetic inheritance in humans.
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Affiliation(s)
- Douglas M Ruden
- Wayne State University, Institute for Environmental Health Sciences, 2727 2 Ave, Room 4000, Detroit, MI 48201, USA
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Krauss V, Reuter G. DNA methylation in Drosophila--a critical evaluation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:177-91. [PMID: 21507351 DOI: 10.1016/b978-0-12-387685-0.00003-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Drosophila belongs to the so-called "Dnmt2 only" organisms, and does not contain any of the canonical DNA methyltransferases (Dnmt1 and Dnmt3). Furthermore, no functional homologs of known 5-methylcytosine reader proteins are found. Nevertheless, there is strong evidence for DNA methylation in this organism. It has been suggested that DNA methylation in Drosophila is simply a byproduct of Dnmt2, which is a DNA methyltransferase (Dnmt) according to structure and type of catalysis but functions in vivo as a tRNA methyltransferase. However, concerning the very specific timing of cytosine methylation in Drosophila, their suggested functions in control of retrotransposon silencing and genome stability, and the obvious DNA methylation activity of Dnmt2 enzymes in the protozoans Dictyostelium discoideum and Entamoeba histolytica, we tend to disagree with this notation. Dnmt2 probably serves, and not only in Drosophila, as a methyltransferase of both specific DNA and tRNA targets.
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Affiliation(s)
- Veiko Krauss
- Developmental Genetics, Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg, Halle/S, Germany
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40
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Abstract
Epigenetic modifications are widely accepted as playing a critical role in the regulation of gene expression and thereby contributing to the determination of the phenotype of multicellular organisms. In general, these marks are cleared and re-established each generation, but there have been reports in a number of model organisms that at some loci in the genome this clearing is incomplete. This phenomenon is referred to as transgenerational epigenetic inheritance. Moreover, recent evidence shows that the environment can stably influence the establishment of the epigenome. Together, these findings suggest that an environmental event in one generation could affect the phenotype in subsequent generations, and these somewhat Lamarckian ideas are stimulating interest from a broad spectrum of biologists, from ecologists to health workers.
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Affiliation(s)
- Lucia Daxinger
- Epigenetics Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, Queensland 4006, Australia
| | - Emma Whitelaw
- Epigenetics Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, Queensland 4006, Australia
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41
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Franklin TB, Russig H, Weiss IC, Gräff J, Linder N, Michalon A, Vizi S, Mansuy IM. Epigenetic transmission of the impact of early stress across generations. Biol Psychiatry 2010; 68:408-15. [PMID: 20673872 DOI: 10.1016/j.biopsych.2010.05.036] [Citation(s) in RCA: 679] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 04/13/2010] [Accepted: 05/06/2010] [Indexed: 12/20/2022]
Abstract
BACKGROUND Traumatic experiences in early life are risk factors for the development of behavioral and emotional disorders. Such disorders can persist through adulthood and have often been reported to be transmitted across generations. METHODS To investigate the transgenerational effect of early stress, mice were exposed to chronic and unpredictable maternal separation from postnatal day 1 to 14. RESULTS We show that chronic and unpredictable maternal separation induces depressive-like behaviors and alters the behavioral response to aversive environments in the separated animals when adult. Most of the behavioral alterations are further expressed by the offspring of males subjected to maternal separation, despite the fact that these males are reared normally. Chronic and unpredictable maternal separation also alters the profile of DNA methylation in the promoter of several candidate genes in the germline of the separated males. Comparable changes in DNA methylation are also present in the brain of the offspring and are associated with altered gene expression. CONCLUSIONS These findings highlight the negative impact of early stress on behavioral responses across generations and on the regulation of DNA methylation in the germline.
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Affiliation(s)
- Tamara B Franklin
- Brain Research Institute, Medical Faculty of University of Zürich, Zürich, Switzerland
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42
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Yazbek SN, Spiezio SH, Nadeau JH, Buchner DA. Ancestral paternal genotype controls body weight and food intake for multiple generations. Hum Mol Genet 2010; 19:4134-44. [PMID: 20696673 DOI: 10.1093/hmg/ddq332] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Current treatments have largely failed to slow the rapidly increasing world-wide prevalence of obesity and its co-morbidities. Despite a strong genetic contribution to obesity (40-70%), only a small percentage of heritability is explained with current knowledge of monogenic abnormalities, common sequence variants and conventional modes of inheritance. Epigenetic effects are rarely tested in humans because of difficulties arranging studies that distinguish conventional and transgenerational inheritance while simultaneously controlling environmental factors and learned behaviors. However, growing evidence from model organisms implicates genetic and environmental factors in one generation that affect phenotypes in subsequent generations. In this report, we provide the first evidence for paternal transgenerational genetic effects on body weight and food intake. This test focused on the obesity-resistant 6C2d congenic strain, which carries the Obrq2a(A/J) allele on an otherwise C57BL/6J background. Various crosses between 6C2d and the control C57BL/6J strain showed that the Obrq2a(A/J) allele in the paternal or grandpaternal generation was sufficient to inhibit diet-induced obesity and reduce food intake in the normally obesity-susceptible, high food intake C57BL/6J strain. These obesity-resistant and reduced food intake phenotypes were transmitted through the paternal lineage but not the maternal lineage with equal strength for at least two generations. Eliminating social interaction between the father and both his offspring and the pregnant dam did not significantly affect food intake levels, demonstrating that the phenotype is transmitted through the male germline rather than through social interactions. Persistence of these phenotypes across multiple generations raises the possibility that transgenerational genetic effects contribute to current metabolic conditions.
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Affiliation(s)
- Soha N Yazbek
- Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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43
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Mirabello L, Savage SA, Korde L, Gadalla SM, Greene MH. LINE-1 methylation is inherited in familial testicular cancer kindreds. BMC MEDICAL GENETICS 2010; 11:77. [PMID: 20478068 PMCID: PMC2880977 DOI: 10.1186/1471-2350-11-77] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 05/17/2010] [Indexed: 11/23/2022]
Abstract
Background Testicular germ cell tumors (TGCT) are the most frequent cancers among young men. There is a clear familial component to TGCT etiology, but no high-penetrance susceptibility gene has been identified. Epigenetic aberrations of the genome represent an alternative mechanism for cancer susceptibility; and, studies suggest that epigenetic changes that influence cancer risk can be inherited through the germline. Global DNA hypomethylation has been associated with the risk of cancers of the bladder and head/neck. Methods We performed a pilot study of global methylation at long interspersed nuclear elements-1 (LINE-1) in peripheral blood DNA isolated from 466 family members of 101 multiple-case testicular cancer families. Results Investigating the correlation of LINE-1 methylation levels among parent-child pairs independent of affection status (n = 355) revealed a strong positive association only between mother-daughter (r = 0.48, P = <0.001) and father-daughter pairs (r = 0.31, P = 0.02), suggesting gender-specific inheritance of methylation. Incorporating cancer status, we observed a strong correlation in LINE-1 methylation levels only among affected father-affected son pairs (r = 0.49, P = 0.03). There was a marginally significant inverse association between lower LINE-1 methylation levels and increased TGCT risk, compared with healthy male relatives (P = 0.049). Conclusions Our data suggest that heritability of LINE-1 methylation may be gender-specific. Further, the strong correlation between LINE-1 methylation levels among affected father-affected son pairs suggests that transgenerational inheritance of an epigenetic event may be associated with disease risk. Larger studies are needed to clarify these preliminary observations.
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Affiliation(s)
- Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
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44
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Skinner MK, Manikkam M, Guerrero-Bosagna C. Epigenetic transgenerational actions of environmental factors in disease etiology. Trends Endocrinol Metab 2010; 21:214-22. [PMID: 20074974 PMCID: PMC2848884 DOI: 10.1016/j.tem.2009.12.007] [Citation(s) in RCA: 464] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 12/09/2009] [Accepted: 12/14/2009] [Indexed: 12/26/2022]
Abstract
The ability of environmental factors to promote a phenotype or disease state not only in the individual exposed but also in subsequent progeny for successive generations is termed transgenerational inheritance. The majority of environmental factors such as nutrition or toxicants such as endocrine disruptors do not promote genetic mutations or alterations in DNA sequence. However, these factors do have the capacity to alter the epigenome. Epimutations in the germline that become permanently programmed can allow transmission of epigenetic transgenerational phenotypes. This review provides an overview of the epigenetics and biology of how environmental factors can promote transgenerational phenotypes and disease.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4236, USA.
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45
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Hitchins MP. Inheritance of epigenetic aberrations (constitutional epimutations) in cancer susceptibility. ADVANCES IN GENETICS 2010; 70:201-43. [PMID: 20920750 DOI: 10.1016/b978-0-12-380866-0.60008-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pathogenic role for heritable mutations in the DNA sequence of tumor suppressor and DNA repair genes has been well established in familial cancer syndromes. These germ line mutations confer a high risk of developing particular types of cancer, according to the gene affected, at a young age of onset when compared to sporadically arising cancers of a similar type. The widespread role for epigenetic dysregulation in the development and progression of sporadic cancers is also well recognized. However, it has only become apparent in recent years that epigenetic aberrations can also occur constitutionally to confer a similar cancer phenotype as a genetic mutation within the same gene. These epigenetic errors are termed "constitutional epimutations" and are characterized by promoter methylation and transcriptional silencing of a single allele of the gene in normal somatic tissues in the absence of a sequence mutation within the affected locus. This is best exemplified in Lynch syndrome, which is an autosomal dominant cancer susceptibility syndrome characterized by the early development of colorectal, uterine, and additional cancers exhibiting microsatellite instability due to impaired mismatch repair. Lynch syndrome is usually caused by heterozygous loss-of-function germ line mutations of the mismatch repair genes, namely MLH1, MSH2, MSH6, and PMS2. Tumors develop following an acquired somatic loss of the remaining functional allele. However, a subset of Lynch syndrome cases without genetic mutations instead has a constitutional epimutation of MLH1 or MSH2. These epimutations are associated with distinct patterns of inheritance depending on the nature of the mechanisms underlying them.
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Affiliation(s)
- Megan P Hitchins
- Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
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46
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Nadeau JH. Transgenerational genetic effects on phenotypic variation and disease risk. Hum Mol Genet 2009; 18:R202-10. [PMID: 19808797 DOI: 10.1093/hmg/ddp366] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Traditionally, we understand that individual phenotypes result primarily from inherited genetic variants together with environmental exposures. However, many studies showed that a remarkable variety of factors including environmental agents, parental behaviors, maternal physiology, xenobiotics, nutritional supplements and others lead to epigenetic changes that can be transmitted to subsequent generations without continued exposure. Recent discoveries show transgenerational epistasis and transgenerational genetic effects where genetic factors in one generation affect phenotypes in subsequent generation without inheritance of the genetic variant in the parents. Together these discoveries implicate a key signaling pathway, chromatin remodeling, methylation, RNA editing and microRNA biology. This exceptional mode of inheritance complicates the search for disease genes and represents perhaps an adaptation to transmit useful gene expression profiles from one generation to the next. In this review, I present evidence for these transgenerational genetic effects, identify their common features, propose a heuristic model to guide the search for mechanisms, discuss the implications, and pose questions whose answers will begin to reveal the underlying mechanisms.
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Affiliation(s)
- Joseph H Nadeau
- Department of Genetics, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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47
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Skinner MK, Guerrero-Bosagna C. Environmental signals and transgenerational epigenetics. Epigenomics 2009; 1:111-117. [PMID: 20563319 DOI: 10.2217/epi.09.11] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The ability of an environmental factor or toxicant to promote a phenotype or disease state not only in the individual exposed, but also in subsequent progeny for multiple generations, is termed transgenerational inheritance. The majority of environmental agents do not promote genetic mutations or alterations in DNA sequence, but do have the capacity to alter the epigenome. Although most environmental exposures will influence somatic cells and not allow the transgenerational transmission of a phenotype, the ability of an environmental factor to reprogram the germline epigenome can promote a transgenerational inheritance of phenotypes and disease states. A limited number of critical developmental periods exist when environmental signals can produce a significant epigenetic reprogramming of the germline. In this review, the ability of environmental factors or toxicants to promote epigenetic transgenerational phenotypes is reviewed.
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48
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Muir WJ, McKechanie AG. Can epigenetics help in the discovery of therapeutics for psychiatric disorders, especially schizophrenia? Expert Opin Drug Discov 2009; 4:621-7. [PMID: 23489155 DOI: 10.1517/17460440902895446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Psychiatric disorders have a heterogeneous biological basis, where environmental factors interplay with non-mendelian genetics to produce complex cognitive/behavioural syndromes such as schizophrenia. Recent findings indicate a proportion of schizophrenia is associated with genomic copy number variation, suggesting that alteration of gene expression levels rather than direct mutation may play a role. Epigenetic mechanisms could be the crucial link between external stimuli and gene expression, influencing schizophrenia risk. These are dynamic reversible systems that offer much promise as targets for future therapies.
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Affiliation(s)
- Walter J Muir
- Reader in Psychiatry University of Edinburgh, Royal Edinburgh Hospital, School of Molecular and Clinical Medicine, Division of Psychiatry, EH10 5HF, Edinburgh, UK
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49
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Milagro FI, Campión J, García-Díaz DF, Goyenechea E, Paternain L, Martínez JA. High fat diet-induced obesity modifies the methylation pattern of leptin promoter in rats. J Physiol Biochem 2009; 65:1-9. [DOI: 10.1007/bf03165964] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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50
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Fleming JL, Huang THM, Toland AE. The role of parental and grandparental epigenetic alterations in familial cancer risk. Cancer Res 2008; 68:9116-21. [PMID: 19010880 DOI: 10.1158/0008-5472.can-08-2184] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Epigenetic alterations of the genome such as DNA promoter methylation and chromatin remodeling play an important role in tumorigenesis. These modifications take place throughout development with subsequent events occurring later in adulthood. Recent studies, however, suggest that some epigenetic alterations that influence cancer risk are inherited through the germline from parent to child and are observed in multiple generations. Epigenetic changes may be inherited as Mendelian, non-Mendelian, or environmentally induced traits. Here, we will discuss Mendelian, non-Mendelian, and environmentally induced patterns of multigenerational epigenetic alterations as well as some possible mechanisms for how these events may be occurring.
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Affiliation(s)
- Jessica L Fleming
- Human Cancer Genetics Program and the Ohio State Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, USA
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