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Food abundance in men before puberty predicts a range of cancers in grandsons. Nat Commun 2022; 13:7507. [PMID: 36473854 PMCID: PMC9726939 DOI: 10.1038/s41467-022-35217-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Nutritional conditions early in human life may influence phenotypic characteristics in later generations. A male-line transgenerational pathway, triggered by the early environment, has been postulated with support from animal and a small number of human studies. Here we analyse individuals born in Uppsala Sweden 1915-29 with linked data from their children and parents, which enables us to explore the hypothesis that pre-pubertal food abundance may trigger a transgenerational effect on cancer events. We used cancer registry and cause-of-death data to analyse 3422 cancer events in grandchildren (G2) by grandparental (G0) food access. We show that variation in harvests and food access in G0 predicts cancer occurrence in G2 in a specific way: abundance among paternal grandfathers, but not any other grandparent, predicts cancer occurrence in grandsons but not in granddaughters. This male-line response is observed for several groups of cancers, suggesting a general susceptibility, possibly acquired in early embryonic development. We observed no transgenerational influence in the middle generation.
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2
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Aagaard A, Liu S, Tregenza T, Braad Lund M, Schramm A, Verhoeven KJF, Bechsgaard J, Bilde T. Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola. Mol Ecol 2022; 31:5765-5783. [PMID: 36112081 PMCID: PMC9827990 DOI: 10.1111/mec.16696] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 02/06/2023]
Abstract
Understanding the role of genetic and nongenetic variants in modulating phenotypes is central to our knowledge of adaptive responses to local conditions and environmental change, particularly in species with such low population genetic diversity that it is likely to limit their evolutionary potential. A first step towards uncovering the molecular mechanisms underlying population-specific responses to the environment is to carry out environmental association studies. We associated climatic variation with genetic, epigenetic and microbiome variation in populations of a social spider with extremely low standing genetic diversity. We identified genetic variants that are associated strongly with environmental variation, particularly with average temperature, a pattern consistent with local adaptation. Variation in DNA methylation in many genes was strongly correlated with a wide set of climate parameters, thereby revealing a different pattern of associations than that of genetic variants, which show strong correlations to a more restricted range of climate parameters. DNA methylation levels were largely independent of cis-genetic variation and of overall genetic population structure, suggesting that DNA methylation can work as an independent mechanism. Microbiome composition also correlated with environmental variation, but most strong associations were with precipitation-related climatic factors. Our results suggest a role for both genetic and nongenetic mechanisms in shaping phenotypic responses to local environments.
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Affiliation(s)
- Anne Aagaard
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Shenglin Liu
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Tom Tregenza
- Centre for Ecology & Conservation, School of BiosciencesUniversity of ExeterPenryn CampusUK
| | - Marie Braad Lund
- Section for Microbiology, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Andreas Schramm
- Section for Microbiology, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Koen J. F. Verhoeven
- Terrestrial Ecology DepartmentNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Jesper Bechsgaard
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Trine Bilde
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
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Harney E, Paterson S, Collin H, Chan BH, Bennett D, Plaistow SJ. Pollution induces epigenetic effects that are stably transmitted across multiple generations. Evol Lett 2022; 6:118-135. [PMID: 35386832 PMCID: PMC8966472 DOI: 10.1002/evl3.273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
It has been hypothesized that the effects of pollutants on phenotypes can be passed to subsequent generations through epigenetic inheritance, affecting populations long after the removal of a pollutant. But there is still little evidence that pollutants can induce persistent epigenetic effects in animals. Here, we show that low doses of commonly used pollutants induce genome‐wide differences in cytosine methylation in the freshwater crustacean Daphnia pulex. Uniclonal populations were either continually exposed to pollutants or switched to clean water, and methylation was compared to control populations that did not experience pollutant exposure. Although some direct changes to methylation were only present in the continually exposed populations, others were present in both the continually exposed and switched to clean water treatments, suggesting that these modifications had persisted for 7 months (>15 generations). We also identified modifications that were only present in the populations that had switched to clean water, indicating a long‐term legacy of pollutant exposure distinct from the persistent effects. Pollutant‐induced differential methylation tended to occur at sites that were highly methylated in controls. Modifications that were observed in both continually and switched treatments were highly methylated in controls and showed reduced methylation in the treatments. On the other hand, modifications found just in the switched treatment tended to have lower levels of methylation in the controls and showed increase methylation in the switched treatment. In a second experiment, we confirmed that sublethal doses of the same pollutants generate effects on life histories for at least three generations following the removal of the pollutant. Our results demonstrate that even low doses of pollutants can induce transgenerational epigenetic effects that are stably transmitted over many generations. Persistent effects are likely to influence phenotypic development, which could contribute to the rapid adaptation, or extinction, of populations confronted by anthropogenic stressors.
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Affiliation(s)
- Ewan Harney
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
- Current address: Institute of Evolutionary Biology (CSIC‐UPF) CMIMA Building Barcelona 08003 Spain
| | - Steve Paterson
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Hélène Collin
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Brian H.K. Chan
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
- Current address: Faculty of Biology, Medicine and Health The University of Manchester Manchester M13 9PT United Kingdom
| | - Daimark Bennett
- Molecular and Physiology Cell Signalling, Institute of Systems, Molecular and Integrative Biology University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Stewart J. Plaistow
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
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4
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Hossin MZ, Falkstedt D, Allebeck P, Mishra G, Koupil I. Early life programming of adult ischemic heart disease within and across generations: The role of the socioeconomic context. Soc Sci Med 2021; 275:113811. [PMID: 33713928 DOI: 10.1016/j.socscimed.2021.113811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/22/2021] [Accepted: 02/27/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND The developmental origins of ischemic heart disease (IHD) have been widely documented but little is known about their persistence across more than one generation. This study aimed to investigate whether the effects of early life disadvantages on adult IHD have changed between generations and are mediated by adult socioeconomic circumstances, and further explore the transgenerational effects of grandparental and parental exposures to disadvantaged circumstances on adult offspring's IHD. METHODS We used register-based data from the Uppsala Multigenerational Study, Sweden. The study populations were the parents born 1915-1929 and their offspring born 1932-1972 with available obstetric data. The offspring were further linked to grandparents who had their socioeconomic and demographic data recorded. The outcome was incident IHD assessed at ages 32-75 during a follow-up from January 1, 1964 till December 31, 2008. The exposures included birthweight standardized-for-gestational age, ponderal index, gestational length, and parental socioeconomic position (SEP). Education and income were analyzed as mediators. Potential transgenerational associations were explored by linking offspring IHD to parents' standardized birthweight and gestational length, grandparental SEP, and to grandmothers' age, parity, and marital status at parental birth. All associations were examined in Cox proportional hazard regression models. RESULTS Lower standardized birthweight and lower parental SEP were found to be associated with higher IHD rates in both generations, with no evidence of effect modification by generation. Education and income did not mediate the association between standardized birthweight and IHD. Disadvantaged grandparental SEP, younger and older childbearing ages of grandmothers, and paternal preterm birth affected offspring's IHD independent of parental education, income, or IHD history. CONCLUSIONS The findings point to similar magnitudes of IHD inequalities by early life disadvantages across two historical periods and the existence of transgenerational effects on IHD. Epigenetic dysregulation involving the germline is a plausible candidate mechanism underlying the transgenerational associations that warrant further research.
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Affiliation(s)
| | - Daniel Falkstedt
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden.
| | - Peter Allebeck
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden.
| | - Gita Mishra
- School of Public Health, The University of Queensland, Herston, Australia.
| | - Ilona Koupil
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden; Department of Public Health Sciences, Stockholm University, Stockholm, Sweden.
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5
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Sundman AS, Pértille F, Lehmann Coutinho L, Jazin E, Guerrero-Bosagna C, Jensen P. DNA methylation in canine brains is related to domestication and dog-breed formation. PLoS One 2020; 15:e0240787. [PMID: 33119634 PMCID: PMC7595415 DOI: 10.1371/journal.pone.0240787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/02/2020] [Indexed: 11/19/2022] Open
Abstract
Epigenetic factors such as DNA methylation act as mediators in the interaction between genome and environment. Variation in the epigenome can both affect phenotype and be inherited, and epigenetics has been suggested to be an important factor in the evolutionary process. During domestication, dogs have evolved an unprecedented between-breed variation in morphology and behavior in an evolutionary short period. In the present study, we explore DNA methylation differences in brain, the most relevant tissue with respect to behavior, between wolf and dog breeds. We optimized a combined method of genotype-by-sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) for its application in canines. Genomic DNA from the frontal cortex of 38 dogs of 8 breeds and three wolves was used. GBS and GBS-MeDIP libraries were prepared and sequenced on Illuma HiSeq2500 platform. The reduced sample represented 1.18 ± 0.4% of the total dog genome (2,4 billion BP), while the GBS-MeDIP covered 11,250,788 ± 4,042,106 unique base pairs. We find substantial DNA methylation differences between wolf and dog and between the dog breeds. The methylation profiles of the different groups imply that epigenetic factors may have been important in the speciation from dog to wolf, but also in the divergence of different dog breeds. Specifically, we highlight methylation differences in genes related to behavior and morphology. We hypothesize that these differences are involved in the phenotypic variation found among dogs, whereas future studies will have to find the specific mechanisms. Our results not only add an intriguing new dimension to dog breeding but are also useful to further understanding of epigenetic involvement.
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Affiliation(s)
- Ann-Sofie Sundman
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Fábio Pértille
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Elena Jazin
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Carlos Guerrero-Bosagna
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Per Jensen
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
- * E-mail:
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6
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Walker C, Burggren W. Remodeling the epigenome and (epi)cytoskeleton: a new paradigm for co-regulation by methylation. ACTA ACUST UNITED AC 2020; 223:223/13/jeb220632. [PMID: 32620673 DOI: 10.1242/jeb.220632] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The epigenome determines heritable patterns of gene expression in the absence of changes in DNA sequence. The result is programming of different cellular-, tissue- and organ-specific phenotypes from a single organismic genome. Epigenetic marks that comprise the epigenome (e.g. methylation) are placed upon or removed from chromatin (histones and DNA) to direct the activity of effectors that regulate gene expression and chromatin structure. Recently, the cytoskeleton has been identified as a second target for the cell's epigenetic machinery. Several epigenetic 'readers, writers and erasers' that remodel chromatin have been discovered to also remodel the cytoskeleton, regulating structure and function of microtubules and actin filaments. This points to an emerging paradigm for dual-function remodelers with 'chromatocytoskeletal' activity that can integrate cytoplasmic and nuclear functions. For example, the SET domain-containing 2 methyltransferase (SETD2) has chromatocytoskeletal activity, methylating both histones and microtubules. The SETD2 methyl mark on chromatin is required for efficient DNA repair, and its microtubule methyl mark is required for proper chromosome segregation during mitosis. This unexpected convergence of SETD2 activity on histones and microtubules to maintain genomic stability suggests the intriguing possibility of an expanded role in the cell for chromatocytoskeletal proteins that read, write and erase methyl marks on the cytoskeleton as well as chromatin. Coordinated use of methyl marks to remodel both the epigenome and the (epi)cytoskeleton opens the possibility for integrated regulation (which we refer to as 'epiregulation') of other higher-level functions, such as muscle contraction or learning and memory, and could even have evolutionary implications.
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Affiliation(s)
- Cheryl Walker
- Center for Precision Environmental Health, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Warren Burggren
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
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Ibhazehiebo K, Rho JM, Kurrasch DM. Metabolism-based drug discovery in zebrafish: An emerging strategy to uncover new anti-seizure therapies. Neuropharmacology 2020; 167:107988. [PMID: 32070912 DOI: 10.1016/j.neuropharm.2020.107988] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 02/01/2020] [Accepted: 02/03/2020] [Indexed: 12/20/2022]
Abstract
As one of the most common neurological disorders, epilepsy can occur throughout the lifespan and from a multiplicity of causes, including genetic mutations, inflammation, neurotrauma, or brain malformations. Although pharmacological agents are the mainstay of treatment for seizure control, an unyielding 30-40% of patients remain refractory to these medications and continue to experience spontaneous recurrent seizures with attendant life-long cognitive, behavioural, and mental health issues, as well as an increased risk for sudden unexpected death. Despite over eight decades of antiseizure drug (ASD) discovery and the approval of dozens of new medications, the percentage of this refractory population remains virtually unchanged, suggesting that drugs with new and unexpected mechanisms of action are needed. In this brief review, we discuss the need for new animal models of epilepsy, with a particular focus on the advantages and disadvantages of zebrafish. We also outline the evidence that epilepsy is characterized by derangements in mitochondrial function and introduce the rationale and promise of bioenergetics as a functional readout assay to uncover novel ASDs. We also consider limitations of a zebrafish metabolism-based drug screening approach. Our goal is to discuss the opportunities and challenges of further development of mitochondrial screening strategies for the development of novel ASDs. This article is part of the special issue entitled 'New Epilepsy Therapies for the 21st Century - From Antiseizure Drugs to Prevention, Modification and Cure of Epilepsy'.
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Affiliation(s)
- Kingsley Ibhazehiebo
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Canada
| | - Jong M Rho
- Alberta Children's Hospital Research Institute, University of Calgary, Canada; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Canada; Department of Neurosciences and Pediatrics, University of California San Diego, Rady Children's Hospital San Diego, California, USA
| | - Deborah M Kurrasch
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Canada.
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8
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Liu Y, Weyrich LS, Llamas B. More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment. Mol Biol Evol 2020; 37:307-319. [PMID: 31638147 DOI: 10.1093/molbev/msz231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Whether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.
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Affiliation(s)
- Yichen Liu
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
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9
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Cauceglia JW, Nelson AC, Rubinstein ND, Kukreja S, Sasso LN, Beaufort JA, Rando OJ, Potts WK. Transitions in paternal social status predict patterns of offspring growth and metabolic transcription. Mol Ecol 2020; 29:624-638. [PMID: 31885115 DOI: 10.1111/mec.15346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 11/27/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
Abstract
One type of parental effect occurs when changes in parental phenotype or environment trigger changes to offspring phenotype. Such nongenetic parental effects can be precisely triggered in response to an environmental cue in time-locked fashion, or in other cases, persist for multiple generations after the cue has been removed, suggesting multiple timescales of action. For parental effects to serve as reliable signals of current environmental conditions, they should be reversible, such that when cues change, offspring phenotypes change in accordance. Social hierarchy is a prevalent feature of the environment, and current parental social status could signal the environment in which offspring will be born. Here, we sought to address parental effects of social status and their timescale of action in mice. We show that territorial competition in seminatural environments affects offspring growth. Although dominant males are not heavier than nondominant or control males, they produce faster growing offspring, particularly sons. The timing, effect-size, and sex-specificity of this association are modulated by maternal social experience. We show that a change in paternal social status is sufficient to modulate offspring weight: from one breeding cycle to the next, status-ascending males produce heavier sons than before, and status-descending males produce lighter sons than before. Current paternal status is also highly predictive of liver transcription in sons, including molecular pathways controlling oxidative phosphorylation and iron metabolism. These results are consistent with a parental effect of social experience, although alternative explanations are considered. In summary, changes in paternal social status are associated with changes in offspring growth and metabolism.
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Affiliation(s)
- Joseph W Cauceglia
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Adam C Nelson
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | | | - Shweta Kukreja
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lynsey N Sasso
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - John A Beaufort
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Wayne K Potts
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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10
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Bertozzi TM, Ferguson-Smith AC. Metastable epialleles and their contribution to epigenetic inheritance in mammals. Semin Cell Dev Biol 2020; 97:93-105. [PMID: 31551132 DOI: 10.1016/j.semcdb.2019.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 02/02/2023]
Abstract
Many epigenetic differences between individuals are driven by genetic variation. Mammalian metastable epialleles are unusual in that they show variable DNA methylation states between genetically identical individuals. The occurrence of such states across generations has resulted in their consideration by many as strong evidence for epigenetic inheritance in mammals, with the classic Avy and AxinFu mouse models - each products of repeat element insertions - being the most widely accepted examples. Equally, there has been interest in exploring their use as epigenetic biosensors given their susceptibility to environmental compromise. Here we review the classic murine metastable epialleles as well as more recently identified candidates, with the aim of providing a more holistic understanding of their biology. We consider the extent to which epigenetic inheritance occurs at metastable epialleles and explore the limited mechanistic insights into the establishment of their variable epigenetic states. We discuss their environmental modulation and their potential relevance in genome regulation. In light of recent whole-genome screens for novel metastable epialleles, we point out the need to reassess their biological relevance in multi-generational studies and we highlight their value as a model to study repeat element silencing as well as the mechanisms and consequences of mammalian epigenetic stochasticity.
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Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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11
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CDX1/2 and KLF5 Expression and Epigenetic Modulation of Sonic Hedgehog Signaling in Gastric Adenocarcinoma. Pathol Oncol Res 2019; 25:1215-1222. [DOI: 10.1007/s12253-019-00594-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 01/15/2019] [Indexed: 01/06/2023]
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12
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Radziejewska A, Chmurzynska A. Folate and choline absorption and uptake: Their role in fetal development. Biochimie 2018; 158:10-19. [PMID: 30529042 DOI: 10.1016/j.biochi.2018.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 12/29/2022]
Abstract
SCOPE In this review, we attempt to assess how choline and folate transporters affect fetal development. We focus on how the expression of these transporters in response to choline and folate intake affects transport effectiveness. We additionally describe allelic variants of the genes encoding these transporters and their phenotypic effects. METHODS AND RESULTS We made an extensive review of recent articles describing role of choline and folate - with particularly emphasize on their transporters - in fetal development. Folate and choline are necessary for the proper functioning of the cell and body. During pregnancy, the requirements of these nutrients increase because of elevated maternal demand and the rapid division of fetal cells. The concentrations of folate and choline in cells depend on food intake, the absorption of nutrients, and the cellular transport system, which is tissue-specific and developmentally regulated. Relatively few studies have investigated the role of choline transporters in fetal development. CONCLUSIONS In this review we show relations between functioning of folate and choline transporters and fetal development.
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Affiliation(s)
- Anna Radziejewska
- Institute of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poland
| | - Agata Chmurzynska
- Institute of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poland.
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13
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Hur SSJ, Cropley JE, Suter CM. Paternal epigenetic programming: evolving metabolic disease risk. J Mol Endocrinol 2017; 58:R159-R168. [PMID: 28100703 DOI: 10.1530/jme-16-0236] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/05/2017] [Indexed: 02/03/2023]
Abstract
Parental health or exposures can affect the lifetime health outcomes of offspring, independently of inherited genotypes. Such 'epigenetic' effects occur over a broad range of environmental stressors, including defects in parental metabolism. Although maternal metabolic effects are well documented, it has only recently been established that that there is also an independent paternal contribution to long-term metabolic health. Both paternal undernutrition and overnutrition can induce metabolic phenotypes in immediate offspring, and in some cases, the induced phenotype can affect multiple generations, implying inheritance of an acquired trait. The male lineage transmission of metabolic disease risk in these cases implicates a heritable factor carried by sperm. Sperm-based transmission provides a tractable system to interrogate heritable epigenetic factors influencing metabolism, and as detailed here, animal models of paternal programming have already provided some significant insights. Here, we review the evidence for paternal programming of metabolism in humans and animal models, and the available evidence on potential underlying mechanisms. Programming by paternal metabolism can be observed in multiple species across animal phyla, suggesting that this phenomenon may have a unique evolutionary significance.
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Affiliation(s)
- Suzy S J Hur
- Victor Chang Cardiac Research InstituteDarlinghurst, New South Wales, Australia
- Faculty of MedicineUniversity of New South Wales, Kensington, New South Wales, Australia
| | - Jennifer E Cropley
- Victor Chang Cardiac Research InstituteDarlinghurst, New South Wales, Australia
- Faculty of MedicineUniversity of New South Wales, Kensington, New South Wales, Australia
| | - Catherine M Suter
- Victor Chang Cardiac Research InstituteDarlinghurst, New South Wales, Australia
- Faculty of MedicineUniversity of New South Wales, Kensington, New South Wales, Australia
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14
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Oettlé AC, Demeter FP, L'abbé EN. Ancestral Variations in the Shape and Size of the Zygoma. Anat Rec (Hoboken) 2016; 300:196-208. [DOI: 10.1002/ar.23469] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/16/2016] [Accepted: 07/25/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Anna C. Oettlé
- Department of Anatomy, School of Medicine, Faculty of Health Sciences; University of Pretoria; Arcadia 0007 Republic of South Africa
| | - Fabrice P. Demeter
- Department of Anatomy, School of Medicine, Faculty of Health Sciences; University of Pretoria; Arcadia 0007 Republic of South Africa
- Musée de l'Homme, HNS; UMR7206, 17 Place du Trocadéro Paris 75116 France
| | - Ericka N. L'abbé
- Department of Anatomy, School of Medicine, Faculty of Health Sciences; University of Pretoria; Arcadia 0007 Republic of South Africa
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15
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Moore DS. Behavioral epigenetics. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 9. [PMID: 27906527 DOI: 10.1002/wsbm.1333] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 12/26/2022]
Abstract
Why do we grow up to have the traits we do? Most 20th century scientists answered this question by referring only to our genes and our environments. But recent discoveries in the emerging field of behavioral epigenetics have revealed factors at the interface between genes and environments that also play crucial roles in development. These factors affect how genes work; scientists now know that what matters as much as which genes you have (and what environments you encounter) is how your genes are affected by their contexts. The discovery that what our genes do depends in part on our experiences has shed light on how Nature and Nurture interact at the molecular level inside of our bodies. Data emerging from the world's behavioral epigenetics laboratories support the idea that a person's genes alone cannot determine if, for example, he or she will end up shy, suffering from cardiovascular disease, or extremely smart. Among the environmental factors that can influence genetic activity are parenting styles, diets, and social statuses. In addition to influencing how doctors treat diseases, discoveries about behavioral epigenetics are likely to alter how biologists think about evolution, because some epigenetic effects of experience appear to be transmissible from generation to generation. This domain of research will likely change how we think about the origins of human nature. WIREs Syst Biol Med 2017, 9:e1333. doi: 10.1002/wsbm.1333 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- David S Moore
- Pitzer College & Claremont Graduate University, Claremont, CA, USA
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16
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Cropley JE, Eaton SA, Aiken A, Young PE, Giannoulatou E, Ho JWK, Buckland ME, Keam SP, Hutvagner G, Humphreys DT, Langley KG, Henstridge DC, Martin DIK, Febbraio MA, Suter CM. Male-lineage transmission of an acquired metabolic phenotype induced by grand-paternal obesity. Mol Metab 2016; 5:699-708. [PMID: 27656407 PMCID: PMC5021672 DOI: 10.1016/j.molmet.2016.06.008] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 12/22/2022] Open
Abstract
Objective Parental obesity can induce metabolic phenotypes in offspring independent of the inherited DNA sequence. Here we asked whether such non-genetic acquired metabolic traits can be passed on to a second generation that has never been exposed to obesity, even as germ cells. Methods We examined the F1, F2, and F3 a/a offspring derived from F0 matings of obese prediabetic Avy/a sires and lean a/a dams. After F0, only lean a/a mice were used for breeding. Results We found that F1 sons of obese founder males exhibited defects in glucose and lipid metabolism, but only upon a post-weaning dietary challenge. F1 males transmitted these defects to their own male progeny (F2) in the absence of the dietary challenge, but the phenotype was largely attenuated by F3. The sperm of F1 males exhibited changes in the abundance of several small RNA species, including the recently reported diet-responsive tRNA-derived fragments. Conclusions These data indicate that induced metabolic phenotypes may be propagated for a generation beyond any direct exposure to an inducing factor. This non-genetic inheritance likely occurs via the actions of sperm noncoding RNA. Paternal obesity induces latent defects in metabolism in F1 sons. Metabolic disease in F1 sons is exposed by short challenge with a Western diet. F1 sons transmit their phenotype to F2 grandsons in the absence of dietary challenge. F1 sperm exhibit changes to prominent small RNA species.
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Affiliation(s)
- Jennifer E Cropley
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales, Kensington, NSW, 2052, Australia.
| | - Sally A Eaton
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales, Kensington, NSW, 2052, Australia
| | - Alastair Aiken
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Paul E Young
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Eleni Giannoulatou
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Joshua W K Ho
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales, Kensington, NSW, 2052, Australia
| | - Michael E Buckland
- Brain and Mind Research Institute, University of Sydney, Sydney, NSW, 2006, Australia
| | - Simon P Keam
- Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Gyorgy Hutvagner
- Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - David T Humphreys
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Katherine G Langley
- Cellular and Molecular Metabolism Laboratory, Baker IDI Diabetes and Heart Research Institute, Melbourne, VIC, 3004, Australia
| | - Darren C Henstridge
- Cellular and Molecular Metabolism Laboratory, Baker IDI Diabetes and Heart Research Institute, Melbourne, VIC, 3004, Australia
| | - David I K Martin
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA
| | - Mark A Febbraio
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Catherine M Suter
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales, Kensington, NSW, 2052, Australia.
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18
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Schrey AW, Robbins TR, Lee J, Dukes DW, Ragsdale AK, Thawley CJ, Langkilde T. Epigenetic response to environmental change: DNA methylation varies with invasion status. ENVIRONMENTAL EPIGENETICS 2016; 2:dvw008. [PMID: 29492288 PMCID: PMC5804522 DOI: 10.1093/eep/dvw008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 06/08/2023]
Abstract
Epigenetic mechanisms may be important for a native species' response to rapid environmental change. Red Imported Fire Ants (Solenopsis invicta Santschi, 1916) were recently introduced to areas occupied by the Eastern Fence Lizard (Sceloporus undulatus Bosc & Daudin, 1801). Behavioral, morphological and physiological phenotypes of the Eastern Fence Lizard have changed following invasion, creating a natural biological system to investigate environmentally induced epigenetic changes. We tested for variation in DNA methylation patterns in Eastern Fence Lizard populations associated with different histories of invasion by Red Imported Fire Ants. At methylation sensitive amplified fragment length polymorphism loci, we detected a higher diversity of methylation in Eastern Fence Lizard populations from Fire Ant uninvaded versus invaded sites, and uninvaded sites had higher methylation. Our results suggest that invasive species may alter methylation frequencies and the pattern of methylation among native individuals. While our data indicate a high level of intrinsic variability in DNA methylation, DNA methylation at some genomic loci may underlie observed phenotypic changes in Eastern Fence Lizard populations in response to invasion of Red Imported Fire Ants. This process may be important in facilitating adaptation of native species to novel pressures imposed by a rapidly changing environment.
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Affiliation(s)
- Aaron W. Schrey
- Department of Biology, Armstrong State University, 11935 Abercorn Street, Savannah,
GA 31419
| | - Travis R. Robbins
- Biology, Chemistry & Environmental Science, Northern New Mexico College, 921 N.
Paseo De Oñate, Española, NM 87532, USA
- Biology Department, Center for Brain Behavior and Cognition, Intercollegiate
Graduate Degree Program in Ecology, 208 Mueller Laboratory, Pennsylvania State University,
University Park, PA 16802, USA
| | - Jacob Lee
- Department of Biology, Armstrong State University, 11935 Abercorn Street, Savannah,
GA 31419
| | - David W. Dukes
- Department of Biology, Armstrong State University, 11935 Abercorn Street, Savannah,
GA 31419
| | - Alexandria K. Ragsdale
- Department of Biology, Armstrong State University, 11935 Abercorn Street, Savannah,
GA 31419
| | - Christopher J. Thawley
- Biology Department, Center for Brain Behavior and Cognition, Intercollegiate
Graduate Degree Program in Ecology, 208 Mueller Laboratory, Pennsylvania State University,
University Park, PA 16802, USA
| | - Tracy Langkilde
- Biology Department, Center for Brain Behavior and Cognition, Intercollegiate
Graduate Degree Program in Ecology, 208 Mueller Laboratory, Pennsylvania State University,
University Park, PA 16802, USA
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O’Dea RE, Noble DWA, Johnson SL, Hesselson D, Nakagawa S. The role of non-genetic inheritance in evolutionary rescue: epigenetic buffering, heritable bet hedging and epigenetic traps. ENVIRONMENTAL EPIGENETICS 2016; 2:dvv014. [PMID: 29492283 PMCID: PMC5804513 DOI: 10.1093/eep/dvv014] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 11/30/2015] [Accepted: 12/09/2015] [Indexed: 05/17/2023]
Abstract
Rapid environmental change is predicted to compromise population survival, and the resulting strong selective pressure can erode genetic variation, making evolutionary rescue unlikely. Non-genetic inheritance may provide a solution to this problem and help explain the current lack of fit between purely genetic evolutionary models and empirical data. We hypothesize that epigenetic modifications can facilitate evolutionary rescue through 'epigenetic buffering'. By facilitating the inheritance of novel phenotypic variants that are generated by environmental change-a strategy we call 'heritable bet hedging'-epigenetic modifications could maintain and increase the evolutionary potential of a population. This process may facilitate genetic adaptation by preserving existing genetic variation, releasing cryptic genetic variation and/or facilitating mutations in functional loci. Although we show that examples of non-genetic inheritance are often maladaptive in the short term, accounting for phenotypic variance and non-adaptive plasticity may reveal important evolutionary implications over longer time scales. We also discuss the possibility that maladaptive epigenetic responses may be due to 'epigenetic traps', whereby evolutionarily novel factors (e.g. endocrine disruptors) hack into the existing epigenetic machinery. We stress that more ecologically relevant work on transgenerational epigenetic inheritance is required. Researchers conducting studies on transgenerational environmental effects should report measures of phenotypic variance, so that the possibility of both bet hedging and heritable bet hedging can be assessed. Future empirical and theoretical work is required to assess the relative importance of genetic and epigenetic variation, and their interaction, for evolutionary rescue.
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Affiliation(s)
- Rose E. O’Dea
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel W. A. Noble
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sheri L. Johnson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Daniel Hesselson
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, UNSW, Australia, Sydney, NSW, Australia
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Department of Zoology, University of Otago, Dunedin, New Zealand
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
- *Correspondence address. School of BEES, UNSW, Sydney, NSW 2052, Australia, Tel:
+61-2-9385-8084
; Fax:
+61-2-9385-9138
; E-mail:
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Szarc vel Szic K, Declerck K, Vidaković M, Vanden Berghe W. From inflammaging to healthy aging by dietary lifestyle choices: is epigenetics the key to personalized nutrition? Clin Epigenetics 2015; 7:33. [PMID: 25861393 PMCID: PMC4389409 DOI: 10.1186/s13148-015-0068-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 03/09/2015] [Indexed: 01/12/2023] Open
Abstract
The progressively older population in developed countries is reflected in an increase in the number of people suffering from age-related chronic inflammatory diseases such as metabolic syndrome, diabetes, heart and lung diseases, cancer, osteoporosis, arthritis, and dementia. The heterogeneity in biological aging, chronological age, and aging-associated disorders in humans have been ascribed to different genetic and environmental factors (i.e., diet, pollution, stress) that are closely linked to socioeconomic factors. The common denominator of these factors is the inflammatory response. Chronic low-grade systemic inflammation during physiological aging and immunosenescence are intertwined in the pathogenesis of premature aging also defined as ‘inflammaging.’ The latter has been associated with frailty, morbidity, and mortality in elderly subjects. However, it is unknown to what extent inflammaging or longevity is controlled by epigenetic events in early life. Today, human diet is believed to have a major influence on both the development and prevention of age-related diseases. Most plant-derived dietary phytochemicals and macro- and micronutrients modulate oxidative stress and inflammatory signaling and regulate metabolic pathways and bioenergetics that can be translated into stable epigenetic patterns of gene expression. Therefore, diet interventions designed for healthy aging have become a hot topic in nutritional epigenomic research. Increasing evidence has revealed that complex interactions between food components and histone modifications, DNA methylation, non-coding RNA expression, and chromatin remodeling factors influence the inflammaging phenotype and as such may protect or predispose an individual to many age-related diseases. Remarkably, humans present a broad range of responses to similar dietary challenges due to both genetic and epigenetic modulations of the expression of target proteins and key genes involved in the metabolism and distribution of the dietary constituents. Here, we will summarize the epigenetic actions of dietary components, including phytochemicals, and macro- and micronutrients as well as metabolites, that can attenuate inflammaging. We will discuss the challenges facing personalized nutrition to translate highly variable interindividual epigenetic diet responses to potential individual health benefits/risks related to aging disease.
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Affiliation(s)
- Katarzyna Szarc vel Szic
- Lab Protein Science, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Ken Declerck
- Lab Protein Science, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Melita Vidaković
- Department of Molecular Biology, Institute for Biological Research, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia
| | - Wim Vanden Berghe
- Lab Protein Science, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
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21
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Nongenetic inheritance and transgenerational epigenetics. Trends Mol Med 2014; 21:134-44. [PMID: 25601643 DOI: 10.1016/j.molmed.2014.12.004] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 11/21/2022]
Abstract
The idea that inherited genotypes define phenotypes has been paramount in modern biology. The question remains, however, whether stable phenotypes could be also inherited from parents independently of the genetic sequence per se. Recent data suggest that parental experiences can be transmitted behaviorally, through in utero exposure of the developing fetus to the maternal environment, or through either the male or female germline. The challenge is to delineate a plausible mechanism. In the past decade it has been proposed that epigenetic mechanisms are involved in multigenerational transmission of phenotypes and transgenerational inheritance. The prospect that ancestral experiences are written in our epigenome has immense implications for our understanding of human behavior, health, and disease.
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22
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O'Neill RJ, Vrana PB, Rosenfeld CS. Maternal methyl supplemented diets and effects on offspring health. Front Genet 2014; 5:289. [PMID: 25206362 PMCID: PMC4143751 DOI: 10.3389/fgene.2014.00289] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/05/2014] [Indexed: 12/21/2022] Open
Abstract
Women seeking to become pregnant and pregnant women are currently advised to consume high amounts of folic acid and other methyl donors to prevent neural tube defects in their offspring. These diets can alter methylation patterns of several biomolecules, including nucleic acids, and histone proteins. Limited animal model data suggests that developmental exposure to these maternal methyl supplemented (MS) diets leads to beneficial epimutations. However, other rodent and humans studies have yielded opposing findings with such diets leading to promiscuous epimutations that are likely associated with negative health outcomes. Conflict exists to whether these maternal diets are preventative or exacerbate the risk for Autism Spectrum Disorders (ASD) in children. This review will discuss the findings to date on the potential beneficial and aversive effects of maternal MS diets. We will also consider how other factors might influence the effects of MS diets. Current data suggest that there is cause for concern as maternal MS diets may lead to epimutations that underpin various diseases, including neurobehavioral disorders. Further studies are needed to explore the comprehensive effects maternal MS diets have on the offspring epigenome and subsequent overall health.
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Affiliation(s)
- Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA ; Institute for Systems Genomics, University of Connecticut Storrs, CT, USA
| | - Paul B Vrana
- Peromyscus Genetic Stock Center, University of South Carolina Columbia, SC, USA ; Department of Biological Sciences, University of South Carolina Columbia, SC, USA
| | - Cheryl S Rosenfeld
- Department of Biomedical Sciences, Bond Life Sciences Center, University of Missouri Columbia, MO, USA ; Bond Life Sciences Center, University of Missouri Columbia, MO, USA ; Genetics Area Program Faculty Member, Bond Life Sciences Center, University of Missouri Columbia, MO, USA
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24
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Furrow RE. Epigenetic inheritance, epimutation, and the response to selection. PLoS One 2014; 9:e101559. [PMID: 25019291 PMCID: PMC4096402 DOI: 10.1371/journal.pone.0101559] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/07/2014] [Indexed: 12/30/2022] Open
Abstract
There has been minimal theoretical exploration of the role of epigenetic variation in the response to natural selection. Using a population genetic model, I derive formulae that characterize the response of epigenetic variation to selection over multiple generations. Unlike genetic models in which mutation rates are assumed to be low relative to the strength of selection, the response to selection decays quickly due to a rapid lowering of parent-offspring epiallelic correlation. This effect is separate from the slowing response caused by a reduction in epigenetic variation. These results suggest that epigenetic variation may be less responsive to natural selection than is genetic variation, even in cases where levels of heritability appear similar.
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Affiliation(s)
- Robert E. Furrow
- Department of Biology, Stanford University, Stanford, California, United States of America
- * E-mail:
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25
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Bégin P, Nadeau KC. Epigenetic regulation of asthma and allergic disease. Allergy Asthma Clin Immunol 2014; 10:27. [PMID: 24932182 PMCID: PMC4057652 DOI: 10.1186/1710-1492-10-27] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/18/2014] [Indexed: 01/18/2023] Open
Abstract
Epigenetics of asthma and allergic disease is a field that has expanded greatly in the last decade. Previously thought only in terms of cell differentiation, it is now evident the epigenetics regulate many processes. With T cell activation, commitment toward an allergic phenotype is tightly regulated by DNA methylation and histone modifications at the Th2 locus control region. When normal epigenetic control is disturbed, either experimentally or by environmental exposures, Th1/Th2 balance can be affected. Epigenetic marks are not only transferred to daughter cells with cell replication but they can also be inherited through generations. In animal models, with constant environmental pressure, epigenetically determined phenotypes are amplified through generations and can last up to 2 generations after the environment is back to normal. In this review on the epigenetic regulation of asthma and allergic diseases we review basic epigenetic mechanisms and discuss the epigenetic control of Th2 cells. We then cover the transgenerational inheritance model of epigenetic traits and discuss how this could relate the amplification of asthma and allergic disease prevalence and severity through the last decades. Finally, we discuss recent epigenetic association studies for allergic phenotypes and related environmental risk factors as well as potential underlying mechanisms for these associations.
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Affiliation(s)
- Philippe Bégin
- Allergy, Immunology, and Rheumatology Division, Stanford University, 269 Campus Drive, Stanford, California, USA
| | - Kari C Nadeau
- Allergy, Immunology, and Rheumatology Division, Stanford University, 269 Campus Drive, Stanford, California, USA
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Börsch-Haubold AG, Montero I, Konrad K, Haubold B. Genome-wide quantitative analysis of histone H3 lysine 4 trimethylation in wild house mouse liver: environmental change causes epigenetic plasticity. PLoS One 2014; 9:e97568. [PMID: 24849289 PMCID: PMC4029994 DOI: 10.1371/journal.pone.0097568] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/17/2014] [Indexed: 01/05/2023] Open
Abstract
In mammals, exposure to toxic or disease-causing environments can change epigenetic marks that are inherited independently of the intrauterine environment. Such inheritance of molecular phenotypes may be adaptive. However, studies demonstrating molecular evidence for epigenetic inheritance have so far relied on extreme treatments, and are confined to inbred animals. We therefore investigated whether epigenomic changes could be detected after a non-drastic change in the environment of an outbred organism. We kept two populations of wild-caught house mice (Mus musculus domesticus) for several generations in semi-natural enclosures on either standard diet and light cycle, or on an energy-enriched diet with longer daylight to simulate summer. As epigenetic marker for active chromatin we quantified genome-wide histone-3 lysine-4 trimethylation (H3K4me3) from liver samples by chromatin immunoprecipitation and high-throughput sequencing as well as by quantitative polymerase chain reaction. The treatment caused a significant increase of H3K4me3 at metabolic genes such as lipid and cholesterol regulators, monooxygenases, and a bile acid transporter. In addition, genes involved in immune processes, cell cycle, and transcription and translation processes were also differently marked. When we transferred young mice of both populations to cages and bred them under standard conditions, most of the H3K4me3 differences were lost. The few loci with stable H3K4me3 changes did not cluster in metabolic functional categories. This is, to our knowledge, the first quantitative study of an epigenetic marker in an outbred mammalian organism. We demonstrate genome-wide epigenetic plasticity in response to a realistic environmental stimulus. In contrast to disease models, the bulk of the epigenomic changes we observed were not heritable.
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Affiliation(s)
- Angelika G. Börsch-Haubold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
| | - Inka Montero
- Institute for Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Kathryn Konrad
- Cologne Center for Genomics, University of Cologne, Köln, Germany
| | - Bernhard Haubold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Jiang X, West AA, Caudill MA. Maternal choline supplementation: a nutritional approach for improving offspring health? Trends Endocrinol Metab 2014; 25:263-73. [PMID: 24680198 DOI: 10.1016/j.tem.2014.02.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/28/2014] [Accepted: 02/05/2014] [Indexed: 12/15/2022]
Abstract
The modulatory role of choline on the fetal epigenome and the impact of in utero choline supply on fetal programming and health are of great interest. Studies in animals and/or humans suggest that maternal choline supplementation during pregnancy benefits important physiologic systems such as offspring cognitive function, response to stress, and cerebral inhibition. Because alterations in offspring phenotype frequently coincide with epigenetic modifications and changes in gene expression, maternal choline supplementation may be a nutritional strategy to improve lifelong health of the child. Future studies are warranted to elucidate further the effect of choline on the fetal epigenome and to determine the level of maternal choline intake required for optimal offspring physiologic function.
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Affiliation(s)
- Xinyin Jiang
- Department of Health and Nutrition Sciences, Brooklyn College, Brooklyn, NY 11210, USA
| | - Allyson A West
- Division of Nutritional Sciences, Cornell University, Ithaca 14853, NY, USA
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca 14853, NY, USA.
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Suter CM, Boffelli D, Martin DIK. A role for epigenetic inheritance in modern evolutionary theory? A comment in response to Dickins and Rahman. Proc Biol Sci 2013; 280:20130903; discussion 20131820. [PMID: 24089330 DOI: 10.1098/rspb.2013.0903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Catherine M Suter
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, , 405 Liverpool Street, Darlinghurst, New South Wales 2010, Australia, Center for Genetics, Children's Hospital Oakland Research Institute, , 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
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Pathways by which the interplay of organismic and environmental factors lead to phenotypic variation within and across generations. ADVANCES IN CHILD DEVELOPMENT AND BEHAVIOR 2013; 44:325-54. [PMID: 23834011 DOI: 10.1016/b978-0-12-397947-6.00012-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The range of responses made to environmental exigencies by animals, including humans, may be impacted by the experiences of their progenitors. In mammals, pathways have been documented ranging from transactions between a mother and her developing fetus in the womb through continuity of parenting practices and cultural inheritance. In addition, phenotypic plasticity may be constrained by factors transmitted by the gametes that are involved in the regulation of gene expression rather than modifications to the genome itself. Possible mediators for this kind of inheritance are examined, and the conditions that might have led to the evolution of such transmission are considered. Anticipatory adjustments to possible environmental exigencies are likely to occur when such conditions recur regularly, but intermittently across generations and endure for substantial periods of time, and when adjusting to them after the fact is likely to be biologically costly, even life-threatening. It appears that physical growth and responses to nutrient availability are domains in which anticipatory, epigenetically inherited adjustments occur. In addition, given the fact that humans have oppressed one another repeatedly and for relatively long periods of time, such behavioral tendencies as boldness or innovativeness may be behavioral traits subject to such effects. The implications of these factors for research and policy are discussed.
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Jablonka E. Epigenetic inheritance and plasticity: The responsive germline. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 111:99-107. [DOI: 10.1016/j.pbiomolbio.2012.08.014] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 08/24/2012] [Accepted: 08/28/2012] [Indexed: 02/03/2023]
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Bohacek J, Gapp K, Saab BJ, Mansuy IM. Transgenerational epigenetic effects on brain functions. Biol Psychiatry 2013; 73:313-20. [PMID: 23062885 DOI: 10.1016/j.biopsych.2012.08.019] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 08/07/2012] [Accepted: 08/19/2012] [Indexed: 12/21/2022]
Abstract
Psychiatric diseases are multifaceted disorders with complex etiology, recognized to have strong heritable components. Despite intense research efforts, genetic loci that substantially account for disease heritability have not yet been identified. Over the last several years, epigenetic processes have emerged as important factors for many brain diseases, and the discovery of epigenetic processes in germ cells has raised the possibility that they may contribute to disease heritability and disease risk. This review examines epigenetic mechanisms in complex diseases and summarizes the most illustrative examples of transgenerational epigenetic inheritance in mammals and their relevance for brain function. Environmental factors that can affect molecular processes and behavior in exposed individuals and their offspring, and their potential epigenetic underpinnings, are described. Possible routes and mechanisms of transgenerational transmission are proposed, and the major questions and challenges raised by this emerging field of research are considered.
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Affiliation(s)
- Johannes Bohacek
- Brain Research Institute, University of Zurich/Swiss Federal Institute of Technology, Zurich, Switzerland
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Jensen P. Transgenerational epigenetic effects on animal behaviour. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:447-54. [PMID: 23369895 DOI: 10.1016/j.pbiomolbio.2013.01.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 12/18/2012] [Accepted: 01/07/2013] [Indexed: 01/02/2023]
Abstract
Over the last decade a shift in paradigm has occurred with respect to the interaction between environment and genes. It is now clear that animal genomes are regulated to a large extent as a result of input from environmental events and experiences, which cause short- and long-term modifications in epigenetic markings of DNA and histones. In this review, the evidence that such epigenetic modifications can affect the behaviour of animals is explored, and whether such acquired behaviour alterations can transfer across generation borders. First, the mechanisms by which experiences cause epigenetic modifications are examined. This includes, for example, methylation of cytosine in CpG positions and acetylation of histones, and studies showing that this can be modified by early experiences. Secondly, the evidence that specific modifications in the epigenome can be the cause of behaviour variation is reviewed. Thirdly, the extent to which this phenotypically active epigenetic variants can be inherited either through the germline or through reoccurring environmental conditions is examined. A particularly interesting observation is that epigenetic modifications are often linked to stress, and may possibly be mediated by steroid effects. Finally, the idea that transgenerationally stable epigenetic variants may serve as substrates for natural selection is explored, and it is speculated that they may even predispose for directed, non-random mutations.
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Affiliation(s)
- Per Jensen
- IFM Biology, AVIAN Behaviour Genomics and Physiology group, Linköping University, 581 83 Linköping, Sweden.
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Bohacek J, Mansuy IM. Epigenetic inheritance of disease and disease risk. Neuropsychopharmacology 2013; 38:220-36. [PMID: 22781843 PMCID: PMC3521963 DOI: 10.1038/npp.2012.110] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/08/2012] [Accepted: 05/08/2012] [Indexed: 12/11/2022]
Abstract
Epigenetic marks in an organism can be altered by environmental factors throughout life. Although changes in the epigenetic code can be positive, some are associated with severe diseases, in particular, cancer and neuropsychiatric disorders. Recent evidence has indicated that certain epigenetic marks can be inherited, and reshape developmental and cellular features over generations. This review examines the challenging possibility that epigenetic changes induced by environmental factors can contribute to some of the inheritance of disease and disease risk. This concept has immense implications for the understanding of biological functions and disease etiology, and provides potential novel strategies for diagnosis and treatment. Examples of epigenetic inheritance relevant to human disease, such as the detrimental effects of traumatic stress or drug/toxic exposure on brain functions, are reviewed. Different possible routes of transmission of epigenetic information involving the germline or germline-independent transfer are discussed, and different mechanisms for the maintenance and transmission of epigenetic information like chromatin remodeling and small noncoding RNAs are considered. Future research directions and remaining major challenges in this field are also outlined. Finally, the adaptive value of epigenetic inheritance, and the cost and benefit of allowing acquired epigenetic marks to persist across generations is critically evaluated.
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Affiliation(s)
- Johannes Bohacek
- Brain Research Institute, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Isabelle M Mansuy
- Brain Research Institute, University of Zurich/ETH Zurich, Zurich, Switzerland
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Millan MJ. An epigenetic framework for neurodevelopmental disorders: from pathogenesis to potential therapy. Neuropharmacology 2012; 68:2-82. [PMID: 23246909 DOI: 10.1016/j.neuropharm.2012.11.015] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 11/11/2012] [Accepted: 11/22/2012] [Indexed: 12/12/2022]
Abstract
Neurodevelopmental disorders (NDDs) are characterized by aberrant and delayed early-life development of the brain, leading to deficits in language, cognition, motor behaviour and other functional domains, often accompanied by somatic symptoms. Environmental factors like perinatal infection, malnutrition and trauma can increase the risk of the heterogeneous, multifactorial and polygenic disorders, autism and schizophrenia. Conversely, discrete genetic anomalies are involved in Down, Rett and Fragile X syndromes, tuberous sclerosis and neurofibromatosis, the less familiar Phelan-McDermid, Sotos, Kleefstra, Coffin-Lowry and "ATRX" syndromes, and the disorders of imprinting, Angelman and Prader-Willi syndromes. NDDs have been termed "synaptopathies" in reference to structural and functional disturbance of synaptic plasticity, several involve abnormal Ras-Kinase signalling ("rasopathies"), and many are characterized by disrupted cerebral connectivity and an imbalance between excitatory and inhibitory transmission. However, at a different level of integration, NDDs are accompanied by aberrant "epigenetic" regulation of processes critical for normal and orderly development of the brain. Epigenetics refers to potentially-heritable (by mitosis and/or meiosis) mechanisms controlling gene expression without changes in DNA sequence. In certain NDDs, prototypical epigenetic processes of DNA methylation and covalent histone marking are impacted. Conversely, others involve anomalies in chromatin-modelling, mRNA splicing/editing, mRNA translation, ribosome biogenesis and/or the regulatory actions of small nucleolar RNAs and micro-RNAs. Since epigenetic mechanisms are modifiable, this raises the hope of novel therapy, though questions remain concerning efficacy and safety. The above issues are critically surveyed in this review, which advocates a broad-based epigenetic framework for understanding and ultimately treating a diverse assemblage of NDDs ("epigenopathies") lying at the interface of genetic, developmental and environmental processes. This article is part of the Special Issue entitled 'Neurodevelopmental Disorders'.
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Affiliation(s)
- Mark J Millan
- Unit for Research and Discovery in Neuroscience, IDR Servier, 125 chemin de ronde, 78290 Croissy sur Seine, Paris, France.
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Jiménez-Chillarón JC, Díaz R, Martínez D, Pentinat T, Ramón-Krauel M, Ribó S, Plösch T. The role of nutrition on epigenetic modifications and their implications on health. Biochimie 2012; 94:2242-63. [DOI: 10.1016/j.biochi.2012.06.012] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/11/2012] [Indexed: 02/06/2023]
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Abstract
The biological and medical importance of epigenetics is nowtaken for granted, but the significance of one aspect of it—epigenetic inheritance—is less widely recognized. New datasuggest that not only is it ubiquitous, but both the generationand the transmission of epigenetic variations may be affectedby developmental conditions. Population studies, formalmodels, and research on genomic and ecological stressesall suggest that epigenetic inheritance is important in bothmicro-and macroevolutionary change.
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Boffelli D, Martin DIK. Epigenetic inheritance: a contributor to species differentiation? DNA Cell Biol 2012; 31 Suppl 1:S11-6. [PMID: 22966965 DOI: 10.1089/dna.2012.1643] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Multiple epigenetic states can be associated with the same genome, and transmitted through the germline for generations, to create the phenomenon of epigenetic inheritance. This form of inheritance is mediated by complex and highly diverse components of the chromosome that associate with DNA, control its transcription, and are inherited alongside it. But, how extensive, and how stable, is the information carried in the germline by the epigenome? Several known examples of epigenetic inheritance demonstrate that it has the ability to create selectable traits, and thus to mediate Darwinian evolution. Here we discuss the possibility that epigenetic inheritance is responsible for some stable characteristics of species, focusing on a recent comparison of the human and chimpanzee methylomes which reveals that somatic methylation states are related to methylation states in the germline. Interpretation of this finding highlights the potential significance of germline epigenetic states, as well as the challenge of investigating a form of inheritance with complex and unfamiliar rules.
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Affiliation(s)
- Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
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Zucchi FCR, Yao Y, Metz GA. The secret language of destiny: stress imprinting and transgenerational origins of disease. Front Genet 2012; 3:96. [PMID: 22675331 PMCID: PMC3366387 DOI: 10.3389/fgene.2012.00096] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 05/10/2012] [Indexed: 12/24/2022] Open
Abstract
Epigenetic regulation modulates gene expression without altering the DNA sequence to facilitate rapid adjustments to dynamically changing environmental conditions. The formation of an epigenetic memory allows passing on this information to subsequent generations. Here we propose that epigenetic memories formed by adverse environmental conditions and stress represent a critical determinant of health and disease in the F3 generation and beyond. Transgenerational programming of epigenetic regulation may represent a key to understand adult-onset complex disease pathogenesis and cumulative effects of life span and familial disease etiology. Ultimately, the mechanisms of generating an epigenetic memory may become of potentially promising diagnostic and therapeutic relevance due to their reversible nature. Exploring the role of environmental factors, such as stress, in causing variations in epigenetic profiles may lead to new avenues of personalized, preventive medicine based on epigenetic signatures and interventions.
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Affiliation(s)
- Fabiola C R Zucchi
- Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
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