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Ectopic expression of the Stabilin2 gene triggered by an intracisternal A particle (IAP) element in DBA/2J strain of mice. Mamm Genome 2020; 31:2-16. [PMID: 31912264 PMCID: PMC7060167 DOI: 10.1007/s00335-019-09824-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/29/2019] [Indexed: 12/21/2022]
Abstract
Stabilin2 (Stab2) encodes a large transmembrane protein which is predominantly expressed in the liver sinusoidal endothelial cells (LSECs) and functions as a scavenger receptor for various macromolecules including hyaluronans (HA). In DBA/2J mice, plasma HA concentration is ten times higher than in 129S6 or C57BL/6J mice, and this phenotype is genetically linked to the Stab2 locus. Stab2 mRNA in the LSECs was significantly lower in DBA/2J than in 129S6, leading to reduced STAB2 proteins in the DBA/2J LSECs. We found a retrovirus-derived transposable element, intracisternal A particle (IAP), in the promoter region of Stab2DBA which likely interferes with normal expression in the LSECs. In contrast, in other tissues of DBA/2J mice, the IAP drives high ectopic Stab2DBA transcription starting within the 5′ long terminal repeat of IAP in a reverse orientation and continuing through the downstream Stab2DBA. Ectopic transcription requires the Stab2-IAP element but is dominantly suppressed by the presence of loci on 59.7–73.0 Mb of chromosome (Chr) 13 from C57BL/6J, while the same region in 129S6 requires additional loci for complete suppression. Chr13:59.9–73 Mb contains a large number of genes encoding Krüppel-associated box-domain zinc-finger proteins that target transposable elements-derived sequences and repress their expression. Despite the high amount of ectopic Stab2DBA transcript in tissues other than liver, STAB2 protein was undetectable and unlikely to contribute to the plasma HA levels of DBA/2J mice. Nevertheless, the IAP insertion and its effects on the transcription of the downstream Stab2DBA exemplify that stochastic evolutional events could significantly influence susceptibility to complex but common diseases.
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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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53
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Perera BP, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC. The role of environmental exposures and the epigenome in health and disease. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:176-192. [PMID: 31177562 PMCID: PMC7252203 DOI: 10.1002/em.22311] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/02/2023]
Abstract
The genetic material of every organism exists within the context of regulatory networks that govern gene expression, collectively called the epigenome. Epigenetics has taken center stage in the study of diseases such as cancer and diabetes, but its integration into the field of environmental health is still emerging. As the Environmental Mutagenesis and Genomics Society (EMGS) celebrates its 50th Anniversary this year, we have come together to review and summarize the seminal advances in the field of environmental epigenomics. Specifically, we focus on the role epigenetics may play in multigenerational and transgenerational transmission of environmentally induced health effects. We also summarize state of the art techniques for evaluating the epigenome, environmental epigenetic analysis, and the emerging field of epigenome editing. Finally, we evaluate transposon epigenetics as they relate to environmental exposures and explore the role of noncoding RNA as biomarkers of environmental exposures. Although the field has advanced over the past several decades, including being recognized by EMGS with its own Special Interest Group, recently renamed Epigenomics, we are excited about the opportunities for environmental epigenetic science in the next 50 years. Environ. Mol. Mutagen. 61:176-192, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Bambarendage P.U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, St. Paul, Minnesota
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Correspondence to: Dana C. Dolinoy, Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan.
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Ciuculete DM, Voisin S, Kular L, Welihinda N, Jonsson J, Jagodic M, Mwinyi J, Schiöth HB. Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression. Epigenetics 2019; 15:646-663. [PMID: 31852353 PMCID: PMC7574381 DOI: 10.1080/15592294.2019.1700628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-Åsberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (praw<1e-4) and susceptibility for suicidal symptoms (padj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (padj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University , Footscray, Australian
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Nipuni Welihinda
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Jörgen Jonsson
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University , Moscow, Russia
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55
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Affiliation(s)
- Chathura J Gunasekara
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert A Waterland
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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56
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Vishwakarma M, Di Russo J. Why does epithelia display heterogeneity? Bridging physical and biological concepts. Biophys Rev 2019; 11:683-687. [PMID: 31494837 PMCID: PMC6815311 DOI: 10.1007/s12551-019-00583-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Medhavi Vishwakarma
- School of Cellular and Molecular Medicine, University Walk, University of Bristol, Bristol, BS1 8TD, UK.
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.
| | - Jacopo Di Russo
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.
- Interdisciplinary Centre for Clinical Research, RWTH Aachen University, Pauwelstrasse 30, 52074, Aachen, Germany.
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Fernandez-Twinn DS, Hjort L, Novakovic B, Ozanne SE, Saffery R. Intrauterine programming of obesity and type 2 diabetes. Diabetologia 2019; 62:1789-1801. [PMID: 31451874 PMCID: PMC6731191 DOI: 10.1007/s00125-019-4951-9] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/05/2019] [Indexed: 12/16/2022]
Abstract
The type 2 diabetes epidemic and one of its predisposing factors, obesity, are major influences on global health and economic burden. It is accepted that genetics and the current environment contribute to this epidemic; however, in the last two decades, both human and animal studies have consolidated considerable evidence supporting the 'developmental programming' of these conditions, specifically by the intrauterine environment. Here, we review the various in utero exposures that are linked to offspring obesity and diabetes in later life, including epidemiological insights gained from natural historical events, such as the Dutch Hunger Winter, the Chinese famine and the more recent Quebec Ice Storm. We also describe the effects of gestational exposure to endocrine disruptors, maternal infection and smoking to the fetus in relation to metabolic programming. Causal evidence from animal studies, motivated by human observations, is also discussed, as well as some of the proposed underlying molecular mechanisms for developmental programming of obesity and type 2 diabetes, including epigenetics (e.g. DNA methylation and histone modifications) and microRNA interactions. Finally, we examine the effects of non-pharmacological interventions, such as improving maternal dietary habits and/or increasing physical activity, on the offspring epigenome and metabolic outcomes.
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Affiliation(s)
- Denise S Fernandez-Twinn
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Level 4, Box 289, Addenbrooke's Treatment Centre, Cambridge, CB2 0QQ, UK
| | - Line Hjort
- Department of Endocrinology, the Diabetes and Bone-metabolic Research Unit, Rigshospitalet, Copenhagen, Denmark
- Department of Obstetrics, Center for Pregnant Women with Diabetes, Rigshospitalet, Copenhagen, Denmark
| | - Boris Novakovic
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Susan E Ozanne
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Level 4, Box 289, Addenbrooke's Treatment Centre, Cambridge, CB2 0QQ, UK.
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia.
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Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, provides a powerful model of the complex interplay between genetic and epigenetic mechanisms of chromatin regulation. FSHD is caused by dysregulation of a macrosatellite repeat, either by contraction of the repeat or by mutations in silencing proteins. Both cases lead to chromatin relaxation and, in the context of a permissive allele, aberrant expression of the DUX4 gene in skeletal muscle. DUX4 is a pioneer transcription factor that activates a program of gene expression during early human development, after which its expression is silenced in most somatic cells. When misexpressed in FSHD skeletal muscle, the DUX4 program leads to accumulated muscle pathology. Epigenetic regulators of the disease locus represent particularly attractive therapeutic targets for FSHD, as many are not global modifiers of the genome, and altering their expression or activity should allow correction of the underlying defect.
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MESH Headings
- CRISPR-Cas Systems
- Chromatin/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Human, Pair 4
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Gene Editing
- Genetic Loci
- Genome, Human
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Facioscapulohumeral/classification
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Muscular Dystrophy, Facioscapulohumeral/pathology
- Mutation
- Severity of Illness Index
- DNA Methyltransferase 3B
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Affiliation(s)
- Charis L Himeda
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
| | - Peter L Jones
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
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59
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Germ cell-mediated mechanisms of epigenetic inheritance. Semin Cell Dev Biol 2019; 97:116-122. [PMID: 31404658 DOI: 10.1016/j.semcdb.2019.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/15/2019] [Accepted: 07/25/2019] [Indexed: 01/07/2023]
Abstract
It is well established that lifestyle and other environmental factors have the potential to shape our own health and future. Research from the last two decades, however, provides mounting evidence that parental exposures or experiences such as dietary challenges, toxin exposure, or stress can impact the health and future of our offspring. There are indications that both the paternal and maternal germline are able to store information of the parental environment and pass certain information on to their progeny. These intergenerational effects are mediated by epigenetic mechanisms. This review summarizes and discusses insights into germline epigenetic plasticity caused by environmental stimuli and how such alterations are transmitted to induce a stable phenotype in the offspring.
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60
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Behavioral Epigenetics: Perspectives Based on Experience-Dependent Epigenetic Inheritance. EPIGENOMES 2019; 3:epigenomes3030018. [PMID: 34968228 PMCID: PMC8594690 DOI: 10.3390/epigenomes3030018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 11/16/2022] Open
Abstract
Epigenetic regulation plays an important role in gene regulation, and epigenetic markers such as DNA methylation and histone modifications are generally described as switches that regulate gene expression. Behavioral epigenetics is defined as the study of how epigenetic alterations induced by experience and environmental stress may affect animal behavior. It studies epigenetic alterations due to environmental enrichment. Generally, molecular processes underlying epigenetic regulation in behavioral epigenetics include DNA methylation, post-translational histone modifications, noncoding RNA activity, and other unknown molecular processes. Whether the inheritance of epigenetic features will occur is a crucial question. In general, the mechanism underlying inheritance can be explained by two main phenomena: Germline-mediated epigenetic inheritance and interact epigenetic inheritance of somatic cells through germline. In this review, we focus on examining behavioral epigenetics based on its possible modes of inheritance and discuss the considerations in the research of epigenetic transgenerational inheritance.
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61
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Phillips CM, Chen LW, Heude B, Bernard JY, Harvey NC, Duijts L, Mensink-Bout SM, Polanska K, Mancano G, Suderman M, Shivappa N, Hébert JR. Dietary Inflammatory Index and Non-Communicable Disease Risk: A Narrative Review. Nutrients 2019; 11:E1873. [PMID: 31408965 PMCID: PMC6722630 DOI: 10.3390/nu11081873] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/30/2019] [Accepted: 08/05/2019] [Indexed: 12/13/2022] Open
Abstract
There are over 1,000,000 publications on diet and health and over 480,000 references on inflammation in the National Library of Medicine database. In addition, there have now been over 30,000 peer-reviewed articles published on the relationship between diet, inflammation, and health outcomes. Based on this voluminous literature, it is now recognized that low-grade, chronic systemic inflammation is associated with most non-communicable diseases (NCDs), including diabetes, obesity, cardiovascular disease, cancers, respiratory and musculoskeletal disorders, as well as impaired neurodevelopment and adverse mental health outcomes. Dietary components modulate inflammatory status. In recent years, the Dietary Inflammatory Index (DII®), a literature-derived dietary index, was developed to characterize the inflammatory potential of habitual diet. Subsequently, a large and rapidly growing body of research investigating associations between dietary inflammatory potential, determined by the DII, and risk of a wide range of NCDs has emerged. In this narrative review, we examine the current state of the science regarding relationships between the DII and cancer, cardiometabolic, respiratory and musculoskeletal diseases, neurodevelopment, and adverse mental health outcomes. We synthesize the findings from recent studies, discuss potential underlying mechanisms, and look to the future regarding novel applications of the adult and children's DII (C-DII) scores and new avenues of investigation in this field of nutritional research.
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Affiliation(s)
- Catherine M Phillips
- HRB Centre for Diet and Health Research, School of Public Health, Physiotherapy, and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland.
- HRB Centre for Diet and Health Research, School of Public Health, University College Cork, Western Gateway Building, Western Rd, Cork, Co. Cork, Ireland.
| | - Ling-Wei Chen
- HRB Centre for Diet and Health Research, School of Public Health, Physiotherapy, and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Barbara Heude
- Research Team on the Early Life Origins of Health (EAROH), Centre for Research in Epidemiology and Statistics (CRESS), INSERM, Université de Paris, F-94807 Villejuif, France
| | - Jonathan Y Bernard
- Research Team on the Early Life Origins of Health (EAROH), Centre for Research in Epidemiology and Statistics (CRESS), INSERM, Université de Paris, F-94807 Villejuif, France
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
- Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Sara M Mensink-Bout
- The Generation R Study Group, Erasmus MC, University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Kinga Polanska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, 91-348 Lodz, Poland
| | - Giulia Mancano
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Nitin Shivappa
- Cancer Prevention and Control Program and Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - James R Hébert
- Cancer Prevention and Control Program and Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
- Connecting Health Innovations LLC, Columbia, SC 29201, USA
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62
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Xavier MJ, Roman SD, Aitken RJ, Nixon B. Transgenerational inheritance: how impacts to the epigenetic and genetic information of parents affect offspring health. Hum Reprod Update 2019; 25:518-540. [DOI: 10.1093/humupd/dmz017] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/19/2019] [Accepted: 04/04/2019] [Indexed: 12/18/2022] Open
Abstract
Abstract
BACKGROUND
A defining feature of sexual reproduction is the transmission of genomic information from both parents to the offspring. There is now compelling evidence that the inheritance of such genetic information is accompanied by additional epigenetic marks, or stable heritable information that is not accounted for by variations in DNA sequence. The reversible nature of epigenetic marks coupled with multiple rounds of epigenetic reprogramming that erase the majority of existing patterns have made the investigation of this phenomenon challenging. However, continual advances in molecular methods are allowing closer examination of the dynamic alterations to histone composition and DNA methylation patterns that accompany development and, in particular, how these modifications can occur in an individual’s germline and be transmitted to the following generation. While the underlying mechanisms that permit this form of transgenerational inheritance remain unclear, it is increasingly apparent that a combination of genetic and epigenetic modifications plays major roles in determining the phenotypes of individuals and their offspring.
OBJECTIVE AND RATIONALE
Information pertaining to transgenerational inheritance was systematically reviewed focusing primarily on mammalian cells to the exclusion of inheritance in plants, due to inherent differences in the means by which information is transmitted between generations. The effects of environmental factors and biological processes on both epigenetic and genetic information were reviewed to determine their contribution to modulating inheritable phenotypes.
SEARCH METHODS
Articles indexed in PubMed were searched using keywords related to transgenerational inheritance, epigenetic modifications, paternal and maternal inheritable traits and environmental and biological factors influencing transgenerational modifications. We sought to clarify the role of epigenetic reprogramming events during the life cycle of mammals and provide a comprehensive review of how the genomic and epigenomic make-up of progenitors may determine the phenotype of its descendants.
OUTCOMES
We found strong evidence supporting the role of DNA methylation patterns, histone modifications and even non-protein-coding RNA in altering the epigenetic composition of individuals and producing stable epigenetic effects that were transmitted from parents to offspring, in both humans and rodent species. Multiple genomic domains and several histone modification sites were found to resist demethylation and endure genome-wide reprogramming events. Epigenetic modifications integrated into the genome of individuals were shown to modulate gene expression and activity at enhancer and promoter domains, while genetic mutations were shown to alter sequence availability for methylation and histone binding. Fundamentally, alterations to the nuclear composition of the germline in response to environmental factors, ageing, diet and toxicant exposure have the potential to become hereditably transmitted.
WIDER IMPLICATIONS
The environment influences the health and well-being of progeny by working through the germline to introduce spontaneous genetic mutations as well as a variety of epigenetic changes, including alterations in DNA methylation status and the post-translational modification of histones. In evolutionary terms, these changes create the phenotypic diversity that fuels the fires of natural selection. However, rather than being adaptive, such variation may also generate a plethora of pathological disease states ranging from dominant genetic disorders to neurological conditions, including spontaneous schizophrenia and autism.
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Affiliation(s)
- Miguel João Xavier
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Shaun D Roman
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Chemical Biology and Clinical Pharmacology, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - R John Aitken
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Brett Nixon
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
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63
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Presence/absence of a CACTA transposon in the CYC2c gene of two genotypes of Helianthus × multiflorus cv. “Meteor” characterized by a radiate inflorescence with different shape of disk flower corollas. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00301-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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64
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Clark J, Martin E, Bulka CM, Smeester L, Santos HP, O'Shea TM, Fry RC. Associations between placental CpG methylation of metastable epialleles and childhood body mass index across ages one, two and ten in the Extremely Low Gestational Age Newborns (ELGAN) cohort. Epigenetics 2019; 14:1102-1111. [PMID: 31216936 DOI: 10.1080/15592294.2019.1633865] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Developmental Origins of Health and Disease (DOHaD) hypothesis posits that in utero and early life conditions can disrupt normal fetal development and program susceptibility to later-life disease. Metastable epialleles are genomic loci in which CpG methylation patterning is responsive to maternal diet and conserved across time and tissues. Thus, these sites could serve as 'signatures' of gestational environment conditions. Here, we sought to determine if methylation of metastable epialleles was associated with changes in childhood body mass index (BMI) z-scores across ages one, two and ten in the Extremely Low Gestational Age Newborns (ELGAN) cohort. CpG methylation of 250 probes (corresponding to 111 genes) within metastable epiallele regions was measured in placental tissue. Linear mixed effects models were fit to evaluate the overall and sex-stratified associations between methylation and changes in BMI z-score over time. In total, 26 probes were associated (p < 0.05) with changes in BMI z-score overall, including probes within Mesoderm Specific Transcript (MEST) and Histone Deacetylase 4 (HDAC4), which have previously been associated with childhood obesity and adipogenesis. Sex-stratified analyses revealed a significant association, after adjusting for multiple comparisons (q < 0.05), within female placentas for one probe annotated to the imprinted gene PLAG1 Like Zinc Finger 1 (PLAGL1). These findings suggest epigenetic marks may be involved in programming susceptibility to obesity in utero and highlight the potential to use placental tissues in predicting growth rate trajectories among premature infants.
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Affiliation(s)
- Jeliyah Clark
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina , Chapel Hill , NC , USA
| | - Elizabeth Martin
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park , NC , USA
| | - Catherine M Bulka
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina , Chapel Hill , NC , USA
| | - Lisa Smeester
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina , Chapel Hill , NC , USA.,Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina , Chapel Hill , NC , USA
| | - Hudson P Santos
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina , Chapel Hill , NC , USA.,School of Nursing, University of North Carolina , Chapel Hill , NC , USA
| | - T Michael O'Shea
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of North Carolina , Chapel Hill , NC , USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina , Chapel Hill , NC , USA.,Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina , Chapel Hill , NC , USA
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Epigenetic regulation of POMC; implications for nutritional programming, obesity and metabolic disease. Front Neuroendocrinol 2019; 54:100773. [PMID: 31344387 DOI: 10.1016/j.yfrne.2019.100773] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/18/2019] [Accepted: 07/20/2019] [Indexed: 01/07/2023]
Abstract
Proopiomelanocortin (POMC) is a key mediator of satiety. Epigenetic marks such as DNA methylation may modulate POMC expression and provide a biological link between early life exposures and later phenotype. Animal studies suggest epigenetic marks at POMC are influenced by maternal energy excess and restriction, prenatal stress and Triclosan exposure. Postnatal factors including energy excess, folate, vitamin A, conjugated linoleic acid and leptin may also affect POMC methylation. Recent human studies suggest POMC DNA methylation is influenced by maternal nutrition in early pregnancy and associated with childhood and adult obesity. Studies in children propose a link between POMC DNA methylation and elevated lipids and insulin, independent of body habitus. This review brings together evidence from animal and human studies and suggests that POMC is sensitive to nutritional programming and is associated with a wide range of weight-related and metabolic outcomes.
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Lee YS, Kunkeaw N, Lee YS. Protein kinase R and its cellular regulators in cancer: An active player or a surveillant? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1558. [PMID: 31231984 DOI: 10.1002/wrna.1558] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Abstract
Protein kinase R (PKR), originally known as an antiviral protein, senses various stresses as well as pathogen-driven double-stranded RNAs. Thereby activated PKR provokes diverse downstream events, including eIF2α phosphorylation and nuclear factor kappa-light-chain-enhancer of activated B cells activation. Consequently, PKR induces apoptosis and inflammation, both of which are highly important in cancer as much as its original antiviral role. Therefore, cellular proteins and RNAs should tightly control PKR activity. PKR and its regulators are often dysregulated in cancer and it is undoubted that such dysregulation contributes to tumorigenesis. However, PKR's precise role in cancer is still in debate, due to incomprehensible and even contradictory data. In this review, we introduce important cellular PKR regulators and discuss about their roles in cancer. Among them, we pay particular attention to nc886, a PKR repressor noncoding RNA that has been identified relatively recently, because its expression pattern in cancer can explain interesting yet obscure oncologic aspects of PKR. Based on nc886 and its regulation of PKR, we have proposed a tumor surveillance model, which reconciles contradictory data about PKR in cancer. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Nawapol Kunkeaw
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Yeon-Su Lee
- Division of Clinical Research, Research Institute, National Cancer Center, Goyang, Korea
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Gunasekara CJ, Scott CA, Laritsky E, Baker MS, MacKay H, Duryea JD, Kessler NJ, Hellenthal G, Wood AC, Hodges KR, Gandhi M, Hair AB, Silver MJ, Moore SE, Prentice AM, Li Y, Chen R, Coarfa C, Waterland RA. A genomic atlas of systemic interindividual epigenetic variation in humans. Genome Biol 2019; 20:105. [PMID: 31155008 PMCID: PMC6545702 DOI: 10.1186/s13059-019-1708-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND DNA methylation is thought to be an important determinant of human phenotypic variation, but its inherent cell type specificity has impeded progress on this question. At exceptional genomic regions, interindividual variation in DNA methylation occurs systemically. Like genetic variants, systemic interindividual epigenetic variants are stable, can influence phenotype, and can be assessed in any easily biopsiable DNA sample. We describe an unbiased screen for human genomic regions at which interindividual variation in DNA methylation is not tissue-specific. RESULTS For each of 10 donors from the NIH Genotype-Tissue Expression (GTEx) program, CpG methylation is measured by deep whole-genome bisulfite sequencing of genomic DNA from tissues representing the three germ layer lineages: thyroid (endoderm), heart (mesoderm), and brain (ectoderm). We develop a computational algorithm to identify genomic regions at which interindividual variation in DNA methylation is consistent across all three lineages. This approach identifies 9926 correlated regions of systemic interindividual variation (CoRSIVs). These regions, comprising just 0.1% of the human genome, are inter-correlated over long genomic distances, associated with transposable elements and subtelomeric regions, conserved across diverse human ethnic groups, sensitive to periconceptional environment, and associated with genes implicated in a broad range of human disorders and phenotypes. CoRSIV methylation in one tissue can predict expression of associated genes in other tissues. CONCLUSIONS In addition to charting a previously unexplored molecular level of human individuality, this atlas of human CoRSIVs provides a resource for future population-based investigations into how interindividual epigenetic variation modulates risk of disease.
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Affiliation(s)
- Chathura J Gunasekara
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - C Anthony Scott
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Eleonora Laritsky
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maria S Baker
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Harry MacKay
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jack D Duryea
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Noah J Kessler
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Keneba, The Gambia
- Department of Women and Children's Health, King's College London, London, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Alexis C Wood
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kelly R Hodges
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Manisha Gandhi
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Amy B Hair
- Department of Pediatrics - Neonatology, Baylor College of Medicine, Houston, TX, USA
| | - Matt J Silver
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Keneba, The Gambia
| | - Sophie E Moore
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Keneba, The Gambia
- Department of Women and Children's Health, King's College London, London, UK
| | - Andrew M Prentice
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Keneba, The Gambia
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
| | - Robert A Waterland
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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68
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Mohandas N, Loke YJ, Hopkins S, Mackenzie L, Bennett C, Berkovic SF, Vadlamudi L, Craig JM. Evidence for type-specific DNA methylation patterns in epilepsy: a discordant monozygotic twin approach. Epigenomics 2019; 11:951-968. [DOI: 10.2217/epi-2018-0136] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: Epilepsy is a common neurological disorder characterized by recurrent seizures. We performed epigenetic analyses between and within 15 monozygotic (MZ) twin pairs discordant for focal or generalized epilepsy. Methods: DNA methylation analysis was performed using Illumina Infinium MethylationEPIC arrays, in blood and buccal samples. Results: Differentially methylated regions between epilepsy types associated with PM20D1 and GFPT2 genes in both tissues. Within MZ discordant twin pairs, differentially methylated regions associated with OTX1 and ARID5B genes for generalized epilepsy and TTC39C and DLX5 genes for focal epilepsy. Conclusion: This is the first epigenome-wide association study, utilizing the discordant MZ co-twin model, to deepen our understanding of the neurobiology of epilepsy.
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Affiliation(s)
- Namitha Mohandas
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Flemington Road, Parkville, Victoria, Australia
| | - Yuk Jing Loke
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
| | - Stephanie Hopkins
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- School of Medicine & Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Lisa Mackenzie
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
| | - Carmen Bennett
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, University of Melbourne, Austin Health, Victoria, Australia
| | - Lata Vadlamudi
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
- Royal Brisbane & Women's Hospital, Queensland, Australia
| | - Jeffrey M Craig
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Flemington Road, Parkville, Victoria, Australia
- Centre for Molecular & Medical Research, School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
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69
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Küpers LK, Monnereau C, Sharp GC, Yousefi P, Salas LA, Ghantous A, Page CM, Reese SE, Wilcox AJ, Czamara D, Starling AP, Novoloaca A, Lent S, Roy R, Hoyo C, Breton CV, Allard C, Just AC, Bakulski KM, Holloway JW, Everson TM, Xu CJ, Huang RC, van der Plaat DA, Wielscher M, Merid SK, Ullemar V, Rezwan FI, Lahti J, van Dongen J, Langie SAS, Richardson TG, Magnus MC, Nohr EA, Xu Z, Duijts L, Zhao S, Zhang W, Plusquin M, DeMeo DL, Solomon O, Heimovaara JH, Jima DD, Gao L, Bustamante M, Perron P, Wright RO, Hertz-Picciotto I, Zhang H, Karagas MR, Gehring U, Marsit CJ, Beilin LJ, Vonk JM, Jarvelin MR, Bergström A, Örtqvist AK, Ewart S, Villa PM, Moore SE, Willemsen G, Standaert ARL, Håberg SE, Sørensen TIA, Taylor JA, Räikkönen K, Yang IV, Kechris K, Nawrot TS, Silver MJ, Gong YY, Richiardi L, Kogevinas M, Litonjua AA, Eskenazi B, Huen K, Mbarek H, Maguire RL, Dwyer T, Vrijheid M, Bouchard L, Baccarelli AA, Croen LA, Karmaus W, Anderson D, de Vries M, Sebert S, Kere J, Karlsson R, Arshad SH, Hämäläinen E, Routledge MN, Boomsma DI, Feinberg AP, Newschaffer CJ, Govarts E, Moisse M, Fallin MD, Melén E, Prentice AM, Kajantie E, Almqvist C, Oken E, Dabelea D, Boezen HM, Melton PE, Wright RJ, Koppelman GH, Trevisi L, Hivert MF, Sunyer J, Munthe-Kaas MC, Murphy SK, Corpeleijn E, Wiemels J, Holland N, Herceg Z, Binder EB, Davey Smith G, Jaddoe VWV, Lie RT, Nystad W, London SJ, Lawlor DA, Relton CL, Snieder H, Felix JF. Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight. Nat Commun 2019; 10:1893. [PMID: 31015461 PMCID: PMC6478731 DOI: 10.1038/s41467-019-09671-3] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 02/18/2019] [Indexed: 12/16/2022] Open
Abstract
Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from -183 to 178 grams per 10% increase in methylation (PBonferroni < 1.06 x 10-7). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10-74) and BMI in pregnancy (3/914, p = 1.13x10-3), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.
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Affiliation(s)
- Leanne K Küpers
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
- Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
| | - Claire Monnereau
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Paul Yousefi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Oslo Centre for Biostatisitcs and Epidemology, Oslo University Hospital, Oslo, Norway
| | - Sarah E Reese
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Allen J Wilcox
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Anne P Starling
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Samantha Lent
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ritu Roy
- HDF Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Computational Biology and Informatics, UCSF, San Francisco, CA, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Catherine Allard
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Allan C Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John W Holloway
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Todd M Everson
- Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA, USA
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Diana A van der Plaat
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Jari Lahti
- Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jenny van Dongen
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sabine A S Langie
- VITO - Health, Mol, Belgium
- Theoretical Physics, Faculty of Sciences, Hasselt University, Hasselt, Belgium
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Maria C Magnus
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Zongli Xu
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Shanshan Zhao
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
| | - Weiming Zhang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- MRC/PHE Centre for Environment and Health School of Public Health Imperial College London, St Mary's Campus, Norfolk Place, London, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Olivia Solomon
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Joosje H Heimovaara
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mariona Bustamante
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Patrice Perron
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, QC, Canada
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, QC, Canada
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California Davis MIND Institute, Sacramento, CA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
| | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA, USA
| | | | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Center for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Anne K Örtqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Pia M Villa
- Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sophie E Moore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
- Department of Women and Children's Health, King's College London, London, UK
| | - Gonneke Willemsen
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ivana V Yang
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katerina Kechris
- Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Yun Yun Gong
- School of Food Sciences and Nutrition, University of Leeds, Leeds, UK
| | - Lorenzo Richiardi
- Department of Medical Sciences, University of Turin, Turin, Italy
- AOU Citta della Salute e della Sceinza, CPO Piemonte, Turin, Italy
| | - Manolis Kogevinas
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brenda Eskenazi
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
- Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, CA, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Hamdi Mbarek
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Community and Family Medicine, Duke University Medical Center, Raleigh, NC, USA
| | - Terence Dwyer
- The George Institute for Global Health, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Martine Vrijheid
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Luigi Bouchard
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- ECOGENE-21 Biocluster, Chicoutimi Hospital, Saguenay, QC, Canada
| | - Andrea A Baccarelli
- Laboratory of Precision Environmental Biosciences, Columbia University Mailman School of Public Health, New York, NY, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Lisa A Croen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Maaike de Vries
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department for Genomics of Common Diseases, School of Public Health, Imperial College London, London, UK
| | - Juha Kere
- Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Esa Hämäläinen
- HUSLAB and the Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | | | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | | | | | - Matthieu Moisse
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children's Hospital, Stockholm, Sweden
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Eero Kajantie
- National Institute for Health and Welfare, Helsinki and Oulu, Oulu, Finland
- Hospital for Children and Adolescents, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, and Department of Pediatrics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Phillip E Melton
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia
| | - Rosalind J Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Letizia Trevisi
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Marie-France Hivert
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, QC, Canada
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Jordi Sunyer
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Monica C Munthe-Kaas
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Pediatric Oncology and Hematology, Oslo University Hospital, Oslo, Norway
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Eva Corpeleijn
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Joseph Wiemels
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Nina Holland
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Altanta, GA, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rolv T Lie
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Wenche Nystad
- Department for Non-Communicable Diseases, Norwegian Institute for Public Health, Oslo, Norway
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands.
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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70
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Gagnier L, Belancio VP, Mager DL. Mouse germ line mutations due to retrotransposon insertions. Mob DNA 2019; 10:15. [PMID: 31011371 PMCID: PMC6466679 DOI: 10.1186/s13100-019-0157-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/01/2019] [Indexed: 12/24/2022] Open
Abstract
Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans.
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Affiliation(s)
- Liane Gagnier
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
| | - Victoria P. Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - Dixie L. Mager
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
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71
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Cecil CAM, Walton E, Pingault JB, Provençal N, Pappa I, Vitaro F, Côté S, Szyf M, Tremblay RE, Tiemeier H, Viding E, McCrory EJ. DRD4 methylation as a potential biomarker for physical aggression: An epigenome-wide, cross-tissue investigation. Am J Med Genet B Neuropsychiatr Genet 2018; 177:746-764. [PMID: 30411855 DOI: 10.1002/ajmg.b.32689] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 08/23/2018] [Accepted: 09/21/2018] [Indexed: 12/13/2022]
Abstract
Epigenetic processes that regulate gene expression, such as DNA methylation (DNAm), have been linked to individual differences in physical aggression. Yet, it is currently unclear whether: (a) DNAm patterns in humans associate with physical aggression independently of other co-occurring psychiatric and behavioral symptoms; (b) whether these patterns are observable across multiple tissues; and (c) whether they may function as a causal versus noncausal biomarker of physical aggression. Here, we used a multisample, cross-tissue design to address these questions. First, we examined genome-wide DNAm patterns (buccal swabs; Illumina 450k) associated with engagement in physical fights in a sample of high-risk youth (n = 119; age = 16-24 years; 53% female). We identified one differentially methylated region in DRD4, which survived genome-wide correction, associated with physical aggression above and beyond co-occurring symptomatology (e.g., ADHD, substance use), and showed strong cross-tissue concordance with both blood and brain. Second, we found that DNAm sites within this region were also differentially methylated in an independent sample of young adults, between individuals with a history of chronic-high versus low physical aggression (peripheral T cells; ages 26-28). Finally, we ran a Mendelian randomization analysis using GWAS data from the EAGLE consortium to test for a causal association of DRD4 methylation with physical aggression. Only one genetic instrument was eligible for the analysis, and results provided no evidence for a causal association. Overall, our findings lend support for peripheral DRD4 methylation as a potential biomarker of physically aggressive behavior, with no evidence yet of a causal relationship.
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Affiliation(s)
- Charlotte A M Cecil
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.,Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Esther Walton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Jean-Baptiste Pingault
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
| | - Nadine Provençal
- Faculty of Health Sciences, Simon Fraser University, Burnaby and BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Irene Pappa
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Frank Vitaro
- Department of Psychoeducation, Université de Montréal, Montréal, Québec, Canada
| | - Sylvana Côté
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada.,Department of Psychology, Université de Montréal, Montréal, Québec, Canada
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Québec, Canada
| | - Richard E Tremblay
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada.,Department of Psychology, Université de Montréal, Montréal, Québec, Canada
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Essi Viding
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
| | - Eamon J McCrory
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
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72
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James P, Sajjadi S, Tomar AS, Saffari A, Fall CHD, Prentice AM, Shrestha S, Issarapu P, Yadav DK, Kaur L, Lillycrop K, Silver M, Chandak GR. Candidate genes linking maternal nutrient exposure to offspring health via DNA methylation: a review of existing evidence in humans with specific focus on one-carbon metabolism. Int J Epidemiol 2018; 47:1910-1937. [PMID: 30137462 PMCID: PMC6280938 DOI: 10.1093/ije/dyy153] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2018] [Indexed: 12/13/2022] Open
Abstract
Background Mounting evidence suggests that nutritional exposures during pregnancy influence the fetal epigenome, and that these epigenetic changes can persist postnatally, with implications for disease risk across the life course. Methods We review human intergenerational studies using a three-part search strategy. Search 1 investigates associations between preconceptional or pregnancy nutritional exposures, focusing on one-carbon metabolism, and offspring DNA methylation. Search 2 considers associations between offspring DNA methylation at genes found in the first search and growth-related, cardiometabolic and cognitive outcomes. Search 3 isolates those studies explicitly linking maternal nutritional exposure to offspring phenotype via DNA methylation. Finally, we compile all candidate genes and regions of interest identified in the searches and describe their genomic locations, annotations and coverage on the Illumina Infinium Methylation beadchip arrays. Results We summarize findings from the 34 studies found in the first search, the 31 studies found in the second search and the eight studies found in the third search. We provide details of all regions of interest within 45 genes captured by this review. Conclusions Many studies have investigated imprinted genes as priority loci, but with the adoption of microarray-based platforms other candidate genes and gene classes are now emerging. Despite a wealth of information, the current literature is characterized by heterogeneous exposures and outcomes, and mostly comprise observational associations that are frequently underpowered. The synthesis of current knowledge provided by this review identifies research needs on the pathway to developing possible early life interventions to optimize lifelong health.
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Affiliation(s)
- Philip James
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Sara Sajjadi
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ashutosh Singh Tomar
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ayden Saffari
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Caroline H D Fall
- MRC Life course Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Andrew M Prentice
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, India
| | - Prachand Issarapu
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Dilip Kumar Yadav
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Lovejeet Kaur
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Karen Lillycrop
- Research Centre for Biological Sciences, Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Matt Silver
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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73
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Kazachenka A, Bertozzi TM, Sjoberg-Herrera MK, Walker N, Gardner J, Gunning R, Pahita E, Adams S, Adams D, Ferguson-Smith AC. Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance. Cell 2018; 175:1259-1271.e13. [PMID: 30454646 PMCID: PMC6242299 DOI: 10.1016/j.cell.2018.09.043] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/19/2018] [Accepted: 09/19/2018] [Indexed: 01/07/2023]
Abstract
Generally repressed by epigenetic mechanisms, retrotransposons represent around 40% of the murine genome. At the Agouti viable yellow (Avy) locus, an endogenous retrovirus (ERV) of the intracisternal A particle (IAP) class retrotransposed upstream of the agouti coat-color locus, providing an alternative promoter that is variably DNA methylated in genetically identical individuals. This results in variable expressivity of coat color that is inherited transgenerationally. Here, a systematic genome-wide screen identifies multiple C57BL/6J murine IAPs with Avy epigenetic properties. Each exhibits a stable methylation state within an individual but varies between individuals. Only in rare instances do they act as promoters controlling adjacent gene expression. Their methylation state is locus-specific within an individual, and their flanking regions are enriched for CTCF. Variably methylated IAPs are reprogrammed after fertilization and re-established as variable loci in the next generation, indicating reconstruction of metastable epigenetic states and challenging the generalizability of non-genetic inheritance at these regions.
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Affiliation(s)
| | - Tessa M Bertozzi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | | | - Nic Walker
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Joseph Gardner
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Richard Gunning
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Elena Pahita
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Sarah Adams
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - David Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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74
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James PT, Dominguez-Salas P, Hennig BJ, Moore SE, Prentice AM, Silver MJ. Maternal One-Carbon Metabolism and Infant DNA Methylation between Contrasting Seasonal Environments: A Case Study from The Gambia. Curr Dev Nutr 2018. [PMCID: PMC6351729 DOI: 10.1093/cdn/nzy082] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background The periconceptional period is a time in which environmentally induced changes to the epigenome could have significant consequences for offspring health. Metastable epialleles (MEs) are genomic loci demonstrating interindividual variation in DNA methylation with intraindividual crosstissue correlation, suggesting that methylation states are established in the very early embryo before gastrulation. In our previous Gambian studies, we have shown that ME methylation states in the offspring are predicted by maternal concentrations of certain nutritional biomarkers around the time of conception. Objective We aimed to assess whether the profile of maternal biomarker predictors of offspring methylation differs between rainy and dry seasons in a population of rural Gambians, using a larger set of 50 recently identified MEs. Methods We measured 1-carbon biomarkers in maternal plasma back-extrapolated to conception, and cytosine-phosphate-guanine (CpG) methylation at 50 ME loci in their infants’ blood at a mean age of 3.3 mo (n = 120 mother-child pairs). We tested for interactions between seasonality and effects of biomarker concentrations on mean ME methylation z score. We used backward stepwise linear regression to select the profile of nutritional predictors of methylation in each season and repeated this analysis with biomarker principal components (PCs) to capture biomarker covariation. Results We found preliminary evidence of seasonal differences in biomarker-methylation associations for folate, choline, and homocysteine (interaction P values ≤0.03). Furthermore, in stratified analyses, biomarker predictors of methylation changed between seasons. In the dry season, vitamin B-2 and methionine were positive predictors. In the rainy season, however, choline and vitamin B-6 were positive predictors, and folate and vitamin B-12 were negative predictors. PC1 captured covariation in the folate metabolism cycle and predicted methylation in dry season conceptions. PC2 represented the betaine remethylation pathway and predicted rainy season methylation. Conclusions Underlying nutritional status may modify the association between nutritional biomarkers and methylation, and should be considered in future studies.
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Affiliation(s)
- Philip T James
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
- Address correspondence to PTJ (e-mail: )
| | - Paula Dominguez-Salas
- Department of Production and Population Health, Royal Veterinary College, London, United Kingdom
| | - Branwen J Hennig
- Population Health, Science Division, Wellcome Trust, London, United Kingdom
| | - Sophie E Moore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Women and Children's Health, King's College London, London, United Kingdom
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
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75
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Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science 2018; 361:eaar3146. [PMID: 30139913 PMCID: PMC6198826 DOI: 10.1126/science.aar3146] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 05/07/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
To assess the impact of genetic variation in regulatory loci on human health, we constructed a high-resolution map of allelic imbalances in DNA methylation, histone marks, and gene transcription in 71 epigenomes from 36 distinct cell and tissue types from 13 donors. Deep whole-genome bisulfite sequencing of 49 methylomes revealed sequence-dependent CpG methylation imbalances at thousands of heterozygous regulatory loci. Such loci are enriched for stochastic switching, which is defined as random transitions between fully methylated and unmethylated states of DNA. The methylation imbalances at thousands of loci are explainable by different relative frequencies of the methylated and unmethylated states for the two alleles. Further analyses provided a unifying model that links sequence-dependent allelic imbalances of the epigenome, stochastic switching at gene regulatory loci, and disease-associated genetic variation.
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Affiliation(s)
- Vitor Onuchic
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Eugene Lurie
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Ivenise Carrero
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Piotr Pawliczek
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Ronak Y Patel
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Zhuoyi Huang
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Robert C Altshuler
- NIH Roadmap Epigenomics Project
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhizhuo Zhang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - R Alan Harris
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Cristian Coarfa
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Lillian Ashmore
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Jessica W Bertol
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Walid D Fakhouri
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Fuli Yu
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Manolis Kellis
- NIH Roadmap Epigenomics Project
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Aleksandar Milosavljevic
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA.
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
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Story Jovanova O, Nedeljkovic I, Spieler D, Walker RM, Liu C, Luciano M, Bressler J, Brody J, Drake AJ, Evans KL, Gondalia R, Kunze S, Kuhnel B, Lahti J, Lemaitre RN, Marioni RE, Swenson B, Himali JJ, Wu H, Li Y, McRae AF, Russ TC, Stewart J, Wang Z, Zhang G, Ladwig KH, Uitterlinden AG, Guo X, Peters A, Räikkönen K, Starr JM, Waldenberger M, Wray NR, Whitsel EA, Sotoodehnia N, Seshadri S, Porteous DJ, van Meurs J, Mosley TH, McIntosh AM, Mendelson MM, Levy D, Hou L, Eriksson JG, Fornage M, Deary IJ, Baccarelli A, Tiemeier H, Amin N. DNA Methylation Signatures of Depressive Symptoms in Middle-aged and Elderly Persons: Meta-analysis of Multiethnic Epigenome-wide Studies. JAMA Psychiatry 2018; 75:949-959. [PMID: 29998287 PMCID: PMC6142917 DOI: 10.1001/jamapsychiatry.2018.1725] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
IMPORTANCE Depressive disorders arise from a combination of genetic and environmental risk factors. Epigenetic disruption provides a plausible mechanism through which gene-environment interactions lead to depression. Large-scale, epigenome-wide studies on depression are missing, hampering the identification of potentially modifiable biomarkers. OBJECTIVE To identify epigenetic mechanisms underlying depression in middle-aged and elderly persons, using DNA methylation in blood. DESIGN, SETTING, AND PARTICIPANTS To date, the first cross-ethnic meta-analysis of epigenome-wide association studies (EWAS) within the framework of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium was conducted. The discovery EWAS included 7948 individuals of European origin from 9 population-based cohorts. Participants who were assessed for both depressive symptoms and whole-blood DNA methylation were included in the study. Results of EWAS were pooled using sample-size weighted meta-analysis. Replication of the top epigenetic sites was performed in 3308 individuals of African American and European origin from 2 population-based cohorts. MAIN OUTCOMES AND MEASURES Whole-blood DNA methylation levels were assayed with Illumina-Infinium Human Methylation 450K BeadChip and depressive symptoms were assessed by questionnaire. RESULTS The discovery cohorts consisted of 7948 individuals (4104 [51.6%] women) with a mean (SD) age of 65.4 (5.8) years. The replication cohort consisted of 3308 individuals (2456 [74.2%] women) with a mean (SD) age of 60.3 (6.4) years. The EWAS identified methylation of 3 CpG sites to be significantly associated with increased depressive symptoms: cg04987734 (P = 1.57 × 10-08; n = 11 256; CDC42BPB gene), cg12325605 (P = 5.24 × 10-09; n = 11 256; ARHGEF3 gene), and an intergenic CpG site cg14023999 (P = 5.99 × 10-08; n = 11 256; chromosome = 15q26.1). The predicted expression of the CDC42BPB gene in the brain (basal ganglia) (effect, 0.14; P = 2.7 × 10-03) and of ARHGEF3 in fibroblasts (effect, -0.48; P = 9.8 × 10-04) was associated with major depression. CONCLUSIONS AND RELEVANCE This study identifies 3 methylated sites associated with depressive symptoms. All 3 findings point toward axon guidance as the common disrupted pathway in depression. The findings provide new insights into the molecular mechanisms underlying the complex pathophysiology of depression. Further research is warranted to determine the utility of these findings as biomarkers of depression and evaluate any potential role in the pathophysiology of depression and their downstream clinical effects.
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Affiliation(s)
- Olivera Story Jovanova
- Department of Epidemiology, Erasmus MC-University
Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ivana Nedeljkovic
- Department of Epidemiology, Erasmus MC-University
Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Derek Spieler
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Klinik und Poliklinik für Psychosomatische
Medizin und Psychotherapie des Klinikums Rechts der Isar der Technischen Universität
München, Munich, Germany
| | - Rosie M. Walker
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Centre for Genomic and Experimental Medicine, MRC
Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General
Hospital, Edinburgh, United Kingdom
| | - Chunyu Liu
- The Framingham Heart Study, Framingham,
Massachusetts,The Population Sciences Branch, Division of Intramural
Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland,Boston University School of Public Health, Boston,
Massachusetts
| | - Michelle Luciano
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Department of Psychology, University of Edinburgh,
Edinburgh, United Kingdom
| | - Jan Bressler
- Human Genetics Center, University of Texas Health
Science Center at Houston
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Department of
Medicine, University of Washington, Seattle
| | - Amanda J. Drake
- University/British Heart Foundation Centre for
Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh,
Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Centre for Genomic and Experimental Medicine, MRC
Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General
Hospital, Edinburgh, United Kingdom
| | - Rahul Gondalia
- Department of Epidemiology, University of North
Carolina at Chapel Hill
| | - Sonja Kunze
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz
Zentrum München, Neuherberg, Germany
| | - Brigitte Kuhnel
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz
Zentrum München, Neuherberg, Germany
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of
Medicine, University of Helsinki, Helsinki, Finland
| | - Rozenn N. Lemaitre
- Cardiovascular Health Research Unit, Department of
Medicine, University of Washington, Seattle
| | - Riccardo E. Marioni
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Department of Psychology, University of Edinburgh,
Edinburgh, United Kingdom
| | - Brenton Swenson
- Cardiovascular Health Research Unit, Department of
Medicine, University of Washington, Seattle,Institute for Public Health Genetics, School of
Public Health, University of Washington, Seattle
| | - Jayandra Jung Himali
- The Framingham Heart Study, Framingham,
Massachusetts,Boston University School of Public Health, Boston,
Massachusetts,Boston University School of Medicine, Boston,
Massachusetts
| | - Hongsheng Wu
- Computer Science and Networking, Wentworth Institute
of Technology, Boston, Massachusetts
| | - Yun Li
- Department of Genetics, University of North Carolina
at Chapel Hill,Department of Biostatistics, University of North
Carolina at Chapel Hill,Department of Computer Science, University of North
Carolina at Chapel Hill
| | - Allan F. McRae
- Institute for Molecular Bioscience, The University
of Queensland, Brisbane, Australia,Queensland Brain Institute, The University of
Queensland, Brisbane, Australia
| | - Tom C. Russ
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Alzheimer Scotland Dementia Research Centre,
Edinburgh, United Kingdom,Centre for Dementia Prevention, University of
Edinburgh, Edinburgh, United Kingdom
| | - James Stewart
- Department of Epidemiology, University of North
Carolina at Chapel Hill,Carolina Population Center, University of North
Carolina at Chapel Hill
| | - Zhiying Wang
- Human Genetics Center, University of Texas Health
Science Center at Houston
| | - Guosheng Zhang
- Department of Genetics, University of North Carolina
at Chapel Hill,Department of Biostatistics, University of North
Carolina at Chapel Hill,Department of Computer Science, University of North
Carolina at Chapel Hill
| | - Karl-Heinz Ladwig
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Klinik und Poliklinik für Psychosomatische
Medizin und Psychotherapie des Klinikums Rechts der Isar der Technischen Universität
München, Munich, Germany
| | - Andre G. Uitterlinden
- Department of Epidemiology, Erasmus MC-University
Medical Center Rotterdam, Rotterdam, the Netherlands,Department of Internal Medicine, Erasmus Medical
Center, Rotterdam, the Netherlands
| | - Xiuqing Guo
- The Institute for Translational Genomics and
Population Sciences, Department of Pediatrics, Harbor-University of California Los Angeles
(UCLA) Medical Center
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz
Zentrum München, Neuherberg, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of
Medicine, University of Helsinki, Helsinki, Finland
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Alzheimer Scotland Dementia Research Centre,
Edinburgh, United Kingdom
| | - Melanie Waldenberger
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz
Zentrum München, Neuherberg, Germany
| | - Naomi R. Wray
- Institute for Molecular Bioscience, The University
of Queensland, Brisbane, Australia,Queensland Brain Institute, The University of
Queensland, Brisbane, Australia
| | - Eric A. Whitsel
- Department of Epidemiology, University of North
Carolina at Chapel Hill,Department of Medicine, University of North Carolina
at Chapel Hill
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of
Medicine, University of Washington, Seattle
| | - Sudha Seshadri
- The Framingham Heart Study, Framingham,
Massachusetts,Boston University School of Medicine, Boston,
Massachusetts
| | - David J. Porteous
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Centre for Genomic and Experimental Medicine, MRC
Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General
Hospital, Edinburgh, United Kingdom
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus Medical
Center, Rotterdam, the Netherlands
| | | | - Andrew M. McIntosh
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Division of Psychiatry, The University of Edinburgh,
Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael M. Mendelson
- The Framingham Heart Study, Framingham,
Massachusetts,The Population Sciences Branch, Division of Intramural
Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland,Department of Cardiology, Boston Children’s
Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel Levy
- The Framingham Heart Study, Framingham,
Massachusetts,The Population Sciences Branch, Division of Intramural
Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Lifang Hou
- Feinberg School of Medicine, Northwestern
University, Chicago, Illinois
| | - Johan G. Eriksson
- Department of General Practice and Primary Health
Care, University of Helsinki, Helsinki, Finland
| | - Myriam Fornage
- Human Genetics Center, University of Texas Health
Science Center at Houston,Institute of Molecular Medicine, University of Texas
Health Science Center at Houston
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Department of Psychology, University of Edinburgh,
Edinburgh, United Kingdom
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Harvard
T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus MC-University
Medical Center Rotterdam, Rotterdam, the Netherlands,Department of Child and Adolescent Psychiatry,
Erasmus MC-University Medical Center Rotterdam, Rotterdam, the Netherlands,Department of Social and Behavioral Science, Harvard
T. H. Chan School of Public Health, Boston, Massachusetts
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC-University
Medical Center Rotterdam, Rotterdam, the Netherlands
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77
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Vengadavaradan A, Sathyanarayanan G, Menon V. Course of recurrent depression in monozygotic twins - A case report. Asian J Psychiatr 2018; 36:121-122. [PMID: 30075350 DOI: 10.1016/j.ajp.2018.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/06/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Ashvini Vengadavaradan
- Department of Psychiatry, Jawaharlal Institute of Postgraduate Medical Education and Research, Dhanvanthri Nagar, Puducherry, India.
| | - Gopinath Sathyanarayanan
- Department of Psychiatry, Jawaharlal Institute of Postgraduate Medical Education and Research, Dhanvanthri Nagar, Puducherry, India.
| | - Vikas Menon
- Department of Psychiatry, Jawaharlal Institute of Postgraduate Medical Education and Research, Dhanvanthri Nagar, Puducherry, India.
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78
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Costello KR, Schones DE. Chromatin modifications in metabolic disease: Potential mediators of long-term disease risk. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10:e1416. [PMID: 29369528 PMCID: PMC6002879 DOI: 10.1002/wsbm.1416] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/30/2017] [Accepted: 12/08/2017] [Indexed: 12/29/2022]
Abstract
Metabolic diseases such as obesity and diabetes are complex diseases resulting from multiple genetic and environmental factors, such as diet and activity levels. These factors are well known contributors to the development of metabolic diseases. One manner by which environmental factors can influence metabolic disease progression is through modifications to chromatin. These modifications can lead to altered gene regulatory programs, which alters disease risk. Furthermore, there is evidence that parents exposed to environmental factors can influence the metabolic health of offspring, especially if exposures are during intrauterine growth periods. In this review, we outline the evidence that chromatin modifications are associated with metabolic diseases, including diabetes and obesity. We also consider evidence that these chromatin modifications can lead to long-term disease risk and contribute to disease risk for future generations. This article is categorized under: Biological Mechanisms > Metabolism Developmental Biology > Developmental Processes in Health and Disease Physiology > Organismal Responses to Environment.
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Affiliation(s)
- Kevin R. Costello
- Department of Diabetes Complications and MetabolismIrell & Manella Graduate School, City of HopeDuarteCalifornia
| | - Dustin E. Schones
- Department of Diabetes Complications and MetabolismIrell & Manella Graduate School, City of HopeDuarteCalifornia
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79
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Kessler NJ, Waterland RA, Prentice AM, Silver MJ. Establishment of environmentally sensitive DNA methylation states in the very early human embryo. SCIENCE ADVANCES 2018; 4:eaat2624. [PMID: 30009262 PMCID: PMC6040841 DOI: 10.1126/sciadv.aat2624] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/01/2018] [Indexed: 05/04/2023]
Abstract
The molecular mechanisms responsible for the developmental origins of later disease are currently unknown. We previously demonstrated that women's periconceptional nutrition predicts their offspring's DNA methylation at metastable epialleles (MEs). We present a genome-wide screen yielding 687 MEs and track their trajectories across nine developmental stages in human in vitro fertilization embryos. MEs exhibit highly unusual methylation dynamics across the implantation-gastrulation transition, producing a large excess of intermediate methylation states, suggesting the potential for differential programming in response to external signals. Using a natural experiment in rural Gambia, we show that genomic regions sensitive to season of conception are highly enriched for MEs and show similar atypical methylation patterns. MEs are enriched for proximal enhancers and transcription start sites and are influenced by genotype. Together, these observations position MEs as distinctive epigenomic features programmed in the early embryo, sensitive to genetic and periconceptional environment, and with the potential to influence phenotype.
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Affiliation(s)
- Noah J. Kessler
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Robert A. Waterland
- U.S. Department of Agriculture/Agricultural Research Service Children’s Nutrition Research Center, Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Matt J. Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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80
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Rollo C, Li Y, Jin XL, O'Neill C. Histone 3 lysine 9 acetylation is a biomarker of the effects of culture on zygotes. Reproduction 2018; 154:375-385. [PMID: 28878090 PMCID: PMC5592804 DOI: 10.1530/rep-17-0112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 05/04/2017] [Accepted: 07/04/2017] [Indexed: 01/26/2023]
Abstract
Acetylation of histone proteins is a major determinant of chromatin structure and function. Fertilisation triggers a round of chromatin remodelling that prepares the genome for the first round of transcription from the new embryonic genome. In this study we confirm that fertilisation leads to a marked progressive increase in the level of histone 3 lysine 9 acetylation in both the paternally and maternally derived genomes. The culture of zygotes in simple defined media caused a marked increase in the global level of acetylation and this affected the male pronucleus more than the female. The culture created a marked asymmetry in staining between the two pronuclei that was not readily detected in zygotes collected directly from the reproductive tract and was ameliorated to some extent by optimized culture media. The increased acetylation caused by culture resulted in increased transcription of Hspa1b, a marker of embryonic genome activation. Pharmacological analyses showed the hyperacetylation of H3K9 and the increased expression of Hspa1b caused by culture were due to the altered net activity of a range of histone acetylases and deacetylases. The marked hyperacetylation of histone 3 lysine 9 caused by culture of zygotes may serve as an early biomarker for the effects of culture on the normal function of the embryo. The results also provide further evidence for an effect of the stresses associated with assisted reproductive technologies on the normal patterns of epigenetic reprogramming in the early embryo.
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Affiliation(s)
- C Rollo
- Human Reproduction UnitKolling Institute Sydney Medical, School University of Sydney, Sydney, Australia
| | - Y Li
- Human Reproduction UnitKolling Institute Sydney Medical, School University of Sydney, Sydney, Australia
| | - X L Jin
- Human Reproduction UnitKolling Institute Sydney Medical, School University of Sydney, Sydney, Australia
| | - C O'Neill
- Human Reproduction UnitKolling Institute Sydney Medical, School University of Sydney, Sydney, Australia
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81
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Abstract
Environmental factors, particularly during early life, are important for the later metabolic health of the individual. In our obesogenic environment, it is of major socio-economic importance to investigate the mechanisms that contribute to the risk of metabolic ill health. Increasing evidence from a variety of model organisms suggests that non-genetically determined phenotypes, including metabolic effects such as glucose intolerance and obesity, can be passed between generations, which encourages us to revisit heredity. Inheritance of altered epigenetic information through the germ line has been proposed as one plausible mechanism. Whether the germline epigenome can be altered by environmental conditions such as diet and the extent to which this occurs in humans are the subject of intense current interest and debate, especially given that extensive germline epigenetic reprogramming is known to occur. As epigenetic mechanisms are often highly conserved between organisms, studying epigenetic inheritance in plants and lower metazoans has the potential to inform our investigation in mammals. This Review explores the extent to which epigenetic inheritance contributes to heredity in these different organisms, whether the environment can affect epigenetic inheritance and whether there is any evidence for the inheritance of acquired phenotypes.
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Affiliation(s)
- Elizabeth J Radford
- Department of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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82
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Abstract
PURPOSE OF REVIEW It is becoming increasingly evident that epigenetic mechanisms, particularly DNA methylation, play a role in the regulation of blood lipid levels and lipid metabolism-linked phenotypes and diseases. RECENT FINDINGS Recent genome-wide methylation and candidate gene studies of blood lipids have highlighted several robustly replicated methylation markers across different ethnicities. Furthermore, many of these lipid-related CpG sites associated with blood lipids are also linked to lipid-related phenotypes and diseases. Integrating epigenome-wide association studies (EWAS) data with other layers of molecular data such as genetics or the transcriptome, accompanied by relevant statistical methods (e.g. Mendelian randomization), provides evidence for causal relationships. Recent data suggest that epigenetic changes can be consequences rather than causes of dyslipidemia. There is sparse information on many lipid classes and disorders of lipid metabolism, and also on the interplay of DNA methylation with other epigenetic layers such as histone modifications and regulatory RNAs. SUMMARY The current review provides a literature overview of epigenetic modifications in lipid metabolism and other lipid-related phenotypes and diseases focusing on EWAS of DNA methylation from January 2016 to September 2017. Recent studies strongly support the importance of epigenetic modifications, such as DNA methylation, in lipid metabolism and related diseases for relevant biological insights, reliable biomarkers, and even future therapeutics.
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Affiliation(s)
- Kirstin Mittelstraß
- Research Unit of Molecular Epidemiology
- Institute of Epidemiology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology
- Institute of Epidemiology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
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83
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Pembrey ME. Does cross-generational epigenetic inheritance contribute to cultural continuity? ENVIRONMENTAL EPIGENETICS 2018; 4:dvy004. [PMID: 29732169 PMCID: PMC5920305 DOI: 10.1093/eep/dvy004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 02/28/2018] [Accepted: 03/04/2018] [Indexed: 06/08/2023]
Abstract
Human studies of cross-generational epigenetic inheritance have to consider confounding by social patterning down the generations, often referred to as 'cultural inheritance'. This raises the question to what extent is 'cultural inheritance' itself epigenetically mediated rather than just learnt. Human studies of non-genetic inheritance have demonstrated that, beyond foetal life, experiences occurring in mid-childhood before puberty are the most likely to be associated with cross-generational responses in the next generation(s). It is proposed that cultural continuity is played out along the axis, or 'payoff', between responsiveness and stability. During the formative years of childhood a stable family and/or home permits small children to explore and thereby learn. To counter disruptions to this family home ideal, cultural institutions such as local schools, religious centres and market places emerged to provide ongoing stability, holding the received wisdom of the past in an accessible state. This cultural support allows the growing child to freely indulge their responsiveness. Some of these prepubertal experiences induce epigenetic responses that also transfer molecular signals to the gametes through which they contribute to the conception of future offspring. In parallel co-evolution with growing cultural support for increasing responsiveness, 'runaway' responsiveness is countered by the positive selection of genetic variants that dampen responsiveness. Testing these ideas within longitudinal multigenerational cohorts will need information on ancestors/parents' own communities and experiences (Exposome scans) linked to ongoing Phenome scans on grandchildren; coupled with epigenome analysis, metastable epialleles and DNA methylation age. Interactions with genetic variants affecting responsiveness should help inform the broad hypothesis.
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Affiliation(s)
- Marcus E Pembrey
- Centre for Child and Adolescent Health, University of Bristol, Bristol, UK
- Great Ormond Street Institute of Child Health, Faculty of Population Health Sciences, University College London, London, UK
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84
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McCabe C, Anderson OS, Montrose L, Neier K, Dolinoy DC. Sexually Dimorphic Effects of Early-Life Exposures to Endocrine Disruptors: Sex-Specific Epigenetic Reprogramming as a Potential Mechanism. Curr Environ Health Rep 2018; 4:426-438. [PMID: 28980159 DOI: 10.1007/s40572-017-0170-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
PURPOSE OF REVIEW The genetic material of every organism exists within the context of regulatory networks that govern gene expression-collectively called the epigenome. Animal models and human birth cohort studies have revealed key developmental periods that are important for epigenetic programming and vulnerable to environmental insults. Thus, epigenetics represent a potential mechanism through which sexually dimorphic effects of early-life exposures such as endocrine-disrupting chemicals (EDCs) manifest. RECENT FINDINGS Several animal studies, and to a lesser extent human studies, have evaluated life-course sexually dimorphic health effects following developmental toxicant exposures; many fewer studies, however, have evaluated epigenetics as a mechanism mediating developmental exposures and later outcomes. To evaluate epigenetic reprogramming as a mechanistic link of sexually dimorphic early-life EDCs exposures, the following criteria should be met: (1) well-characterized exposure paradigm that includes relevant windows for developmental epigenetic reprogramming; (2) evaluation of sex-specific exposure-related epigenetic change; and (3) observation of a sexually dimorphic phenotype in either childhood, adolescence, or adulthood.
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Affiliation(s)
- Carolyn McCabe
- Nutritonal Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA
| | - Olivia S Anderson
- Nutritonal Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA
| | - Luke Montrose
- Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA
| | - Kari Neier
- Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA
| | - Dana C Dolinoy
- Nutritonal Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA. .,Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA.
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85
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Van Baak TE, Coarfa C, Dugué PA, Fiorito G, Laritsky E, Baker MS, Kessler NJ, Dong J, Duryea JD, Silver MJ, Saffari A, Prentice AM, Moore SE, Ghantous A, Routledge MN, Gong YY, Herceg Z, Vineis P, Severi G, Hopper JL, Southey MC, Giles GG, Milne RL, Waterland RA. Epigenetic supersimilarity of monozygotic twin pairs. Genome Biol 2018; 19:2. [PMID: 29310692 PMCID: PMC5759268 DOI: 10.1186/s13059-017-1374-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/06/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Monozygotic twins have long been studied to estimate heritability and explore epigenetic influences on phenotypic variation. The phenotypic and epigenetic similarities of monozygotic twins have been assumed to be largely due to their genetic identity. RESULTS Here, by analyzing data from a genome-scale study of DNA methylation in monozygotic and dizygotic twins, we identified genomic regions at which the epigenetic similarity of monozygotic twins is substantially greater than can be explained by their genetic identity. This "epigenetic supersimilarity" apparently results from locus-specific establishment of epigenotype prior to embryo cleavage during twinning. Epigenetically supersimilar loci exhibit systemic interindividual epigenetic variation and plasticity to periconceptional environment and are enriched in sub-telomeric regions. In case-control studies nested in a prospective cohort, blood DNA methylation at these loci years before diagnosis is associated with risk of developing several types of cancer. CONCLUSIONS These results establish a link between early embryonic epigenetic development and adult disease. More broadly, epigenetic supersimilarity is a previously unrecognized phenomenon that may contribute to the phenotypic similarity of monozygotic twins.
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Affiliation(s)
- Timothy E Van Baak
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Giovanni Fiorito
- Department of Medical Sciences, University of Torino and Italian Institute for Genomic Medicine, Torino, Italy
| | - Eleonora Laritsky
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maria S Baker
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Noah J Kessler
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Jianrong Dong
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jack D Duryea
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Matt J Silver
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Ayden Saffari
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Andrew M Prentice
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Sophie E Moore
- MRC Unit The Gambia, Keneba, Gambia
- Division of Women's Health, King's College London, London, UK
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | | | - Yun Yun Gong
- School of Food Science & Nutrition, University of Leeds, Leeds, UK
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Paolo Vineis
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
- Italian Institute for Genomic Medicine, Torino, Italy
| | - Gianluca Severi
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
- Italian Institute for Genomic Medicine, Torino, Italy
- CESP Inserm, Facultés de medicine Université Paris-Sud, Paris, France
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Roger L Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Robert A Waterland
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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86
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Frías-Lasserre D, Villagra CA. The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution. Front Microbiol 2017; 8:2483. [PMID: 29312192 PMCID: PMC5744636 DOI: 10.3389/fmicb.2017.02483] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022] Open
Abstract
Neo-Darwinian explanations of organic evolution have settled on mutation as the principal factor in producing evolutionary novelty. Mechanistic characterizations have been also biased by the classic dogma of molecular biology, where only proteins regulate gene expression. This together with the rearrangement of genetic information, in terms of genes and chromosomes, was considered the cornerstone of evolution at the level of natural populations. This predominant view excluded both alternative explanations and phenomenologies that did not fit its paradigm. With the discovery of non-coding RNAs (ncRNAs) and their role in the control of genetic expression, new mechanisms arose providing heuristic power to complementary explanations to evolutionary processes overwhelmed by mainstream genocentric views. Viruses, epimutation, paramutation, splicing, and RNA editing have been revealed as paramount functions in genetic variations, phenotypic plasticity, and diversity. This article discusses how current epigenetic advances on ncRNAs have changed the vision of the mechanisms that generate variation, how organism-environment interaction can no longer be underestimated as a driver of organic evolution, and how it is now part of the transgenerational inheritance and evolution of species.
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Affiliation(s)
- Daniel Frías-Lasserre
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
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87
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Stern S, Kirst C, Bargmann CI. Neuromodulatory Control of Long-Term Behavioral Patterns and Individuality across Development. Cell 2017; 171:1649-1662.e10. [DOI: 10.1016/j.cell.2017.10.041] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 09/10/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022]
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88
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Patkin E, Grudinina N, Sasina L, Noniashvili E, Pavlinova L, Suchkova I, Kustova M, Kolmakov N, Van Truong T, Sofronov G. Asymmetric DNA methylation between sister chromatids of metaphase chromosomes in mouse embryos upon bisphenol A action. Reprod Toxicol 2017; 74:1-9. [DOI: 10.1016/j.reprotox.2017.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/24/2017] [Accepted: 08/18/2017] [Indexed: 12/17/2022]
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89
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Prentice S. They Are What You Eat: Can Nutritional Factors during Gestation and Early Infancy Modulate the Neonatal Immune Response? Front Immunol 2017; 8:1641. [PMID: 29234319 PMCID: PMC5712338 DOI: 10.3389/fimmu.2017.01641] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/09/2017] [Indexed: 12/17/2022] Open
Abstract
The ontogeny of the human immune system is sensitive to nutrition even in the very early embryo, with both deficiency and excess of macro- and micronutrients being potentially detrimental. Neonates are particularly vulnerable to infectious disease due to the immaturity of the immune system and modulation of nutritional immunity may play a role in this sensitivity. This review examines whether nutrition around the time of conception, throughout pregnancy, and in early neonatal life may impact on the developing infant immune system.
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Affiliation(s)
- Sarah Prentice
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
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90
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Abstract
Analyzing the conditions in which past individuals lived is key to understanding the environments and cultural transitions to which humans had to adapt. Here, we suggest a methodology to probe into past environments, using reconstructed premortem DNA methylation maps of ancient individuals. We review a large body of research showing that differential DNA methylation is associated with changes in various external and internal factors, and propose that loci whose DNA methylation level is environmentally responsive could serve as markers to infer about ancient daily life, diseases, nutrition, exposure to toxins, and more. We demonstrate this approach by showing that hunger-related DNA methylation changes are found in ancient hunter-gatherers. The strategy we present here opens a window to reconstruct previously inaccessible aspects of the lives of past individuals.
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Affiliation(s)
- David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Anat Malul
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
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91
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Haertle L, Maierhofer A, Böck J, Lehnen H, Böttcher Y, Blüher M, Schorsch M, Potabattula R, El Hajj N, Appenzeller S, Haaf T. Hypermethylation of the non-imprinted maternal MEG3 and paternal MEST alleles is highly variable among normal individuals. PLoS One 2017; 12:e0184030. [PMID: 28854270 PMCID: PMC5576652 DOI: 10.1371/journal.pone.0184030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/16/2017] [Indexed: 01/09/2023] Open
Abstract
Imprinted genes show parent-specific activity (functional haploidy), which makes them particularly vulnerable to epigenetic dysregulation. Here we studied the methylation profiles of oppositely imprinted genes at single DNA molecule resolution by two independent parental allele-specific deep bisulfite sequencing (DBS) techniques. Using Roche (GSJunior) next generation sequencing technology, we analyzed the maternally imprinted MEST promoter and the paternally imprinted MEG3 intergenic (IG) differentially methylated region (DMR) in fetal cord blood, adult blood, and visceral adipose tissue. Epimutations were defined as paternal or maternal alleles with >50% aberrantly (de)methylated CpG sites, showing the wrong methylation imprint. The epimutation rates (range 2–66%) of the paternal MEST and the maternal MEG3 IG DMR allele, which should be completely unmethylated, were significantly higher than those (0–15%) of the maternal MEST and paternal MEG3 alleles, which are expected to be fully methylated. This hypermethylation of the non-imprinted allele (HNA) was independent of parental origin. Very low epimutation rates in sperm suggest that HNA occurred after fertilization. DBS with Illumina (MiSeq) technology confirmed HNA for the MEST promoter and the MEG3 IG DMR, and to a lesser extent, for the paternally imprinted secondary MEG3 promoter and the maternally imprinted PEG3 promoter. HNA leads to biallelic methylation of imprinted genes in a considerable proportion of normal body cells (somatic mosaicism) and is highly variable between individuals. We propose that during development and differentiation maintenance of differential methylation at most imprinting control regions may become to some extent redundant. The accumulation of stochastic and environmentally-induced methylation errors on the non-imprinted allele may increase epigenetic diversity between cells and individuals.
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Affiliation(s)
- Larissa Haertle
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Anna Maierhofer
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Julia Böck
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Harald Lehnen
- Department of Gynecology and Obstetrics, Municipal Clinics, Mönchengladbach, Germany
| | - Yvonne Böttcher
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, Leipzig, Germany
- Institute of Clinical Medicine, University of Oslo, Lørenskog, Norway
| | - Matthias Blüher
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, Leipzig, Germany
| | | | - Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Silke Appenzeller
- Core Unit Systems Medicine, Julius Maximilians University, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Julius Maximilians University, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- * E-mail:
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92
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Stevens AJ, Rucklidge JJ, Kennedy MA. Epigenetics, nutrition and mental health. Is there a relationship? Nutr Neurosci 2017; 21:602-613. [PMID: 28553986 DOI: 10.1080/1028415x.2017.1331524] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many aspects of human development and disease are influenced by the interaction between genetic and environmental factors. Understanding how our genes respond to the environment is central to managing health and disease, and is one of the major contemporary challenges in human genetics. Various epigenetic processes affect chromosome structure and accessibility of deoxyribonucleic acid (DNA) to the enzymatic machinery that leads to expression of genes. One important epigenetic mechanism that appears to underlie the interaction between environmental factors, including diet, and our genome, is chemical modification of the DNA. The best understood of these modifications is methylation of cytosine residues in DNA. It is now recognized that the pattern of methylated cytosines throughout our genomes (the 'methylome') can change during development and in response to environmental cues, often with profound effects on gene expression. Many dietary constituents may indirectly influence genomic pathways that methylate DNA, and there is evidence for biochemical links between nutritional quality and mental health. Deficiency of both macro- and micronutrients has been associated with increased behavioural problems, and nutritional supplementation has proven efficacious in treatment of certain neuropsychiatric disorders. In this review we examine evidence from the fields of nutrition, developmental biology, and mental health that supports dietary impacts on epigenetic processes, particularly DNA methylation. We then consider whether such processes could underlie the demonstrated efficacy of dietary supplementation in treatment of mental disorders, and whether targeted manipulation of DNA methylation patterns using controlled dietary supplementation may be of wider clinical value.
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Affiliation(s)
- Aaron J Stevens
- a Department of Pathology , University of Otago , P.O. Box 4345, Christchurch , New Zealand
| | - Julia J Rucklidge
- b Department of Psychology , University of Canterbury , Christchurch , New Zealand
| | - Martin A Kennedy
- a Department of Pathology , University of Otago , P.O. Box 4345, Christchurch , New Zealand
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93
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Kannan M, Li J, Fritz SE, Husarek KE, Sanford JC, Sullivan TL, Tiwary PK, An W, Boeke JD, Symer DE. Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration. Mob DNA 2017; 8:8. [PMID: 28491150 PMCID: PMC5424313 DOI: 10.1186/s13100-017-0091-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/03/2017] [Indexed: 02/15/2023] Open
Abstract
Background The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. Results Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny. In cancer cell lines, the newly inserted sequences typically underwent rapid transcriptional gene silencing, but they lacked cytosine methylation even after many cell divisions. L1 reporter expression was reversible and oscillated frequently. Silenced or variegated reporter expression was strongly and uniformly reactivated by treatment with inhibitors of histone deacetylation, revealing the mechanism for their silencing. By contrast, de novo integrants retrotransposed by L1 in pluripotent mouse embryonic stem (ES) cells underwent rapid silencing by dense cytosine methylation. Similarly, de novo cytosine methylation also was identified at new integrants when studied in several distinct somatic tissues of adult founder mice. Pre-existing L1 elements in cultured human cancer cells were stably silenced by dense cytosine methylation, whereas their transcription modestly increased when cytosine methylation was experimentally reduced in cells lacking DNA methyltransferases DNMT1 and DNMT3b. As a control, reporter genes mobilized by piggyBac (PB), a DNA transposon, revealed relatively stable and robust expression without apparent silencing in both cultured cancer cells and ES cells. Conclusions We hypothesize that the de novo methylation marks at newly inserted sequences retrotransposed by L1 in early pre-implantation development are maintained or re-established in adult somatic tissues. By contrast, histone deacetylation reversibly silences L1 reporter insertions that had mobilized at later timepoints in somatic development and differentiation, e.g., in cancer cell lines. We conclude that the cellular contexts of L1 retrotransposition can determine expression or silencing of newly integrated sequences. We propose a model whereby reporter expression from somatic TE insertions reflects the timing, molecular mechanism, epigenetic controls and the genomic, cellular and developmental contexts of their integration. Electronic supplementary material The online version of this article (doi:10.1186/s13100-017-0091-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manoj Kannan
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, 333031 Rajasthan India.,Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Present Address: Birla Institute of Technology and Science, Pilani, Dubai campus, Dubai, United Arab Emirates
| | - Jingfeng Li
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH USA.,Department of Internal Medicine, The Ohio State University, Columbus, OH USA
| | - Sarah E Fritz
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Kathryn E Husarek
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: Aventiv Research, Inc., Columbus, OH USA
| | - Jonathan C Sanford
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: Drug Safety Research and Development, Pfizer, Inc., Groton, CT USA
| | - Teresa L Sullivan
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
| | - Pawan Kumar Tiwary
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Present Address: Biocon, Bangalore, India
| | - Wenfeng An
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA.,Present Address: Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD USA
| | - Jef D Boeke
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA.,Present Address: Institute for Systems Genetics, New York University Langone Medical Center, New York, NY USA
| | - David E Symer
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH USA.,Human Cancer Genetics Program, and Department of Biomedical Informatics, The Ohio State University, Columbus, OH USA.,Human Cancer Genetics Program, Department of Cancer Biology and Genetics, and Department of Biomedical Informatics, The Ohio State University, Tzagournis Research Facility, Room 440, 420 West 12th Ave, Columbus, OH 43210 USA
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94
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Abstract
The human epigenome may link environmental exposures and commensal microbiota changes to host pathology in respect to the developmental origins of inflammatory bowel diseases (ulcerative colitis [UC] and Crohn's disease [more appropriately Crohn disease, CD]). Genetic predisposition - prenatal, perinatal and pediatric environmental influences - microbiome aberration (dysbiosis) and immune dysregulation appear to be important elements in disease development, progression and maintenance. The prevalence of combined genetic and epigenetic susceptibility toward UC and CD is calculated herein to be as high as 2%, and approximately 1% for UC and CD in highly developed countries, respectively. This review emphasizes the significant challenges for epigenetic research in inflammatory bowel diseases. Overcoming these challenges, however, could reveal unique opportunities for disease prevention, treatment and possible cure.
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Affiliation(s)
- Richard Kellermayer
- Section of Pediatric Gastroenterology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, USDA/ARS Children's Nutrition Research Center, Houston, TX 77030, USA
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95
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Castillo-Fernandez JE, Loke YJ, Bass-Stringer S, Gao F, Xia Y, Wu H, Lu H, Liu Y, Wang J, Spector TD, Saffery R, Craig JM, Bell JT. DNA methylation changes at infertility genes in newborn twins conceived by in vitro fertilisation. Genome Med 2017; 9:28. [PMID: 28340599 PMCID: PMC5364659 DOI: 10.1186/s13073-017-0413-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 02/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The association of in vitro fertilisation (IVF) and DNA methylation has been studied predominantly at regulatory regions of imprinted genes and at just thousands of the ~28 million CpG sites in the human genome. METHODS We investigated the links between IVF and DNA methylation patterns in whole cord blood cells (n = 98) and cord blood mononuclear cells (n = 82) from newborn twins using genome-wide methylated DNA immunoprecipitation coupled with deep sequencing. RESULTS At a false discovery rate (FDR) of 5%, we identified one significant whole blood DNA methylation change linked to conception via IVF, which was located ~3 kb upstream of TNP1, a gene previously linked to male infertility. The 46 most strongly associated signals (FDR of 25%) included a second region in a gene also previously linked to infertility, C9orf3, suggesting that our findings may in part capture the effect of parental subfertility. Using twin modelling, we observed that individual-specific environmental factors appear to be the main overall contributors of methylation variability at the FDR 25% IVF-associated differentially methylated regions, although evidence for methylation heritability was also obtained at several of these regions. We replicated previous findings of differential methylation associated with IVF at the H19/IGF2 region in cord blood mononuclear cells, and we validated the signal at C9orf3 in monozygotic twins. We also explored the impact of intracytoplasmic sperm injection on the FDR 25% signals for potential effects specific to male or female infertility factors. CONCLUSIONS To our knowledge, this is the most comprehensive study of DNA methylation profiles at birth and IVF conception to date, and our results show evidence for epigenetic modifications that may in part reflect parental subfertility.
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Affiliation(s)
| | - Yuk Jing Loke
- Early Life Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Sebastian Bass-Stringer
- Early Life Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Fei Gao
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | | | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.,King Abdulaziz University, Jeddah, 22254, Saudi Arabia.,Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark.,The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, SE1 7EH, London, UK.
| | - Richard Saffery
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia. .,Cancer, Disease and Developmental Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.
| | - Jeffrey M Craig
- Early Life Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, SE1 7EH, London, UK.
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96
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Wanner N, Bechtel-Walz W. Epigenetics of kidney disease. Cell Tissue Res 2017; 369:75-92. [PMID: 28286899 DOI: 10.1007/s00441-017-2588-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/15/2017] [Indexed: 02/06/2023]
Abstract
DNA methylation and histone modifications determine renal programming and the development and progression of renal disease. The identification of the way in which the renal cell epigenome is altered by environmental modifiers driving the onset and progression of renal diseases has extended our understanding of the pathophysiology of kidney disease progression. In this review, we focus on current knowledge concerning the implications of epigenetic modifications during renal disease from early development to chronic kidney disease progression including renal fibrosis, diabetic nephropathy and the translational potential of identifying new biomarkers and treatments for the prevention and therapy of chronic kidney disease and end-stage kidney disease.
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Affiliation(s)
- Nicola Wanner
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Center for Systems Biology (ZBSA), Albert-Ludwigs-University, Freiburg, Germany. .,Renal Division, University Hospital Freiburg, Breisacher Strasse 66, 79106, Freiburg, Germany.
| | - Wibke Bechtel-Walz
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Renal Division, University Hospital Freiburg, Breisacher Strasse 66, 79106, Freiburg, Germany.
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97
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Yuan C, Zhang Y, Liu Y, Wang S, Wang Z. DNA demethylation mediated by down-regulated TETs in the testes of rare minnow Gobiocypris rarus under bisphenol A exposure. CHEMOSPHERE 2017; 171:355-361. [PMID: 28030787 DOI: 10.1016/j.chemosphere.2016.12.098] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/10/2016] [Accepted: 12/20/2016] [Indexed: 06/06/2023]
Abstract
Inevitable BPA exposure resulted in disturbance of DNA methylation status and our published study suspected that BPA has the potentiality to disturb DNA demethylation and GSH production in Gobiocypris rarus testes. To confirm this conjecture, several experiments were carried out in the present study. Adult male G. rarus was exposed to 1, 15 and 225 μg L-1 (nominal concentration) BPA for two weeks. The levels of 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), glutathione (GSH), and enzyme levels for DNA methylation and GSH synthesis in the testes were detected. Meanwhile, the contents of substrates for GSH synthesis were measured. Furthermore, the transcriptional changes of the studied genes were examined. Results indicated that 1-225 μg L-1 BPA caused decrease of testicular ten-eleven translocation proteins (TETs) with more obvious effects at low concentrations. Moreover, all concentrations of BPA resulted in decrease of 5hmC levels while only 225 μg L-1 BPA resulted in significant increase of 5mC. In addition, all treatments resulted in significant decrease of GSH and the replenishment of GSH might be mainly accomplished by circular synthesis. These results indicated that BPA exposure inhibited TETs-mediated DNA demethylation and the declined DNA demethylation mediated by TETs may result in DNA hypermethylation at 225 μg L-1 BPA. In addition, the changes of DNA methylation status were irrelevant with GSH levels.
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Affiliation(s)
- Cong Yuan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100 China
| | - Yingying Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100 China
| | - Yan Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100 China
| | - Song Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100 China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100 China.
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98
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Bourke L, del Monte-Nieto G, Outhwaite J, Bharti V, Pollock P, Simmons D, Adam A, Hur S, Maghzal G, Whitelaw E, Stocker R, Suter C, Harvey R, Harten S. Loss of Rearranged L-Myc Fusion (RLF) results in defects in heart development in the mouse. Differentiation 2017; 94:8-20. [DOI: 10.1016/j.diff.2016.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 10/25/2016] [Accepted: 11/16/2016] [Indexed: 01/22/2023]
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99
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Vogt G. Facilitation of environmental adaptation and evolution by epigenetic phenotype variation: insights from clonal, invasive, polyploid, and domesticated animals. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx002. [PMID: 29492304 PMCID: PMC5804542 DOI: 10.1093/eep/dvx002] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/28/2017] [Accepted: 02/02/2017] [Indexed: 05/13/2023]
Abstract
There is increasing evidence, particularly from plants, that epigenetic mechanisms can contribute to environmental adaptation and evolution. The present article provides an overview on this topic for animals and highlights the special suitability of clonal, invasive, hybrid, polyploid, and domesticated species for environmental and evolutionary epigenetics. Laboratory and field studies with asexually reproducing animals have shown that epigenetically diverse phenotypes can be produced from the same genome either by developmental stochasticity or environmental induction. The analysis of invasions revealed that epigenetic phenotype variation may help to overcome genetic barriers typically associated with invasions such as bottlenecks and inbreeding. Research with hybrids and polyploids established that epigenetic mechanisms are involved in consolidation of speciation by contributing to reproductive isolation and restructuring of the genome in the neo-species. Epigenetic mechanisms may even have the potential to trigger speciation but evidence is still meager. The comparison of domesticated animals and their wild ancestors demonstrated heritability and selectability of phenotype modulating DNA methylation patterns. Hypotheses, model predictions, and empirical results are presented to explain how epigenetic phenotype variation could facilitate adaptation and speciation. Clonal laboratory lineages, monoclonal invaders, and adaptive radiations of different evolutionary age seem particularly suitable to empirically test the proposed ideas. A respective research agenda is presented.
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Affiliation(s)
- Günter Vogt
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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Navarro E, Funtikova AN, Fíto M, Schröder H. Prenatal nutrition and the risk of adult obesity: Long-term effects of nutrition on epigenetic mechanisms regulating gene expression. J Nutr Biochem 2017; 39:1-14. [DOI: 10.1016/j.jnutbio.2016.03.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 03/23/2016] [Accepted: 03/27/2016] [Indexed: 12/19/2022]
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