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Mann MRW, Suzuki M, Keller Valsecchi CI. Editorial: In celebration of women in developmental epigenetics. Front Cell Dev Biol 2024; 12:1416081. [PMID: 38859963 PMCID: PMC11163029 DOI: 10.3389/fcell.2024.1416081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 06/12/2024] Open
Affiliation(s)
- Mellissa R. W. Mann
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Masako Suzuki
- Department of Nutrition, Texas A&M University, College Station, TX, United States
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2
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van Dongen J, Hubers N, Boomsma DI. New insights into the (epi)genetics of twinning. Hum Reprod 2024; 39:35-42. [PMID: 38052159 PMCID: PMC10767898 DOI: 10.1093/humrep/dead131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 05/24/2023] [Indexed: 12/07/2023] Open
Abstract
Spontaneous dizygotic (DZ) twins, i.e. twins conceived without the use of ARTs, run in families and their prevalence varies widely around the globe. In contrast, monozygotic (MZ) twins occur at a constant rate across time and geographical regions and, with some rare exceptions, do not cluster in families. The leading hypothesis for MZ twins, which arise when a zygote splits during preimplantation stages of development, is random occurrence. We have found the first series of genes underlying the liability of being the mother of DZ twins and have shown that being an MZ twin is strongly associated with a stable DNA methylation signature in child and adult somatic tissues. Because identical twins keep this molecular signature across the lifespan, this discovery opens up completely new possibilities for the retrospective diagnosis of whether a person is an MZ twin whose co-twin may have vanished in the early stages of pregnancy. Here, we summarize the gene finding results for mothers of DZ twins based on genetic association studies followed by meta-analysis, and further present the striking epigenetic results for MZ twins.
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Affiliation(s)
- Jenny van Dongen
- Netherlands Twin Register, Department of Biological Psychology, Amsterdam Reproduction and Development Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Nikki Hubers
- Netherlands Twin Register, Department of Biological Psychology, Amsterdam Reproduction and Development Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, Amsterdam Reproduction and Development Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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3
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Derakhshan M, Kessler NJ, Hellenthal G, Silver MJ. Metastable epialleles in humans. Trends Genet 2024; 40:52-68. [PMID: 38000919 DOI: 10.1016/j.tig.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 11/26/2023]
Abstract
First identified in isogenic mice, metastable epialleles (MEs) are loci where the extent of DNA methylation (DNAm) is variable between individuals but correlates across tissues derived from different germ layers within a given individual. This property, termed systemic interindividual variation (SIV), is attributed to stochastic methylation establishment before germ layer differentiation. Evidence suggests that some putative human MEs are sensitive to environmental exposures in early development. In this review we introduce key concepts pertaining to human MEs, describe methods used to identify MEs in humans, and review their genomic features. We also highlight studies linking DNAm at putative human MEs to early environmental exposures and postnatal (including disease) phenotypes.
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Affiliation(s)
- Maria Derakhshan
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Noah J Kessler
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | | | - Matt J Silver
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia.
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4
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Braz CU, Passamonti MM, Khatib H. Characterization of genomic regions escaping epigenetic reprogramming in sheep. ENVIRONMENTAL EPIGENETICS 2023; 10:dvad010. [PMID: 38496251 PMCID: PMC10944287 DOI: 10.1093/eep/dvad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 03/19/2024]
Abstract
The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.
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Affiliation(s)
- Camila U Braz
- Department of Animal Sciences, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition, Universit’a Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI 53706, USA
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5
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Tam PLF, Leung D. The Molecular Impacts of Retrotransposons in Development and Diseases. Int J Mol Sci 2023; 24:16418. [PMID: 38003607 PMCID: PMC10671454 DOI: 10.3390/ijms242216418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Retrotransposons are invasive genetic elements that constitute substantial portions of mammalian genomes. They have the potential to influence nearby gene expression through their cis-regulatory sequences, reverse transcription machinery, and the ability to mold higher-order chromatin structures. Due to their multifaceted functions, it is crucial for host fitness to maintain strict regulation of these parasitic sequences to ensure proper growth and development. This review explores how subsets of retrotransposons have undergone evolutionary exaptation to enhance the complexity of mammalian genomes. It also highlights the significance of regulating these elements, drawing on recent studies conducted in human and murine systems.
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Affiliation(s)
- Phoebe Lut Fei Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China;
| | - Danny Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China;
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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6
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Xu B, Li X, Zhang S, Lian M, Huang W, Zhang Y, Wang Y, Huang Z. Pan cancer characterization of genes whose expression has been associated with LINE-1 antisense promoter activity. Mob DNA 2023; 14:13. [PMID: 37723560 PMCID: PMC10506190 DOI: 10.1186/s13100-023-00300-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Long interspersed nuclear element-1 (LINE-1 or L1) comprises 17% of the human genome. As the only autonomous and active retrotransposons, L1 may take part in cancer initiation and progression in some ways. The studies of L1 in cancer mainly focus on the impact of L1 insertion into the new genome locus. The L1 5´ untranslated region (UTR) also contains antisense promoter (ASP) activity, generating L1-gene chimeric transcripts to a neighbor exon. Some of these ASP-associated genes have been reported to be overexpressed in cancer and promote cancer cell growth. However, little is known about overall expression patterns and the roles of L1 ASP-associated genes in human cancers. RESULTS L1 ASP-associated genes were frequently dysregulated in cancer and associated with the cell cycle, the PI3K/AKT pathway, and the GTPase signaling pathway. The expression of L1 ASP-associated genes was correlated with tumor patient prognosis. Hub L1 ASP-associated genes CENPU and MCM2 showed a correlation with immune infiltration, clinical T stage, and cancer stemness in pan-cancer. Knockdown of L1 ASP-associated gene LINC00491 resulted in a significant decrease in tumor growth and migration ability. CONCLUSIONS The expression of L1 ASP-associated genes is significantly dysregulated at the pan-cancer level, which is closely related to the tumor microenvironment, progression, and patient prognosis. Hub genes CENPU and MCM2 are expected to be new tumor diagnostic markers and therapeutic targets.
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Affiliation(s)
- Baohong Xu
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Xueer Li
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Shaoqi Zhang
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Meina Lian
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Wenbin Huang
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
| | - Yudong Wang
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China.
| | - Zhiquan Huang
- First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong, China.
- Department of Oral and Maxillofacial Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
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7
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Lechner L, Opitz R, Silver MJ, Krabusch PM, Prentice AM, Field MS, Stachelscheid H, Leitão E, Schröder C, Fernandez Vallone V, Horsthemke B, Jöckel KH, Schmidt B, Nöthen MM, Hoffmann P, Herms S, Kleyn PW, Megges M, Blume-Peytavi U, Weiss K, Mai K, Blankenstein O, Obermayer B, Wiegand S, Kühnen P. Early-set POMC methylation variability is accompanied by increased risk for obesity and is addressable by MC4R agonist treatment. Sci Transl Med 2023; 15:eadg1659. [PMID: 37467315 DOI: 10.1126/scitranslmed.adg1659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/22/2023] [Indexed: 07/21/2023]
Abstract
Increasing evidence points toward epigenetic variants as a risk factor for developing obesity. We analyzed DNA methylation of the POMC (pro-opiomelanocortin) gene, which is pivotal for satiety regulation. We identified sex-specific and nongenetically determined POMC hypermethylation associated with a 1.4-fold (confidence interval, 1.03 to 2.04) increased individual risk of developing obesity. To investigate the early embryonic establishment of POMC methylation states, we established a human embryonic stem cell (hESC) model. Here, hESCs (WA01) were transferred into a naïve state, which was associated with a reduction of DNA methylation. Naïve hESCs were differentiated via a formative state into POMC-expressing hypothalamic neurons, which was accompanied by re-establishment of DNA methylation patterning. We observed that reduced POMC gene expression was associated with increased POMC methylation in POMC-expressing neurons. On the basis of these findings, we treated POMC-hypermethylated obese individuals (n = 5) with an MC4R agonist and observed a body weight reduction of 4.66 ± 2.16% (means ± SD) over a mean treatment duration of 38.4 ± 26.0 weeks. In summary, we identified an epigenetic obesity risk variant at the POMC gene fulfilling the criteria for a metastable epiallele established in early embryonic development that may be addressable by MC4R agonist treatment to reduce body weight.
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Affiliation(s)
- Lara Lechner
- Department of Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany
| | - Robert Opitz
- Institute for Experimental Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany
| | - Matt J Silver
- Medical Research Council Unit, Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, Gambia
| | - Philipp M Krabusch
- Department of Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany
| | - Andrew M Prentice
- Medical Research Council Unit, Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, Gambia
| | - Martha S Field
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Harald Stachelscheid
- Berlin Institute of Health, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, BIH Core Unit Stem Cells and Organoids, 13353 Berlin, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, 45147 Essen, Germany
| | | | - Valeria Fernandez Vallone
- Berlin Institute of Health, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, BIH Core Unit Stem Cells and Organoids, 13353 Berlin, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, 45147 Essen, Germany
| | - Karl-Heinz Jöckel
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, 45147 Essen, Germany
| | - Börge Schmidt
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, 45147 Essen, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Stefan Herms
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | | | - Matthias Megges
- Department of Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany
| | - Ulrike Blume-Peytavi
- Clinical Research Center for Hair and Skin Science, Department of Dermatology and Venerology and Allergology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Katja Weiss
- Klinik für Angeborene Herzfehler - Kinderkardiologie, Deutsches Herzzentrum der Charité, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany
| | - Knut Mai
- Department of Endocrinology, Diabetes, and Nutrition and Charité Center for Cardiovascular Research, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Center for Diabetes Research, 85764 München-Neuherberg, Germany
| | - Oliver Blankenstein
- Department of Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany
- Department Endocrinology and Metabolism, Labor Berlin-Charité Vivantes GmbH, 13353 Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health/Charité- Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Susanna Wiegand
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Center for Social-Pediatric Care/Pediatric Endocrinology and Diabetology, 13353 Berlin, Germany
| | - Peter Kühnen
- Department of Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany
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8
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Epigenetics in fetal alcohol spectrum disorder. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:211-239. [PMID: 37019593 DOI: 10.1016/bs.pmbts.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During pregnancy, alcohol abuse and its detrimental effects on developing offspring are major public health, economic and social challenges. The prominent characteristic attributes of alcohol (ethanol) abuse during pregnancy in humans are neurobehavioral impairments in offspring due to damage to the central nervous system (CNS), causing structural and behavioral impairments that are together named fetal alcohol spectrum disorder (FASD). Development-specific alcohol exposure paradigms were established to recapitulate the human FASD phenotypes and establish the underlying mechanisms. These animal studies have offered some critical molecular and cellular underpinnings likely to account for the neurobehavioral impairments associated with prenatal ethanol exposure. Although the pathogenesis of FASD remains unclear, emerging literature proposes that the various genomic and epigenetic components that cause the imbalance in gene expression can significantly contribute to the development of this disease. These studies acknowledged numerous immediate and enduring epigenetic modifications, such as methylation of DNA, post-translational modifications (PTMs) of histone proteins, and regulatory networks related to RNA, using many molecular approaches. Methylated DNA profiles, PTMs of histone proteins, and RNA-regulated expression of genes are essential for synaptic and cognitive behavior. Thus, offering a solution to many neuronal and behavioral impairments reported in FASD. In the current chapter, we review the recent advances in different epigenetic modifications that cause the pathogenesis of FASD. The information discussed can help better explain the pathogenesis of FASD and thereby might provide a basis for finding novel therapeutic targets and innovative treatment strategies.
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Bock SL, Smaga CR, McCoy JA, Parrott BB. Genome-wide DNA methylation patterns harbour signatures of hatchling sex and past incubation temperature in a species with environmental sex determination. Mol Ecol 2022; 31:5487-5505. [PMID: 35997618 PMCID: PMC9826120 DOI: 10.1111/mec.16670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023]
Abstract
Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic data sets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulphite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligators (Alligator mississippiensis), a TSD species lacking reliable markers of sexual dimorphism in early life stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy (in 20 training samples and four test samples) and past incubation temperature with a mean absolute error of 1.2°C (in four test samples) based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as nonlethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity.
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Affiliation(s)
- Samantha L. Bock
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
| | - Christopher R. Smaga
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
| | - Jessica A. McCoy
- Department of BiologyCollege of CharlestonCharlestonSouth CarolinaUSA
| | - Benjamin B. Parrott
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
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10
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Missing Causality and Heritability of Autoimmune Hepatitis. Dig Dis Sci 2022; 68:1585-1604. [PMID: 36261672 DOI: 10.1007/s10620-022-07728-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/10/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND Autoimmune hepatitis has an unknown cause and genetic associations that are not disease-specific or always present. Clarification of its missing causality and heritability could improve prevention and management strategies. AIMS Describe the key epigenetic and genetic mechanisms that could account for missing causality and heritability in autoimmune hepatitis; indicate the prospects of these mechanisms as pivotal factors; and encourage investigations of their pathogenic role and therapeutic potential. METHODS English abstracts were identified in PubMed using multiple key search phases. Several hundred abstracts and 210 full-length articles were reviewed. RESULTS Environmental induction of epigenetic changes is the prime candidate for explaining the missing causality of autoimmune hepatitis. Environmental factors (diet, toxic exposures) can alter chromatin structure and the production of micro-ribonucleic acids that affect gene expression. Epistatic interaction between unsuspected genes is the prime candidate for explaining the missing heritability. The non-additive, interactive effects of multiple genes could enhance their impact on the propensity and phenotype of autoimmune hepatitis. Transgenerational inheritance of acquired epigenetic marks constitutes another mechanism of transmitting parental adaptations that could affect susceptibility. Management strategies could range from lifestyle adjustments and nutritional supplements to precision editing of the epigenetic landscape. CONCLUSIONS Autoimmune hepatitis has a missing causality that might be explained by epigenetic changes induced by environmental factors and a missing heritability that might reflect epistatic gene interactions or transgenerational transmission of acquired epigenetic marks. These unassessed or under-evaluated areas warrant investigation.
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11
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Holland ML, Rakyan VK. A stochastic basis for metabolic phenotypes. Nat Metab 2022; 4:1091-1092. [PMID: 36097184 DOI: 10.1038/s42255-022-00630-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michelle L Holland
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK.
| | - Vardhman K Rakyan
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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12
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Benetatos L, Benetatou A, Vartholomatos G. Epialleles and epiallelic heterogeneity in hematological malignancies. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:139. [PMID: 35834015 DOI: 10.1007/s12032-022-01737-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/22/2022] [Indexed: 10/17/2022]
Abstract
DNA methylation has a well-established role in the pathogenesis, prognosis, and response to treatment in all the spectra of hematological malignancies. However, most of the data reported involve average DNA methylation observed in a sample. The emergence of bisulfite sequencing methods such as enhanced reduced representation that permit analyze adjacent CpGs led to exciting findings. Among these are the epialleles shift and the resulting epigenetic heterogeneity observed in leukemias and lymphomas. Epialleles seem to have an influential role as the cause of mutations that characterize leukemias, may stratify groups with different prognosis and response to treatment, and may be redistributed in the genome at different time points of the disease promoting activation of alternate transcriptional networks. Epiallelic shift may be responsible for the intratumor heterogeneity observed within the cells of the same tumor which increases with disease aggressiveness. It may also responsible for the interpatient heterogeneity explaining why blood cancers exhibit different behavior among different patients. Understanding better epiallelic conformation and the consequent chromatin conformational changes and the pathways that may be affected will permit deeper understanding of hematological malignancies pathogenesis and treatment.
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Affiliation(s)
- Leonidas Benetatos
- Blood Bank, Preveza General Hospital, Selefkias 2, 48100, Preveza, Greece.
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13
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Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei MS, Vander Schaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. CELL GENOMICS 2022; 2:100144. [PMID: 35873672 PMCID: PMC9306256 DOI: 10.1016/j.xgen.2022.100144] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 05/20/2022] [Indexed: 05/21/2023]
Abstract
We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc Min/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.
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Affiliation(s)
- Wanding Zhou
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
| | - Toshinori Hinoue
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bret Barnes
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | - Owen Mitchell
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Waleed Iqbal
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kelly K. Foy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kwang-Ho Lee
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ethan J. Moyer
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra VanderArk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Julie M. Koeman
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Wubin Ding
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Manpreet Kalkat
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Nathan J. Spix
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bryn Eagleson
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Liang Kang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Peter A. Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Connie M. Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Rishi Porecha
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | | | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
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14
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Derakhshan M, Kessler NJ, Ishida M, Demetriou C, Brucato N, Moore G, Fall CHD, Chandak GR, Ricaut FX, Prentice A, Hellenthal G, Silver M. Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo. Nucleic Acids Res 2022; 50:6735-6752. [PMID: 35713545 PMCID: PMC9749461 DOI: 10.1093/nar/gkac503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/06/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
We analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs ('hvCpGs') with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.
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Affiliation(s)
| | - Noah J Kessler
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, UK
| | - Miho Ishida
- UCL Great Ormond Street Institute of Child Health, UK
| | | | - Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | | | - Caroline H D Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton,
Southampton, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular
and Molecular Biology,Hyderabad, India
| | - Francois-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London,
Gower Street, London WC1E 6BT, UK
| | - Matt J Silver
- London School of Hygiene and Tropical Medicine, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
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15
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Postnikova LA, Patkin EL. The possible effect of lactoferrin on the epigenetic characteristics of early mammalian embryos exposed to bisphenol A. Birth Defects Res 2022; 114:1199-1209. [PMID: 35451577 DOI: 10.1002/bdr2.2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 03/15/2022] [Accepted: 03/30/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND The main objective of this review was to state a hypothetical mechanism of the antitoxic effect of lactoferrin (Lf) on embryos exposed to bisphenol A (BPA). On this basis, it is possible to suggest Lf as a potential protective health component before conception upon toxic effects and viral infections. METHODS The narrative review was performed using systematic review methods to identify relevant literature. The resources required for this study were obtained by searching the electronic database PubMed (MEDLINE). Articles were searched using the keywords "BPA," "lactoferrin," "DNA-methylation," "epigenetic," "mammals," "human," and "mouse." The inclusion criteria were as follows: (a) primary or original research; (b) study of epigenetic modification; and (c) study focuses on early mammalian development. RESULTS Presented data demonstrate that Lf can modulate epigenetical characteristic, such as DNA methylation and reactive oxygen species (ROS), and, thereby, may serve as a potential readily available pharmaceutical product. CONCLUSION Suggested hypothesis is based on the important interrelated role of changes in epigenetic modifications and oxidative stress in early embryogenesis under the influence of BPA and virus infection as a cause of the development of pathologies in the adult organism.
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Affiliation(s)
- Liubov A Postnikova
- Federal State Budget Scientific Institution "Institute of Experimental Medicine", St. Petersburg, Russia
| | - Eugene L Patkin
- Federal State Budget Scientific Institution "Institute of Experimental Medicine", St. Petersburg, Russia
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16
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Silver MJ, Saffari A, Kessler NJ, Chandak GR, Fall CHD, Issarapu P, Dedaniya A, Betts M, Moore SE, Routledge MN, Herceg Z, Cuenin C, Derakhshan M, James PT, Monk D, Prentice AM. Environmentally sensitive hotspots in the methylome of the early human embryo. eLife 2022; 11:e72031. [PMID: 35188105 PMCID: PMC8912923 DOI: 10.7554/elife.72031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/18/2022] [Indexed: 11/26/2022] Open
Abstract
In humans, DNA methylation marks inherited from gametes are largely erased following fertilisation, prior to construction of the embryonic methylome. Exploiting a natural experiment of seasonal variation including changes in diet and nutritional status in rural Gambia, we analysed three datasets covering two independent child cohorts and identified 259 CpGs showing consistent associations between season of conception (SoC) and DNA methylation. SoC effects were most apparent in early infancy, with evidence of attenuation by mid-childhood. SoC-associated CpGs were enriched for metastable epialleles, parent-of-origin-specific methylation and germline differentially methylated regions, supporting a periconceptional environmental influence. Many SoC-associated CpGs overlapped enhancers or sites of active transcription in H1 embryonic stem cells and fetal tissues. Half were influenced but not determined by measured genetic variants that were independent of SoC. Environmental 'hotspots' providing a record of environmental influence at periconception constitute a valuable resource for investigating epigenetic mechanisms linking early exposures to lifelong health and disease.
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Affiliation(s)
- Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Ayden Saffari
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Noah J Kessler
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Gririraj R Chandak
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Caroline HD Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General HospitalSouthamptonUnited Kingdom
| | - Prachand Issarapu
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Akshay Dedaniya
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Modupeh Betts
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Sophie E Moore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
- Department of Women and Children's Health, King's College LondonLondonUnited Kingdom
| | - Michael N Routledge
- School of Medicine, University of LeedsLeedsUnited Kingdom
- School of Food and Biological Engineering, Jiangsu UniversityZhenjiangChina
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Maria Derakhshan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Philip T James
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - David Monk
- Biomedical Research Centre, University of East AngliaNorwichUnited Kingdom
- Bellvitge Institute for Biomedical ResearchBarcelonaSpain
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
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17
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Joglekar R, Grenier C, Hoyo C, Hoffman K, Murphy SK. Maternal tobacco smoke exposure is associated with increased DNA methylation at human metastable epialleles in infant cord blood. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac005. [PMID: 35355955 PMCID: PMC8962709 DOI: 10.1093/eep/dvac005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Metastable epialleles (MEs) are genomic regions that are stochastically methylated prior to germ layer specification and exhibit high interindividual but low intra-individual variability across tissues. ME methylation is vulnerable to environmental stressors, including diet. Tobacco smoke (TS) exposure during pregnancy is associated with adverse impacts on fetal health and maternal micronutrient levels as well as altered methylation. Our objective was to determine if maternal smoke exposure impacts methylation at MEs. Consistent with prior studies, we observed reductions in one-carbon pathway micronutrients with gestational TS exposure, including maternal folate (P = 0.02) and vitamins B6 (P = 0.05) and B12 (P = 0.007). We examined putative MEs BOLA3, PAX8, and ZFYVE28 in cord blood specimens from 85 Newborn Epigenetics STudy participants. Gestational TS exposure was associated with elevated DNA methylation at PAX8 (+5.22% average methylation; 95% CI: 0.33% to 10.10%; P = 0.037). In human conceptal kidney tissues, higher PAX8 transcription was associated with lower methylation (R s = 0.55; P = 0.07), suggesting that the methylation levels established at MEs, and their environmentally induced perturbation, may have meaningful, tissue-specific functional consequences. This may be particularly important because PAX8 is implicated in several cancers, including pediatric kidney cancer. Our data are the first to indicate vulnerability of human ME methylation establishment to TS exposure, with a general trend of increasing levels of methylation at these loci. Further investigation is needed to determine how TS exposure-mediated changes in DNA methylation at MEs, and consequent expression levels, might affect smoking-related disease risk.
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Affiliation(s)
- Rashmi Joglekar
- Integrated Toxicology and Environmental Health Program, Nicholas School of the Environment, Duke University, PO Box 90328, Durham, NC 27708, USA
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, Duke University Medical Center, 70 W Main Street, Suite 510, Durham, NC 27701, USA
| | - Carole Grenier
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, Duke University Medical Center, 70 W Main Street, Suite 510, Durham, NC 27701, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, Epidemiology and Environmental Epigenomics Lab, North Carolina State University, 850 Main Campus Drive, Suite 1104, Raleigh, NC 27606, USA
| | - Kate Hoffman
- Division of Environmental Sciences and Policy, Nicholas School of the Environment, Duke University, Grainger Hall, 9 Circuit Drive, Durham, NC 27708, USA
| | - Susan K Murphy
- Integrated Toxicology and Environmental Health Program, Nicholas School of the Environment, Duke University, PO Box 90328, Durham, NC 27708, USA
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, Duke University Medical Center, 70 W Main Street, Suite 510, Durham, NC 27701, USA
- Division of Environmental Sciences and Policy, Nicholas School of the Environment, Duke University, Grainger Hall, 9 Circuit Drive, Durham, NC 27708, USA
- Department of Pathology, Duke University Medical Center, DUMC 3712, Durham, NC 27710, USA
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18
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Epigenomic Modifications in Modern and Ancient Genomes. Genes (Basel) 2022; 13:genes13020178. [PMID: 35205223 PMCID: PMC8872240 DOI: 10.3390/genes13020178] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/26/2022] Open
Abstract
Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to infer epigenetic changes in the past. Investigating genome-wide methylation patterns of ancient humans may ultimately yield in a more comprehensive understanding of how our ancestors have adapted to the changing environment, and modified their lifestyles accordingly. We discuss the difficulties of working with ancient DNA in particular utilizing paleoepigenomic approaches, and assess new paleoepigenomic data, which might be helpful in future studies.
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19
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Candler T, Kessler N, Gunasekara C, Ward K, James P, Laritsky E, Baker M, Dyer R, Elango R, Jeffries D, Waterland R, Moore S, Ludgate M, Prentice A, Silver M. DNA methylation at a nutritionally sensitive region of the PAX8 gene is associated with thyroid volume and function in Gambian children. SCIENCE ADVANCES 2021; 7:eabj1561. [PMID: 34739318 PMCID: PMC8570597 DOI: 10.1126/sciadv.abj1561] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/16/2021] [Indexed: 05/13/2023]
Abstract
PAX8 is a key thyroid transcription factor implicated in thyroid gland differentiation and function, and PAX8 gene methylation is reported to be sensitive to the periconceptional environment. Using a novel recall-by-epigenotype study in Gambian children, we found that PAX8 hypomethylation at age 2 years is associated with a 21% increase in thyroid volume and an increase in free thyroxine (T4) at 5 to 8 years, the latter equivalent to 8.4% of the normal range. Free T4 was associated with a decrease in DXA-derived body fat and bone mineral density. Furthermore, offspring PAX8 methylation was associated with periconceptional maternal nutrition, and methylation variability was influenced by genotype, suggesting that sensitivity to environmental exposures may be under partial genetic control. Together, our results demonstrate a possible link between early environment, PAX8 gene methylation and thyroid gland development and function, with potential implications for early embryonic programming of thyroid-related health and disease.
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Affiliation(s)
- Toby Candler
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Noah Kessler
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chathura Gunasekara
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kate Ward
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
- MRC Lifecourse Epidemiology, University of Southampton, Southampton, UK
| | - Philip James
- Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Eleonora Laritsky
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maria Baker
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Roger Dyer
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Rajavel Elango
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - David Jeffries
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Robert 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
| | - Sophie Moore
- MRC 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
| | - Marian Ludgate
- Thyroid Research Group, School of Medicine, Cardiff University, Cardiff, UK
| | - Andrew Prentice
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Matt Silver
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
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20
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Costello KR, Leung A, Trac C, Lee M, Basam M, Pospisilik JA, Schones DE. Sequence features of retrotransposons allow for epigenetic variability. eLife 2021; 10:71104. [PMID: 34668484 PMCID: PMC8555987 DOI: 10.7554/elife.71104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that make up a large fraction of mammalian genomes. While select TEs have been co-opted in host genomes to have function, the majority of these elements are epigenetically silenced by DNA methylation in somatic cells. However, some TEs in mice, including the Intracisternal A-particle (IAP) subfamily of retrotransposons, have been shown to display interindividual variation in DNA methylation. Recent work has revealed that IAP sequence differences and strain-specific KRAB zinc finger proteins (KZFPs) may influence the methylation state of these IAPs. However, the mechanisms underlying the establishment and maintenance of interindividual variability in DNA methylation still remain unclear. Here, we report that sequence content and genomic context influence the likelihood that IAPs become variably methylated. IAPs that differ from consensus IAP sequences have altered KZFP recruitment that can lead to decreased KAP1 recruitment when in proximity of constitutively expressed genes. These variably methylated loci have a high CpG density, similar to CpG islands, and can be bound by ZF-CxxC proteins, providing a potential mechanism to maintain this permissive chromatin environment and protect from DNA methylation. These observations indicate that variably methylated IAPs escape silencing through both attenuation of KZFP binding and recognition by ZF-CxxC proteins to maintain a hypomethylated state.
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Affiliation(s)
- Kevin R Costello
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, United States
| | - Amy Leung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States
| | - Candi Trac
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States
| | - Michael Lee
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, United States
| | - Mudaser Basam
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States
| | | | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, United States
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21
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Jia FF, Drew AP, Nicholson GA, Corbett A, Kumar KR. Facioscapulohumeral muscular dystrophy type 2: an update on the clinical, genetic, and molecular findings. Neuromuscul Disord 2021; 31:1101-1112. [PMID: 34711481 DOI: 10.1016/j.nmd.2021.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/01/2021] [Accepted: 09/09/2021] [Indexed: 11/25/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a common genetic disease of the skeletal muscle with a characteristic pattern of weakness. Facioscapulohumeral muscular dystrophy type 2 (FSHD2) accounts for approximately 5% of all cases of FSHD and describes patients without a D4Z4 repeat contraction on chromosome 4. Phenotypically FSHD2 shows virtually no difference from FSHD1 and both forms of FSHD arise via a common downstream mechanism of epigenetic derepression of the transcription factor DUX4 in skeletal muscle cells. This results in expression of DUX4 and target genes leading to skeletal muscle toxicity. Over the past decade, major progress has been made in our understanding of the genetic and epigenetic architecture that underlies FSHD2 pathogenesis, as well as the clinical manifestations and disease progression. These include the finding that FSHD2 is a digenic disease and that mutations in the genes SMCHD1, DNMT3B, and more recently LRIF1, can cause FSHD2. FSHD2 is complex and it is important that clinicians keep abreast of recent developments; this review aims to serve as an update of the clinical, genetic, and molecular research into this condition.
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Affiliation(s)
- Fangzhi Frank Jia
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia.
| | - Alexander P Drew
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.
| | - Garth Alexander Nicholson
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| | - Alastair Corbett
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| | - Kishore Raj Kumar
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
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22
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van Dongen J, Gordon SD, McRae AF, Odintsova VV, Mbarek H, Breeze CE, Sugden K, Lundgren S, Castillo-Fernandez JE, Hannon E, Moffitt TE, Hagenbeek FA, van Beijsterveldt CEM, Jan Hottenga J, Tsai PC, Min JL, Hemani G, Ehli EA, Paul F, Stern CD, Heijmans BT, Slagboom PE, Daxinger L, van der Maarel SM, de Geus EJC, Willemsen G, Montgomery GW, Reversade B, Ollikainen M, Kaprio J, Spector TD, Bell JT, Mill J, Caspi A, Martin NG, Boomsma DI. Identical twins carry a persistent epigenetic signature of early genome programming. Nat Commun 2021; 12:5618. [PMID: 34584077 PMCID: PMC8479069 DOI: 10.1038/s41467-021-25583-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/19/2021] [Indexed: 02/08/2023] Open
Abstract
Monozygotic (MZ) twins and higher-order multiples arise when a zygote splits during pre-implantation stages of development. The mechanisms underpinning this event have remained a mystery. Because MZ twinning rarely runs in families, the leading hypothesis is that it occurs at random. Here, we show that MZ twinning is strongly associated with a stable DNA methylation signature in adult somatic tissues. This signature spans regions near telomeres and centromeres, Polycomb-repressed regions and heterochromatin, genes involved in cell-adhesion, WNT signaling, cell fate, and putative human metastable epialleles. Our study also demonstrates a never-anticipated corollary: because identical twins keep a lifelong molecular signature, we can retrospectively diagnose if a person was conceived as monozygotic twin.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands.
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands.
| | - Scott D Gordon
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Veronika V Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Hamdi Mbarek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | | | - Karen Sugden
- Department of Psychology and Neuroscience and Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Sara Lundgren
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | | | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience and Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Catharina E M van Beijsterveldt
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, SD, USA
| | - Franziska Paul
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
| | - Claudio D Stern
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Bruno Reversade
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Medical Genetics Department, KOC University, School of Medicine, Istanbul, Turkey
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Avshalom Caspi
- Department of Psychology and Neuroscience and Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
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23
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Maternal Dietary Quality and Dietary Inflammation Associations with Offspring Growth, Placental Development, and DNA Methylation. Nutrients 2021; 13:nu13093130. [PMID: 34579008 PMCID: PMC8468062 DOI: 10.3390/nu13093130] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/31/2021] [Accepted: 09/04/2021] [Indexed: 12/14/2022] Open
Abstract
The ‘Developmental Origins of Health and Diseases’ hypothesis posits that prenatal maternal diet influences offspring growth and later life health outcomes. Dietary assessment has focused on selected nutrients. However, this approach does not consider the complex interactions between foods and nutrients. To provide a more comprehensive approach to public health, dietary indices have been developed to assess dietary quality, dietary inflammation and risk factors for non-communicable diseases. Thus far, their use in the context of placental development is limited and associations with offspring outcomes have been inconsistent. Although epidemiological studies have focused on the role of maternal diet on foetal programming, the underlying mechanisms are still poorly understood. Some evidence suggests these associations may be driven by placental and epigenetic changes. In this narrative review, we examine the current literature regarding relationships between key validated diet quality scores (Dietary Inflammatory Index [DII], Mediterranean diet [MD], Healthy Eating Index [HEI], Alternative Healthy Eating Index [AHEI], Dietary Approaches to Stop Hypertension [DASH], Glycaemic Index [GI] and Glycaemic Load [GL]) in pregnancy and birth and long-term offspring outcomes. We summarise findings, discuss potential underlying placental and epigenetic mechanisms, in particular DNA methylation, and highlight the need for further research and public health strategies that incorporate diet quality and epigenetics.
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24
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Oocyte age and preconceptual alcohol use are highly correlated with epigenetic imprinting of a noncoding RNA ( nc886). Proc Natl Acad Sci U S A 2021; 118:2026580118. [PMID: 33723081 PMCID: PMC8000112 DOI: 10.1073/pnas.2026580118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genomic imprinting occurs before fertilization, impacts every cell of the developing child, and may be sensitive to environmental perturbations. The noncoding RNA, nc886 (also called VTRNA2-1) is the only known example of the ∼100 human genes imprinted by DNA methylation, that shows polymorphic imprinting in the population. The nc886 gene is part of an ∼1.6-kb differentially methylated region (DMR) that is methylated in the oocyte and silenced on the maternal allele in about 75% of humans worldwide. Here, we show that the presence or absence of imprinting at the nc886 DMR in an individual is consistent across different tissues, confirming that the imprint is established before cellular differentiation and is maintained into adulthood. We investigated the relationships between the frequency of imprinting in newborns and maternal age, alcohol consumption and cigarette smoking before conception in more than 1,100 mother/child pairs from South Africa. The probability of imprinting in newborns was increased in older mothers and decreased in mothers who drank alcohol before conception. On the other hand, cigarette smoking had no apparent relationship with the frequency of imprinting. These data show an epigenetic change during oocyte maturation which is potentially subject to environmental influence. Much focus has been placed on avoiding alcohol consumption during pregnancy, but our data suggest that drinking before conception may affect the epigenome of the newborn.
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25
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Adenine base editing of the DUX4 polyadenylation signal for targeted genetic therapy in facioscapulohumeral muscular dystrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:342-354. [PMID: 34484861 PMCID: PMC8399085 DOI: 10.1016/j.omtn.2021.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/26/2021] [Indexed: 12/26/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by chromatin relaxation of the D4Z4 repeat resulting in misexpression of the D4Z4-encoded DUX4 gene in skeletal muscle. One of the key genetic requirements for the stable production of full-length DUX4 mRNA in skeletal muscle is a functional polyadenylation signal (ATTAAA) in exon three of DUX4 that is used in somatic cells. Base editors hold great promise to treat DNA lesions underlying genetic diseases through their ability to carry out specific and rapid nucleotide mutagenesis even in postmitotic cells such as skeletal muscle. In this study, we present a simple and straightforward strategy for mutagenesis of the somatic DUX4 polyadenylation signal by adenine base editing in immortalized myoblasts derived from independent FSHD-affected individuals. We show that mutating this critical cis-regulatory element results in downregulation of DUX4 mRNA and its direct transcriptional target genes. Our findings identify the somatic DUX4 polyadenylation signal as a therapeutic target and represent the first step toward clinical application of the CRISPR-Cas9 base editing platform for FSHD gene therapy.
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26
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27
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Luperchio TR, Boukas L, Zhang L, Pilarowski G, Jiang J, Kalinousky A, Hansen KD, Bjornsson HT. Leveraging the Mendelian disorders of the epigenetic machinery to systematically map functional epigenetic variation. eLife 2021; 10:65884. [PMID: 34463256 PMCID: PMC8443249 DOI: 10.7554/elife.65884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Although each Mendelian Disorder of the Epigenetic Machinery (MDEM) has a different causative gene, there are shared disease manifestations. We hypothesize that this phenotypic convergence is a consequence of shared epigenetic alterations. To identify such shared alterations, we interrogate chromatin (ATAC-seq) and expression (RNA-seq) states in B cells from three MDEM mouse models (Kabuki [KS] type 1 and 2 and Rubinstein-Taybi type 1 [RT1] syndromes). We develop a new approach for the overlap analysis and find extensive overlap primarily localized in gene promoters. We show that disruption of chromatin accessibility at promoters often disrupts downstream gene expression, and identify 587 loci and 264 genes with shared disruption across all three MDEMs. Subtle expression alterations of multiple, IgA-relevant genes, collectively contribute to IgA deficiency in KS1 and RT1, but not in KS2. We propose that the joint study of MDEMs offers a principled approach for systematically mapping functional epigenetic variation in mammals.
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Affiliation(s)
- Teresa Romeo Luperchio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Leandros Boukas
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Li Zhang
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Genay Pilarowski
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Jenny Jiang
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Allison Kalinousky
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Landspitali University Hospital, Reykjavik, Iceland
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28
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Marttila S, Viiri LE, Mishra PP, Kühnel B, Matias-Garcia PR, Lyytikäinen LP, Ceder T, Mononen N, Rathmann W, Winkelmann J, Peters A, Kähönen M, Hutri-Kähönen N, Juonala M, Aalto-Setälä K, Raitakari O, Lehtimäki T, Waldenberger M, Raitoharju E. Methylation status of nc886 epiallele reflects periconceptional conditions and is associated with glucose metabolism through nc886 RNAs. Clin Epigenetics 2021; 13:143. [PMID: 34294131 PMCID: PMC8296652 DOI: 10.1186/s13148-021-01132-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/13/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Non-coding RNA 886 (nc886) is coded from a maternally inherited metastable epiallele. We set out to investigate the determinants and dynamics of the methylation pattern at the nc886 epiallele and how this methylation status associates with nc886 RNA expression. Furthermore, we investigated the associations between the nc886 methylation status or the levels of nc886 RNAs and metabolic traits in the YFS and KORA cohorts. The association between nc886 epiallele methylation and RNA expression was also validated in induced pluripotent stem cell (iPSC) lines. RESULTS We confirm that the methylation status of the nc886 epiallele is mostly binomial, with individuals displaying either a non- or hemi-methylated status, but we also describe intermediately and close to fully methylated individuals. We show that an individual's methylation status is associated with the mother's age and socioeconomic status, but not with the individual's own genetics. Once established, the methylation status of the nc886 epiallele remains stable for at least 25 years. This methylation status is strongly associated with the levels of nc886 non-coding RNAs in serum, blood, and iPSC lines. In addition, nc886 methylation status associates with glucose and insulin levels during adolescence but not with the indicators of glucose metabolism or the incidence of type 2 diabetes in adulthood. However, the nc886-3p RNA levels also associate with glucose metabolism in adulthood. CONCLUSIONS These results indicate that nc886 metastable epiallele methylation is tuned by the periconceptional conditions and it associates with glucose metabolism through the expression of the ncRNAs coded in the epiallele region.
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Grants
- 755320 Horizon 2020 (Taxinomisis)
- WA 4081/1-1 German Research Foundation
- BB/S020845/1 Biotechnology and Biological Sciences Research Council
- 134309, 126925, 121584, 124282, 129378, 117787, 41071 Academy of Finland
- 286284 and 322098 Academy of Finland
- 01EA1902A Joint Programming Initiative A healthy diet for a healthy life (DIMENSION)
- 848146 Horizon 2020 (To_Aition)
- 9X047, 9S054, and 9AB059 Tampere University Hospital Medical Funds
- 742927 European Research Council (MULTIEPIGEN)
- 285902, 330809 and 338395 academy of finland
- X51001 Tampere University Hospital Medical Funds
- the Social Insurance Institution of Finland
- Kuopio, Tampere, and Turku University Hospital Medical Funds
- Juho Vainion Säätiö
- Paavo Nurmen Säätiö
- Sydäntutkimussäätiö
- Suomen Kulttuurirahasto
- Tampereen Tuberkuloosisäätiö
- Emil Aaltosen Säätiö
- Yrjö Jahnssonin Säätiö
- Signe ja Ane Gyllenbergin Säätiö
- Diabetesliitto
- the Tampere University Hospital Supporting Foundation
- the Finnish Society of Clinical Chemistry
- Foundation of Clinical Chemistry
- Laboratoriolääketieteen edistämissäätiö sr.
- Orionin Tutkimussäätiö
- the Paulo Foundation
- Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz Zentrum München
- German Federal Ministry of Education and Research
- State of Bavaria
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Affiliation(s)
- Saara Marttila
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland.
- Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Leena E Viiri
- Heart Group, Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Brigitte Kühnel
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Pamela R Matias-Garcia
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Tiina Ceder
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Wolfgang Rathmann
- German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research At Heinrich Heine University, Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Neurogenetics and Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Annette Peters
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Nina Hutri-Kähönen
- Tampere Centre for Skills Training and Simulation, Tampere University, Tampere, Finland
| | - Markus Juonala
- Division of Medicine, Department of Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Katriina Aalto-Setälä
- Heart Group, Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Heart Hospital, Tampere University Hospital, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, University of Turku, Turku University Hospital, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Emma Raitoharju
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland.
- Centre for Population Health Research, University of Turku, Turku University Hospital, Turku, Finland.
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29
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Marttila S, Viiri LE, Mishra PP, Kühnel B, Matias-Garcia PR, Lyytikäinen LP, Ceder T, Mononen N, Rathmann W, Winkelmann J, Peters A, Kähönen M, Hutri-Kähönen N, Juonala M, Aalto-Setälä K, Raitakari O, Lehtimäki T, Waldenberger M, Raitoharju E. Methylation status of nc886 epiallele reflects periconceptional conditions and is associated with glucose metabolism through nc886 RNAs. Clin Epigenetics 2021. [PMID: 34294131 DOI: 10.1186/s13148‐021‐01132‐3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Non-coding RNA 886 (nc886) is coded from a maternally inherited metastable epiallele. We set out to investigate the determinants and dynamics of the methylation pattern at the nc886 epiallele and how this methylation status associates with nc886 RNA expression. Furthermore, we investigated the associations between the nc886 methylation status or the levels of nc886 RNAs and metabolic traits in the YFS and KORA cohorts. The association between nc886 epiallele methylation and RNA expression was also validated in induced pluripotent stem cell (iPSC) lines. RESULTS We confirm that the methylation status of the nc886 epiallele is mostly binomial, with individuals displaying either a non- or hemi-methylated status, but we also describe intermediately and close to fully methylated individuals. We show that an individual's methylation status is associated with the mother's age and socioeconomic status, but not with the individual's own genetics. Once established, the methylation status of the nc886 epiallele remains stable for at least 25 years. This methylation status is strongly associated with the levels of nc886 non-coding RNAs in serum, blood, and iPSC lines. In addition, nc886 methylation status associates with glucose and insulin levels during adolescence but not with the indicators of glucose metabolism or the incidence of type 2 diabetes in adulthood. However, the nc886-3p RNA levels also associate with glucose metabolism in adulthood. CONCLUSIONS These results indicate that nc886 metastable epiallele methylation is tuned by the periconceptional conditions and it associates with glucose metabolism through the expression of the ncRNAs coded in the epiallele region.
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Affiliation(s)
- Saara Marttila
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland. .,Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Leena E Viiri
- Heart Group, Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Brigitte Kühnel
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Pamela R Matias-Garcia
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Tiina Ceder
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Wolfgang Rathmann
- German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany.,Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research At Heinrich Heine University, Düsseldorf, Germany.,Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Department of Neurogenetics and Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Annette Peters
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Nina Hutri-Kähönen
- Tampere Centre for Skills Training and Simulation, Tampere University, Tampere, Finland
| | - Markus Juonala
- Division of Medicine, Department of Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Katriina Aalto-Setälä
- Heart Group, Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Heart Hospital, Tampere University Hospital, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku, Turku University Hospital, Turku, Finland.,Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland.,Department of Clinical Physiology and Nuclear Medicine, University of Turku, Turku University Hospital, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Emma Raitoharju
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Pirkanmaa Hospital District and Fimlab Laboratories, Tampere, Finland. .,Centre for Population Health Research, University of Turku, Turku University Hospital, Turku, Finland.
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30
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Rizzardi LF, Hickey PF, Idrizi A, Tryggvadóttir R, Callahan CM, Stephens KE, Taverna SD, Zhang H, Ramazanoglu S, Hansen KD, Feinberg AP. Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits. Genome Biol 2021; 22:116. [PMID: 33888138 PMCID: PMC8061076 DOI: 10.1186/s13059-021-02335-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/30/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND DNA methylation dynamics in the brain are associated with normal development and neuropsychiatric disease and differ across functionally distinct brain regions. Previous studies of genome-wide methylation differences among human brain regions focus on limited numbers of individuals and one to two brain regions. RESULTS Using GTEx samples, we generate a resource of DNA methylation in purified neuronal nuclei from 8 brain regions as well as lung and thyroid tissues from 12 to 23 donors. We identify differentially methylated regions between brain regions among neuronal nuclei in both CpG (181,146) and non-CpG (264,868) contexts, few of which were unique to a single pairwise comparison. This significantly expands the knowledge of differential methylation across the brain by 10-fold. In addition, we present the first differential methylation analysis among neuronal nuclei from basal ganglia tissues and identify unique CpG differentially methylated regions, many associated with ion transport. We also identify 81,130 regions of variably CpG methylated regions, i.e., variable methylation among individuals in the same brain region, which are enriched in regulatory regions and in CpG differentially methylated regions. Many variably methylated regions are unique to a specific brain region, with only 202 common across all brain regions, as well as lung and thyroid. Variably methylated regions identified in the amygdala, anterior cingulate cortex, and hippocampus are enriched for heritability of schizophrenia. CONCLUSIONS These data suggest that epigenetic variation in these particular human brain regions could be associated with the risk for this neuropsychiatric disorder.
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Affiliation(s)
- Lindsay F. Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - Peter F. Hickey
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria Australia
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - Rakel Tryggvadóttir
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - Colin M. Callahan
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - Kimberly E. Stephens
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Pediatrics, Division of Infectious Diseases, University of Arkansas for Medical Sciences, 13 Children’s Way, Little Rock, AR 72202 USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202 USA
| | - Sean D. Taverna
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205 USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205 USA
| | - Sinan Ramazanoglu
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - GTEx Consortium
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria Australia
- Department of Pediatrics, Division of Infectious Diseases, University of Arkansas for Medical Sciences, 13 Children’s Way, Little Rock, AR 72202 USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202 USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205 USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Departments of Biomedical Engineering and Mental Health, Johns Hopkins University Schools of Engineering and Public Health, Baltimore, MD USA
| | - Kasper D. Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Departments of Biomedical Engineering and Mental Health, Johns Hopkins University Schools of Engineering and Public Health, Baltimore, MD USA
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Le Goff A, Allard P, Landecker H. Heritable changeability: Epimutation and the legacy of negative definition in epigenetic concepts. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2021; 86:35-46. [PMID: 33965662 DOI: 10.1016/j.shpsa.2020.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/27/2020] [Indexed: 06/12/2023]
Abstract
Epigenetic concepts are fundamentally shaped by a legacy of negative definition, often understood by what they are not. Yet the function and implication of negative definition for scientific discourse has thus far received scant attention. Using the term epimutation as exemplar, we analyze the paradoxical like-but-unlike structure of a term that must simultaneously connect with but depart from genetic concepts. We assess the historical forces structuring the use of epimutation and like terms such as paramutation. This analysis highlights the positive characteristics defining epimutation: the regularity, oxymoronic temporality, and materiality of stable processes. Integrating historical work, ethnographic observation, and insights from philosophical practice-oriented conceptual analysis, we detail the distinctive epistemic goals the epimutation concept fulfils in medicine, plant biology and toxicology. Epimutation and allied epigenetic terms have succeeded by being mutation-like and recognizable, yet have failed to consolidate for exactly the same reason: they are tied simultaneously by likeness and opposition to nouns that describe things that are assumed to persist unchanged over space and time. Moreover, negative definition casts the genetic-epigenetic relationship as an either/or binary, overshadowing continuities and connections. This analysis is intended to assist practitioners and observers of genetics and epigenetics in recognizing and moving beyond the conceptual legacies of negative definition.
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Affiliation(s)
- Anne Le Goff
- The Institute for Society and Genetics & the EpiCenter, University of California, UCLA Institute for Society and Genetics, 621 Charles E. Young Dr., South Box 957221, 3360 LSB, Los Angeles, USA.
| | - Patrick Allard
- The Institute for Society and Genetics & the EpiCenter, University of California, UCLA Institute for Society and Genetics, 621 Charles E. Young Dr., South Box 957221, 3360 LSB, Los Angeles, USA.
| | - Hannah Landecker
- Department of Sociology, The Institute for Society and Genetics & the EpiCenter, University of California, UCLA Institute for Society and Genetics, 621 Charles E. Young Dr, South Box 957221, 3360 LSB, Los Angeles, USA.
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Bertozzi TM, Takahashi N, Hanin G, Kazachenka A, Ferguson-Smith AC. A spontaneous genetically induced epiallele at a retrotransposon shapes host genome function. eLife 2021; 10:e65233. [PMID: 33755012 PMCID: PMC8084528 DOI: 10.7554/elife.65233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Intracisternal A-particles (IAPs) are endogenous retroviruses (ERVs) responsible for most insertional mutations in the mouse. Full-length IAPs harbour genes flanked by long terminal repeats (LTRs). Here, we identify a solo LTR IAP variant (Iap5-1solo) recently formed in the inbred C57BL/6J mouse strain. In contrast to the C57BL/6J full-length IAP at this locus (Iap5-1full), Iap5-1solo lacks DNA methylation and H3K9 trimethylation. The distinct DNA methylation levels between the two alleles are established during preimplantation development, likely due to loss of KRAB zinc finger protein binding at the Iap5-1solo variant. Iap5-1solo methylation increases and becomes more variable in a hybrid genetic background yet is unresponsive to maternal dietary methyl supplementation. Differential epigenetic modification of the two variants is associated with metabolic differences and tissue-specific changes in adjacent gene expression. Our characterisation of Iap5-1 as a genetically induced epiallele with functional consequences establishes a new model to study transposable element repression and host-element co-evolution.
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Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Nozomi Takahashi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Geula Hanin
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
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Vogt G. Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance. J Biosci 2021. [DOI: 10.1007/s12038-021-00138-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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VTRNA2-1: Genetic Variation, Heritable Methylation and Disease Association. Int J Mol Sci 2021; 22:ijms22052535. [PMID: 33802562 PMCID: PMC7961504 DOI: 10.3390/ijms22052535] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/28/2022] Open
Abstract
VTRNA2-1 is a metastable epiallele with accumulating evidence that methylation at this region is heritable, modifiable and associated with disease including risk and progression of cancer. This study investigated the influence of genetic variation and other factors such as age and adult lifestyle on blood DNA methylation in this region. We first sequenced the VTRNA2-1 gene region in multiple-case breast cancer families in which VTRNA2-1 methylation was identified as heritable and associated with breast cancer risk. Methylation quantitative trait loci (mQTL) were investigated using a prospective cohort study (4500 participants with genotyping and methylation data). The cis-mQTL analysis (334 variants ± 50 kb of the most heritable CpG site) identified 43 variants associated with VTRNA2-1 methylation (p < 1.5 × 10−4); however, these explained little of the methylation variation (R2 < 0.5% for each of these variants). No genetic variants elsewhere in the genome were found to strongly influence VTRNA2-1 methylation. SNP-based heritability estimates were consistent with the mQTL findings (h2 = 0, 95%CI: −0.14 to 0.14). We found no evidence that age, sex, country of birth, smoking, body mass index, alcohol consumption or diet influenced blood DNA methylation at VTRNA2-1. Genetic factors and adult lifestyle play a minimal role in explaining methylation variability at the heritable VTRNA2-1 cluster.
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Bacon ER, Brinton RD. Epigenetics of the developing and aging brain: Mechanisms that regulate onset and outcomes of brain reorganization. Neurosci Biobehav Rev 2021; 125:503-516. [PMID: 33657435 DOI: 10.1016/j.neubiorev.2021.02.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/11/2022]
Abstract
Brain development is a life-long process that encompasses several critical periods of transition, during which significant cognitive changes occur. Embryonic development, puberty, and reproductive senescence are all periods of transition that are hypersensitive to environmental factors. Rather than isolated episodes, each transition builds upon the last and is influenced by consequential changes that occur in the transition before it. Epigenetic marks, such as DNA methylation and histone modifications, provide mechanisms by which early events can influence development, cognition, and health outcomes. For example, parental environment influences imprinting patterns in gamete cells, which ultimately impacts gene expression in the embryo which may result in hypersensitivity to poor maternal nutrition during pregnancy, raising the risks for cognitive impairment later in life. This review explores how epigenetics induce and regulate critical periods, and also discusses how early environmental interactions prime a system towards a particular health outcome and influence susceptibility to disease or cognitive impairment throughout life.
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Affiliation(s)
- Eliza R Bacon
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; The Center for Precision Medicine, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Roberta Diaz Brinton
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; Center for Innovation in Brain Science, School of Medicine, University of Arizona, Tucson, AZ, 85721, USA.
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Elmer JL, Hay AD, Kessler NJ, Bertozzi TM, Ainscough EAC, Ferguson-Smith AC. Genomic properties of variably methylated retrotransposons in mouse. Mob DNA 2021; 12:6. [PMID: 33612119 PMCID: PMC7898769 DOI: 10.1186/s13100-021-00235-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit inter-individual variability in this methylation (VM-IAPs) with implications for genome function. RESULTS Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis. Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. CONCLUSION Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation.
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Affiliation(s)
- Jessica L. Elmer
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Amir D. Hay
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Noah J. Kessler
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Tessa M. Bertozzi
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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Planterose Jiménez B, Liu F, Caliebe A, Montiel González D, Bell JT, Kayser M, Vidaki A. Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity. Genome Biol 2021; 22:18. [PMID: 33402197 PMCID: PMC7786996 DOI: 10.1186/s13059-020-02223-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/07/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Although the genomes of monozygotic twins are practically identical, their methylomes may evolve divergently throughout their lifetime as a consequence of factors such as the environment or aging. Particularly for young and healthy monozygotic twins, DNA methylation divergence, if any, may be restricted to stochastic processes occurring post-twinning during embryonic development and early life. However, to what extent such stochastic mechanisms can systematically provide a stable source of inter-individual epigenetic variation remains uncertain until now. RESULTS We enriched for inter-individual stochastic variation by using an equivalence testing-based statistical approach on whole blood methylation microarray data from healthy adolescent monozygotic twins. As a result, we identified 333 CpGs displaying similarly large methylation variation between monozygotic co-twins and unrelated individuals. Although their methylation variation surpasses measurement error and is stable in a short timescale, susceptibility to aging is apparent in the long term. Additionally, 46% of these CpGs were replicated in adipose tissue. The identified sites are significantly enriched at the clustered protocadherin loci, known for stochastic methylation in developing neurons. We also confirmed an enrichment in monozygotic twin DNA methylation discordance at these loci in whole genome bisulfite sequencing data from blood and adipose tissue. CONCLUSIONS We have isolated a component of stochastic methylation variation, distinct from genetic influence, measurement error, and epigenetic drift. Biomarkers enriched in this component may serve in the future as the basis for universal epigenetic fingerprinting, relevant for instance in the discrimination of monozygotic twin individuals in forensic applications, currently impossible with standard DNA profiling.
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Affiliation(s)
- Benjamin Planterose Jiménez
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
- University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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Nilsson E, Sadler-Riggleman I, Beck D, Skinner MK. Differential DNA methylation in somatic and sperm cells of hatchery vs wild (natural-origin) steelhead trout populations. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab002. [PMID: 34040807 PMCID: PMC8132314 DOI: 10.1093/eep/dvab002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/09/2021] [Accepted: 03/01/2021] [Indexed: 05/06/2023]
Abstract
Environmental factors such as nutrition, stress, and toxicants can influence epigenetic programming and phenotypes of a wide variety of species from plants to humans. The current study was designed to investigate the impacts of hatchery spawning and rearing on steelhead trout (Oncorhynchus mykiss) vs the wild fish on a molecular level. Additionally, epigenetic differences between feeding practices that allow slow growth (2 years) and fast growth (1 year) hatchery trout were investigated. The sperm and red blood cells (RBC) from adult male slow growth/maturation hatchery steelhead, fast growth/maturation hatchery steelhead, and wild (natural-origin) steelhead were collected for DNA preparation to investigate potential alterations in differential DNA methylation regions (DMRs) and genetic mutations, involving copy number variations (CNVs). The sperm and RBC DNA both had a large number of DMRs when comparing the hatchery vs wild steelhead trout populations. The DMRs were cell type specific with negligible overlap. Slow growth/maturation compared to fast growth/maturation steelhead also had a larger number of DMRs in the RBC samples. A number of the DMRs had associated genes that were correlated to various biological processes and pathologies. Observations demonstrate a major epigenetic programming difference between the hatchery and wild natural-origin fish populations, but negligible genetic differences. Therefore, hatchery conditions and growth/maturation rate can alter the epigenetic developmental programming of the steelhead trout. Interestingly, epigenetic alterations in the sperm allow for potential epigenetic transgenerational inheritance of phenotypic variation to future generations. The impacts of hatchery exposures are not only important to consider on the fish exposed, but also on future generations and evolutionary trajectory of fish in the river populations.
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Affiliation(s)
- Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
- Correspondence address. Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA. Tel: +1-509-335-1524; E-mail:
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40
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Anastasiadi D, Shao C, Chen S, Piferrer F. Footprints of global change in marine life: Inferring past environment based on DNA methylation and gene expression marks. Mol Ecol 2020; 30:747-760. [PMID: 33372368 DOI: 10.1111/mec.15764] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/17/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022]
Abstract
Ocean global warming affects the distribution, life history and physiology of marine life. Extreme events, like marine heatwaves, are increasing in frequency and intensity. During sensitive stages of early fish development, the consequences may be long-lasting and mediated by epigenetic mechanisms. Here, we used European sea bass as a model to study the possible long-lasting effects of a marine heatwave during early development. We measured DNA methylation and gene expression in four tissues (brain, muscle, liver and testis) and detected differentially methylated regions (DMRs). Six genes were differentially expressed and contained DMRs three years after exposure to increased temperature, indicating direct phenotypic consequences and representing persistent changes. Interestingly, nine genes contained DMRs around the same genomic regions across tissues, therefore consisting of common footprints of developmental temperature in environmentally responsive loci. These loci are, to our knowledge, the first metastable epialleles (MEs) described in fish. MEs may serve as biomarkers to infer past life history events linked with persistent consequences. These results highlight the importance of subtle phenotypic changes mediated by epigenetics to extreme weather events during sensitive life stages. Also, to our knowledge, it is the first time the molecular effects of a marine heatwave during the lifetime of individuals are assessed. MEs could be used in surveillance programs aimed at determining the footprints of climate change on marine life. Our study paves the way for the identification of conserved MEs that respond equally to environmental perturbations across species. Conserved MEs would constitute a tool of assessment of global change effects in marine life at a large scale.
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Affiliation(s)
- Dafni Anastasiadi
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Songlin Chen
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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Bondada R, Somasundaram S, Marimuthu MP, Badarudeen MA, Puthiyaveedu VK, Maruthachalam R. Natural epialleles of Arabidopsis SUPERMAN display superwoman phenotypes. Commun Biol 2020; 3:772. [PMID: 33319840 PMCID: PMC7738503 DOI: 10.1038/s42003-020-01525-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 11/25/2020] [Indexed: 01/07/2023] Open
Abstract
Epimutations are heritable changes in gene function due to loss or gain of DNA cytosine methylation or chromatin modifications without changes in the DNA sequence. Only a few natural epimutations displaying discernible phenotypes are documented in plants. Here, we report natural epimutations in the cadastral gene, SUPERMAN(SUP), showing striking phenotypes despite normal transcription, discovered in a natural tetraploid, and subsequently in eleven diploid Arabidopsis genetic accessions. This natural lois lane(lol) epialleles behave as recessive mendelian alleles displaying a spectrum of silent to strong superwoman phenotypes affecting only the carpel whorl, in contrast to semi-dominant superman or supersex features manifested by induced epialleles which affect both stamen and carpel whorls. Despite its unknown origin, natural lol epialleles are subjected to the same epigenetic regulation as induced clk epialleles. The existence of superwoman epialleles in diverse wild populations is interpreted in the light of the evolution of unisexuality in plants. Ramesh Bondada et al. report natural epimutations in the Arabidopsis SUPERMAN gene from tetraploid and diploid accessions. The existence of these epialleles in diverse wild populations have the potential to shed light on the evolution of unisexuality in plants.
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Affiliation(s)
- Ramesh Bondada
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Saravanakumar Somasundaram
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | | | - Mohammed Afsal Badarudeen
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Vaishak Kanjirakol Puthiyaveedu
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Ravi Maruthachalam
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India.
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Abstract
The characteristics of fetal membrane cells and their phenotypic adaptations to support pregnancy or promote parturition are defined by global patterns of gene expression controlled by chromatin structure. Heritable epigenetic chromatin modifications that include DNA methylation and covalent histone modifications establish chromatin regions permissive or exclusive of regulatory interactions defining the cell-specific scope and potential of gene activity. Non-coding RNAs acting at the transcriptional and post-transcriptional levels complement the system by robustly stabilizing gene expression patterns and contributing to ordered phenotype transitions. Here we review currently available information about epigenetic gene regulation in the amnion and the chorion laeve. In addition, we provide an overview of epigenetic phenomena in the decidua, which is the maternal tissue fused to the chorion membrane forming the anatomical and functional unit called choriodecidua. The relationship of gene expression with DNA (CpG) methylation, histone acetylation and methylation, micro RNAs, long non-coding RNAs and chromatin accessibility is discussed in the context of normal pregnancy, parturition and pregnancy complications. Data generated using clinical samples and cell culture models strongly suggests that epigenetic events are associated with the phenotypic transitions of fetal membrane cells during the establishment, maintenance and termination of pregnancy potentially driving and consolidating the changes as pregnancy progresses. Disease conditions and environmental factors may produce epigenetic footprints that indicate exposures and mediate adverse pregnancy outcomes. Although knowledge is expanding rapidly, fetal membrane epigenetics is still in an early stage of development necessitating further research to realize its remarkable basic and translational potential.
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Affiliation(s)
- Tamas Zakar
- Department of Maternity & Gynaecology, John Hunter Hospital, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Jonathan W. Paul
- School of Medicine and Public Health, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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Ouni M, Saussenthaler S, Eichelmann F, Jähnert M, Stadion M, Wittenbecher C, Rönn T, Zellner L, Gottmann P, Ling C, Schulze MB, Schürmann A. Epigenetic Changes in Islets of Langerhans Preceding the Onset of Diabetes. Diabetes 2020; 69:2503-2517. [PMID: 32816961 PMCID: PMC7576562 DOI: 10.2337/db20-0204] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/09/2020] [Indexed: 12/19/2022]
Abstract
The identification of individuals with a high risk of developing type 2 diabetes (T2D) is fundamental for prevention. Here, we used a translational approach and prediction criteria to identify changes in DNA methylation visible before the development of T2D. Islets of Langerhans were isolated from genetically identical 10-week-old female New Zealand Obese mice, which differ in their degree of hyperglycemia and in liver fat content. The application of a semiexplorative approach identified 497 differentially expressed and methylated genes (P = 6.42e-09, hypergeometric test) enriched in pathways linked to insulin secretion and extracellular matrix-receptor interaction. The comparison of mouse data with DNA methylation levels of incident T2D cases from the prospective European Prospective Investigation of Cancer (EPIC)-Potsdam cohort, revealed 105 genes with altered DNA methylation at 605 cytosine-phosphate-guanine (CpG) sites, which were associated with future T2D. AKAP13, TENM2, CTDSPL, PTPRN2, and PTPRS showed the strongest predictive potential (area under the receiver operating characteristic curve values 0.62-0.73). Among the new candidates identified in blood cells, 655 CpG sites, located in 99 genes, were differentially methylated in islets of humans with T2D. Using correction for multiple testing detected 236 genes with an altered DNA methylation in blood cells and 201 genes in diabetic islets. Thus, the introduced translational approach identified novel putative biomarkers for early pancreatic islet aberrations preceding T2D.
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Affiliation(s)
- Meriem Ouni
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Sophie Saussenthaler
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Fabian Eichelmann
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
| | - Markus Jähnert
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Mandy Stadion
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Clemens Wittenbecher
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Tina Rönn
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Lisa Zellner
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Pascal Gottmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Matthias B Schulze
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Annette Schürmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
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Odhiambo JF, Pankey CL, Ghnenis AB, Ford SP. A Review of Maternal Nutrition during Pregnancy and Impact on the Offspring through Development: Evidence from Animal Models of Over- and Undernutrition. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17186926. [PMID: 32971930 PMCID: PMC7559343 DOI: 10.3390/ijerph17186926] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 12/22/2022]
Abstract
Similarities in offspring phenotype due to maternal under- or over-nutrition during gestation have been observed in studies conducted at University of Wyoming. In these studies, ewes were either nutrient-restricted (NR) from early to mid-gestation, or fed an obesogenic diet (MO) from preconception through term. Offspring necropsies occurred at mid-gestation, late-gestation, and after parturition. At mid gestation, body weights of NR fetuses were ~30% lighter than controls, whereas MO fetuses were ~30% heavier than those of controls. At birth, lambs born to NR, MO, and control ewes exhibited similar weights. This was a consequence of accelerated fetal growth rates in NR ewes, and reduced fetal growth rates in MO ewes in late gestation, when compared to their respective controls. These fetal growth patterns resulted in remarkably similar effects of increased susceptibility to obesity, cardiovascular disease, and glucose intolerance in offspring programmed mostly during fetal stages of development. These data provide evidence that maternal under- and over-nutrition similarly induce the development of the same cadre of physical and metabolic problems in postnatal life.
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Affiliation(s)
- John F. Odhiambo
- Division of Agricultural Sciences, Florida A&M University, Tallahassee, FL 32307, USA
- Formerly, Department of Animal Science, University of Wyoming, Laramie, WY 82071, USA; (C.L.P.); (A.B.G.); (S.P.F.)
- Correspondence:
| | - Christopher L. Pankey
- Formerly, Department of Animal Science, University of Wyoming, Laramie, WY 82071, USA; (C.L.P.); (A.B.G.); (S.P.F.)
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, Lewisburg, WV 24901, USA
| | - Adel B. Ghnenis
- Formerly, Department of Animal Science, University of Wyoming, Laramie, WY 82071, USA; (C.L.P.); (A.B.G.); (S.P.F.)
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University, Bryan, TX 77807, USA
| | - Stephen P. Ford
- Formerly, Department of Animal Science, University of Wyoming, Laramie, WY 82071, USA; (C.L.P.); (A.B.G.); (S.P.F.)
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Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans-Acting Modifiers. Viruses 2020; 12:v12080810. [PMID: 32727076 PMCID: PMC7472028 DOI: 10.3390/v12080810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation.
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46
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Kartal Ö, Schmid MW, Grossniklaus U. Cell type-specific genome scans of DNA methylation divergence indicate an important role for transposable elements. Genome Biol 2020; 21:172. [PMID: 32660534 PMCID: PMC7359245 DOI: 10.1186/s13059-020-02068-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/10/2020] [Indexed: 01/01/2023] Open
Abstract
In population genomics, genetic diversity measures play an important role in genome scans for divergent sites. In population epigenomics, comparable tools are rare although the epigenome can vary at several levels of organization. We propose a model-free, information-theoretic approach, the Jensen-Shannon divergence (JSD), as a flexible diversity index for epigenomic diversity. Here, we demonstrate how JSD uncovers the relationship between genomic features and cell type-specific methylome diversity in Arabidopsis thaliana. However, JSD is applicable to any epigenetic mark and any collection of individuals, tissues, or cells, for example to assess the heterogeneity in healthy organs and tumors.
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Affiliation(s)
- Önder Kartal
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008 Switzerland
- Creoptix AG, Zugerstrasse 76, Wädenswil, 8820 Switzerland
| | - Marc W. Schmid
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008 Switzerland
- MWSchmid GmbH, Möhrlistrasse 25, Zurich, 8006 Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008 Switzerland
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47
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Leroy JL, Frongillo EA, Dewan P, Black MM, Waterland RA. Can Children Catch up from the Consequences of Undernourishment? Evidence from Child Linear Growth, Developmental Epigenetics, and Brain and Neurocognitive Development. Adv Nutr 2020; 11:1032-1041. [PMID: 32584399 PMCID: PMC7360439 DOI: 10.1093/advances/nmaa020] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/04/2020] [Accepted: 02/12/2020] [Indexed: 11/13/2022] Open
Abstract
Recovery from nutritionally induced height deficits continues to garner attention. The current literature on catch-up growth, however, has 2 important limitations: wide-ranging definitions of catch-up growth are used, and it remains unclear whether children can recover from the broader consequences of undernutrition. We addressed these shortcomings by reviewing the literature on the criteria for catch-up in linear growth and on the potential to recover from undernutrition early in life in 3 domains: linear growth, developmental epigenetics, and child brain and neurocognitive development. Four criteria must be met to demonstrate catch-up growth in height: after a period in which a growth-inhibiting condition (criterion 1) causes a reduction in linear growth velocity (criterion 2), alleviation of the inhibiting condition (criterion 3) leads to higher-than-normal velocity (criterion 4). Accordingly, studies that are observational, do not use absolute height, or have no alleviation of an inhibiting condition cannot be used to establish catch-up growth. Adoption and foster care, which provide dramatic improvements in children's living conditions not typically attained in nutrition interventions, led to some (but incomplete) recovery in linear growth and brain and neurocognitive development. Maternal nutrition around the time of conception was shown to have long-term (potentially permanent) effects on DNA methylation in the offspring. Undernourishment early in life may thus have profound irreversible effects. Scientific, program, and policy efforts should focus on preventing maternal and child undernutrition rather than on correcting its consequences or attempting to prove they can be corrected.
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Affiliation(s)
- Jef L Leroy
- Poverty, Health, and Nutrition Division, International Food Policy Research Institute, Washington, DC, USA
| | - Edward A Frongillo
- Department of Health Promotion, Education, and Behavior, University of South Carolina, Columbia, SC, USA
| | - Pragya Dewan
- Poverty, Health, and Nutrition Division, International Food Policy Research Institute, Washington, DC, USA
| | - Maureen M Black
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
- RTI International, Research Triangle Park, NC, USA
| | - Robert A Waterland
- USDA/Agricultural Research Service Children's Nutrition Research Center, Departments of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
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48
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DNA methylation at the crossroads of gene and environment interactions. Essays Biochem 2020; 63:717-726. [PMID: 31782496 PMCID: PMC6923319 DOI: 10.1042/ebc20190031] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022]
Abstract
DNA methylation is an epigenetic mark involved in regulating genome function and is critical for normal development in mammals. It has been observed that the developmental environment can lead to permanent changes in gene expression and DNA methylation, at least at 'metastable epialleles'. These are defined as regions of the genome that show a variable epigenetic state that is established early in development and maintained through subsequent cell divisions. However, the majority of the known genome does not behave in this manner. Here, we use the developmental origins of adult disease hypothesis to understand environmental epigenomics. Some challenges to studying how DNA methylation is influenced by the environment include identifying DNA methylation changes associated with an environmental exposure in tissues with a complex cellular composition and at genomic regions for which DNA methylation is dynamically regulated in a cell-type specific manner. We also offer a perspective of how emerging technologies may be useful for dissecting the functional contribution of exposure-associated epigenetic changes and highlight recent evidence that suggests that genomic regions that are absent from genome assemblies may be unappreciated hotspots for environmental modulation of the epigenetic state.
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Vukic M, Wu H, Daxinger L. Making headway towards understanding how epigenetic mechanisms contribute to early-life effects. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180126. [PMID: 30966890 DOI: 10.1098/rstb.2018.0126] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It has become clear that in addition to the DNA sequence there is another layer of information, termed epigenetic modifications, that can influence phenotypes and traits. In particular, environmental epigenomics, which addresses the effect of the environment on the epigenome and human health, is becoming an area of great interest for many researchers working in different scientific fields. In this review, we will consider the current evidence that early-life environmental signals can have long-term effects on the epigenome. We will further evaluate how recent technological advances may enable us to unravel the molecular mechanisms underlying these phenomena, which will be crucial for understanding heritability in health and disease. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.
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Affiliation(s)
- Maja Vukic
- Department of Human Genetics, Leiden University Medical Centre , Einthovenweg 20, 2333 ZC Leiden , The Netherlands
| | - Haoyu Wu
- Department of Human Genetics, Leiden University Medical Centre , Einthovenweg 20, 2333 ZC Leiden , The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre , Einthovenweg 20, 2333 ZC Leiden , The Netherlands
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50
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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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