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Vullioud C, Benhaiem S, Meneghini D, Szyf M, Shao Y, Hofer H, East ML, Fickel J, Weyrich A. Epigenetic signatures of social status in wild female spotted hyenas (Crocuta crocuta). Commun Biol 2024; 7:313. [PMID: 38548860 PMCID: PMC10978994 DOI: 10.1038/s42003-024-05926-y] [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: 08/01/2023] [Accepted: 02/16/2024] [Indexed: 04/01/2024] Open
Abstract
In mammalian societies, dominance hierarchies translate into inequalities in health, reproductive performance and survival. DNA methylation is thought to mediate the effects of social status on gene expression and phenotypic outcomes, yet a study of social status-specific DNA methylation profiles in different age classes in a wild social mammal is missing. We tested for social status signatures in DNA methylation profiles in wild female spotted hyenas (Crocuta crocuta), cubs and adults, using non-invasively collected gut epithelium samples. In spotted hyena clans, female social status influences access to resources, foraging behavior, health, reproductive performance and survival. We identified 149 differentially methylated regions between 42 high- and low-ranking female spotted hyenas (cubs and adults). Differentially methylated genes were associated with energy conversion, immune function, glutamate receptor signalling and ion transport. Our results provide evidence that socio-environmental inequalities are reflected at the molecular level in cubs and adults in a wild social mammal.
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Affiliation(s)
- Colin Vullioud
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Sarah Benhaiem
- Department of Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Dorina Meneghini
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | | | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marion L East
- Department of Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- University of Potsdam, Potsdam, Germany
| | - Alexandra Weyrich
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Universität Leipzig, Leipzig, Germany.
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Tando Y, Matsui Y. Inheritance of environment-induced phenotypic changes through epigenetic mechanisms. ENVIRONMENTAL EPIGENETICS 2023; 9:dvad008. [PMID: 38094661 PMCID: PMC10719065 DOI: 10.1093/eep/dvad008] [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: 09/18/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 03/08/2024]
Abstract
Growing evidence suggests that epigenetic changes through various parental environmental factors alter the phenotypes of descendants in various organisms. Environmental factors, including exposure to chemicals, stress and abnormal nutrition, affect the epigenome in parental germ cells by different epigenetic mechanisms, such as DNA methylation, histone modification as well as small RNAs via metabolites. Some current remaining questions are the causal relationship between environment-induced epigenetic changes in germ cells and altered phenotypes of descendants, and the molecular basis of how the abnormal epigenetic changes escape reprogramming in germ cells. In this review, we introduce representative examples of intergenerational and transgenerational inheritance of phenotypic changes through parental environmental factors and the accompanied epigenetic and metabolic changes, with a focus on animal species. We also discuss the molecular mechanisms of epigenomic inheritance and their possible biological significance.
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Affiliation(s)
- Yukiko Tando
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Yasuhisa Matsui
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
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Laine VN, Sepers B, Lindner M, Gawehns F, Ruuskanen S, van Oers K. An ecologist's guide for studying DNA methylation variation in wild vertebrates. Mol Ecol Resour 2023; 23:1488-1508. [PMID: 35466564 DOI: 10.1111/1755-0998.13624] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/29/2022] [Accepted: 04/13/2022] [Indexed: 11/30/2022]
Abstract
The field of molecular biology is advancing fast with new powerful technologies, sequencing methods and analysis software being developed constantly. Commonly used tools originally developed for research on humans and model species are now regularly used in ecological and evolutionary research. There is also a growing interest in the causes and consequences of epigenetic variation in natural populations. Studying ecological epigenetics is currently challenging, especially for vertebrate systems, because of the required technical expertise, complications with analyses and interpretation, and limitations in acquiring sufficiently high sample sizes. Importantly, neglecting the limitations of the experimental setup, technology and analyses may affect the reliability and reproducibility, and the extent to which unbiased conclusions can be drawn from these studies. Here, we provide a practical guide for researchers aiming to study DNA methylation variation in wild vertebrates. We review the technical aspects of epigenetic research, concentrating on DNA methylation using bisulfite sequencing, discuss the limitations and possible pitfalls, and how to overcome them through rigid and reproducible data analysis. This review provides a solid foundation for the proper design of epigenetic studies, a clear roadmap on the best practices for correct data analysis and a realistic view on the limitations for studying ecological epigenetics in vertebrates. This review will help researchers studying the ecological and evolutionary implications of epigenetic variation in wild populations.
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Affiliation(s)
- Veronika N Laine
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Bernice Sepers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, The Netherlands
| | - Melanie Lindner
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Fleur Gawehns
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Biology, University of Turku, Finland
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, The Netherlands
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Weyrich A, Guerrero-Altamirano TP, Yasar S, Czirják GÁ, Wachter B, Fickel J. First Steps towards the Development of Epigenetic Biomarkers in Female Cheetahs ( Acinonyx jubatus). LIFE (BASEL, SWITZERLAND) 2022; 12:life12060920. [PMID: 35743950 PMCID: PMC9225391 DOI: 10.3390/life12060920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Free-ranging cheetahs (Acinonyx jubatus) are generally healthy, whereas cheetahs under human care, such as those in zoological gardens, suffer from ill-defined infectious and degenerative pathologies. These differences are only partially explained by husbandry management programs because both groups share low genetic diversity. However, mounting evidence suggests that physiological differences between populations in different environments can be tracked down to differences in epigenetic signatures. Here, we identified differentially methylated regions (DMRs) between free-ranging cheetahs and conspecifics in zoological gardens and prospect putative links to pathways relevant to immunity, energy balance and homeostasis. Comparing epigenomic DNA methylation profiles obtained from peripheral blood mononuclear cells (PBMCs) from eight free-ranging female cheetahs from Namibia and seven female cheetahs living in zoological gardens within Europe, we identified DMRs of which 22 were hypermethylated and 23 hypomethylated. Hypermethylated regions in cheetahs under human care were located in the promoter region of a gene involved in host-pathogen interactions (KLC1) and in an intron of a transcription factor relevant for the development of pancreatic β-cells, liver, and kidney (GLIS3). The most canonical mechanism of DNA methylation in promoter regions is assumed to repress gene transcription. Taken together, this could indicate that hypermethylation at the promoter region of KLC1 is involved in the reduced immunity in cheetahs under human care. This approach can be generalized to characterize DNA methylation profiles in larger cheetah populations under human care with a more granular longitudinal data collection, which, in the future, could be used to monitor the early onset of pathologies, and ultimately translate into the development of biomarkers with prophylactic and/or therapeutic potential.
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Affiliation(s)
- Alexandra Weyrich
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (T.P.G.-A.); (S.Y.)
- Correspondence: (A.W.); (B.W.); (J.F.)
| | - Tania P. Guerrero-Altamirano
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (T.P.G.-A.); (S.Y.)
- Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Selma Yasar
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (T.P.G.-A.); (S.Y.)
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gábor Á. Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany;
| | - Bettina Wachter
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
- Correspondence: (A.W.); (B.W.); (J.F.)
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (T.P.G.-A.); (S.Y.)
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Correspondence: (A.W.); (B.W.); (J.F.)
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Milošević M, Arsić A, Cvetković Z, Vučić V. Memorable Food: Fighting Age-Related Neurodegeneration by Precision Nutrition. Front Nutr 2021; 8:688086. [PMID: 34422879 PMCID: PMC8374314 DOI: 10.3389/fnut.2021.688086] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Healthcare systems worldwide are seriously challenged by a rising prevalence of neurodegenerative diseases (NDDs), which mostly, but not exclusively, affect the ever-growing population of the elderly. The most known neurodegenerative diseases are Alzheimer's (AD) and Parkinson's disease, multiple sclerosis, and amyotrophic lateral sclerosis, but some viral infections of the brain and traumatic brain injury may also cause NDD. Typical for NDD are the malfunctioning of neurons and their irreversible loss, which often progress irreversibly to dementia and ultimately to death. Numerous factors are involved in the pathogenesis of NDD: genetic variability, epigenetic changes, extent of oxidative/nitrosative stress, mitochondrial dysfunction, and DNA damage. The complex interplay of all the above-mentioned factors may be a fingerprint of neurodegeneration, with different diseases being affected to different extents by particular factors. There is a voluminous body of evidence showing the benefits of regular exercise to brain health and cognitive functions. Moreover, the importance of a healthy diet, balanced in macro- and micro-nutrients, in preventing neurodegeneration and slowing down a progression to full-blown disease is evident. Individuals affected by NDD almost inevitably have low-grade inflammation and anomalies in lipid metabolism. Metabolic and lipid profiles in NDD can be improved by the Mediterranean diet. Many studies have associated the Mediterranean diet with a decreased risk of dementia and AD, but a cause-and-effect relationship has not been deduced. Studies with caloric restriction showed neuroprotective effects in animal models, but the results in humans are inconsistent. The pathologies of NDD are complex and there is a great inter-individual (epi)genetic variance within any population. Furthermore, the gut microbiome, being deeply involved in nutrient uptake and lipid metabolism, also represents a pillar of the gut microbiome-brain axis and is linked with the pathogenesis of NDD. Numerous studies on the role of different micronutrients (omega-3 fatty acids, bioactive polyphenols from fruit and medicinal plants) in the prevention, prediction, and treatment of NDD have been conducted, but we are still far away from a personalized diet plan for individual NDD patients. For this to be realized, large-scale cohorts that would include the precise monitoring of food intake, mapping of genetic variants, epigenetic data, microbiome studies, and metabolome, lipidome, and transcriptome data are needed.
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Affiliation(s)
- Maja Milošević
- Department of Neuroendocrinology, Institute for Medical Research, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Arsić
- Department of Nutritional Biochemistry and Dietology, Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, University of Belgrade, Belgrade, Serbia
| | - Zorica Cvetković
- Department of Hematology, Clinical Hospital Center Zemun, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vesna Vučić
- Department of Nutritional Biochemistry and Dietology, Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, University of Belgrade, Belgrade, Serbia
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Hu J, Wuitchik SJS, Barry TN, Jamniczky HA, Rogers SM, Barrett RDH. Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus). Genetics 2021; 217:1-15. [PMID: 33683369 PMCID: PMC8045681 DOI: 10.1093/genetics/iyab001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24-35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.
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Affiliation(s)
- Juntao Hu
- National Observation and Research Station for Yangtze Estuarine Wetland Ecosystems, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai 200438, China
- Redpath Museum and Department of Biology, McGill University, Montreal, QC H3A 0C4, Canada
| | - Sara J S Wuitchik
- Informatics Group, Harvard University, Cambridge, MA 02138, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Tegan N Barry
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Heather A Jamniczky
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, QC H3A 0C4, Canada
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Rutkowska J, Lagisz M, Bonduriansky R, Nakagawa S. Mapping the past, present and future research landscape of paternal effects. BMC Biol 2020; 18:183. [PMID: 33246472 PMCID: PMC7694421 DOI: 10.1186/s12915-020-00892-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/08/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Although in all sexually reproducing organisms an individual has a mother and a father, non-genetic inheritance has been predominantly studied in mothers. Paternal effects have been far less frequently studied, until recently. In the last 5 years, research on environmentally induced paternal effects has grown rapidly in the number of publications and diversity of topics. Here, we provide an overview of this field using synthesis of evidence (systematic map) and influence (bibliometric analyses). RESULTS We find that motivations for studies into paternal effects are diverse. For example, from the ecological and evolutionary perspective, paternal effects are of interest as facilitators of response to environmental change and mediators of extended heredity. Medical researchers track how paternal pre-fertilization exposures to factors, such as diet or trauma, influence offspring health. Toxicologists look at the effects of toxins. We compare how these three research guilds design experiments in relation to objects of their studies: fathers, mothers and offspring. We highlight examples of research gaps, which, in turn, lead to future avenues of research. CONCLUSIONS The literature on paternal effects is large and disparate. Our study helps in fostering connections between areas of knowledge that develop in parallel, but which could benefit from the lateral transfer of concepts and methods.
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Affiliation(s)
- Joanna Rutkowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, BEES, The University of New South Wales, Sydney, Australia
| | - Malgorzata Lagisz
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, BEES, The University of New South Wales, Sydney, Australia
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, BEES, The University of New South Wales, Sydney, Australia
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, BEES, The University of New South Wales, Sydney, Australia
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Brass KE, Herndon N, Gardner SA, Grindstaff JL, Campbell P. Intergenerational effects of paternal predator cue exposure on behavior, stress reactivity, and neural gene expression. Horm Behav 2020; 124:104806. [PMID: 32534838 DOI: 10.1016/j.yhbeh.2020.104806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022]
Abstract
Predation threat impacts prey behavior, physiology, and fitness. Stress-mediated alterations to the paternal epigenome can be transmitted to offspring via the germline, conferring a potential advantage to offspring in predator-rich environments. While intergenerational epigenetic transmission of paternal experience has been demonstrated in mammals, how paternal predator exposure might alter offspring phenotypes across development is unstudied. We exposed male mice to a predator odor (2,4,5-trimethylthiazoline, TMT) or a neutral odor (banana extract) prior to mating and measured offspring behavioral phenotypes throughout development, together with adult stress reactivity and candidate gene expression in the prefrontal cortex, hippocampus, amygdala, and hypothalamus. We predicted that offspring of TMT-exposed males would be less active, would display elevated anxiety-like behaviors, and would have a more efficient stress response relative to controls, phenotypes that should enhance predator avoidance in a high predation risk environment. Unexpectedly, we found that offspring of TMT-exposed males are more active, exhibit less anxiety-like behavior, and have decreased baseline plasma corticosterone relative to controls. Effects of paternal treatment on neural gene expression were limited to the prefrontal cortex, with increased mineralocorticoid receptor expression and a trend towards increased Bdnf expression in offspring of TMT-exposed males. These results suggest that fathers exposed to predation threat produce offspring that are buffered against non-acute stressors and, potentially, better adapted to a predator-dense environment because they avoid trade-offs between predator avoidance and foraging and reproduction. This study provides evidence that ecologically relevant paternal experience can be transmitted through the germline, and can impact offspring phenotypes throughout development.
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Affiliation(s)
- Kelsey E Brass
- Oklahoma State University, Department of Integrative Biology, Stillwater, OK 74078, USA
| | - Nathan Herndon
- Oklahoma State University, Department of Integrative Biology, Stillwater, OK 74078, USA
| | - Sarah A Gardner
- Oklahoma State University, Department of Integrative Biology, Stillwater, OK 74078, USA; University of California Riverside, Department of Evolution, Ecology, and Organismal Biology, Riverside, CA 92521, USA
| | - Jennifer L Grindstaff
- Oklahoma State University, Department of Integrative Biology, Stillwater, OK 74078, USA
| | - Polly Campbell
- Oklahoma State University, Department of Integrative Biology, Stillwater, OK 74078, USA; University of California Riverside, Department of Evolution, Ecology, and Organismal Biology, Riverside, CA 92521, USA.
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Guerrero TP, Fickel J, Benhaiem S, Weyrich A. Epigenomics and gene regulation in mammalian social systems. Curr Zool 2020; 66:307-319. [PMID: 32440291 PMCID: PMC7233906 DOI: 10.1093/cz/zoaa005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 02/12/2020] [Indexed: 12/19/2022] Open
Abstract
Social epigenomics is a new field of research that studies how the social environment shapes the epigenome and how in turn the epigenome modulates behavior. We focus on describing known gene-environment interactions (GEIs) and epigenetic mechanisms in different mammalian social systems. To illustrate how epigenetic mechanisms integrate GEIs, we highlight examples where epigenetic mechanisms are associated with social behaviors and with their maintenance through neuroendocrine, locomotor, and metabolic responses. We discuss future research trajectories and open questions for the emerging field of social epigenomics in nonmodel and naturally occurring social systems. Finally, we outline the technological advances that aid the study of epigenetic mechanisms in the establishment of GEIs and vice versa.
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Affiliation(s)
- Tania P Guerrero
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
- Faculty of Environment and Natural Resources, Albert Ludwig University of Freiburg, Tennenbacher Str. 4, Freiburg, D-79085, Germany
| | - Jörns Fickel
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
| | - Sarah Benhaiem
- Department Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
| | - Alexandra Weyrich
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
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11
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Tissue-specific epigenetic inheritance after paternal heat exposure in male wild guinea pigs. Mamm Genome 2020; 31:157-169. [PMID: 32285146 PMCID: PMC7369130 DOI: 10.1007/s00335-020-09832-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/19/2020] [Indexed: 12/28/2022]
Abstract
External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 °C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes.
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Liu Y, Weyrich LS, Llamas B. More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment. Mol Biol Evol 2020; 37:307-319. [PMID: 31638147 DOI: 10.1093/molbev/msz231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Whether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.
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Affiliation(s)
- Yichen Liu
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
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Fuso A, Lucarelli M. CpG and Non-CpG Methylation in the Diet–Epigenetics–Neurodegeneration Connection. Curr Nutr Rep 2019; 8:74-82. [DOI: 10.1007/s13668-019-0266-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Weyrich A, Lenz D, Fickel J. Environmental Change-Dependent Inherited Epigenetic Response. Genes (Basel) 2018; 10:genes10010004. [PMID: 30583460 PMCID: PMC6356568 DOI: 10.3390/genes10010004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/11/2018] [Accepted: 12/17/2018] [Indexed: 02/05/2023] Open
Abstract
Epigenetic modifications are a mechanism conveying environmental information to subsequent generations via parental germ lines. Research on epigenetic responses to environmental changes in wild mammals has been widely neglected, as well as studies that compare responses to changes in different environmental factors. Here, we focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to either diet (~40% less protein) or temperature increase (10 °C increased temperature). Because both experiments focused on the liver as the main metabolic and thermoregulation organ, we were able to decipher if epigenetic changes differed in response to different environmental changes. Reduced representation bisulfite sequencing (RRBS) revealed differentially methylated regions (DMRs) in annotated genomic regions in sons sired before (control) and after the fathers’ treatments. We detected both a highly specific epigenetic response dependent on the environmental factor that had changed that was reflected in genes involved in specific metabolic pathways, and a more general response to changes in outer stimuli reflected by epigenetic modifications in a small subset of genes shared between both responses. Our results indicated that fathers prepared their offspring for specific environmental changes by paternally inherited epigenetic modifications, suggesting a strong paternal contribution to adaptive processes.
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Affiliation(s)
- Alexandra Weyrich
- Evolutionary Genetics (Dept.2), Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany.
| | - Dorina Lenz
- Evolutionary Genetics (Dept.2), Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany.
| | - Jörns Fickel
- Evolutionary Genetics (Dept.2), Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany.
- Institute for Biochemistry and Biology, Potsdam University, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
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