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Matlosz S, Franzdóttir SR, Pálsson A, Jónsson ZO. DNA methylation reprogramming in teleosts. Evol Dev 2024:e12486. [PMID: 38783650 DOI: 10.1111/ede.12486] [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: 09/23/2023] [Revised: 04/29/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Early embryonic development is crucially important but also remarkably diverse among animal taxa. Axis formation and cell lineage specification occur due to both spatial and temporal control of gene expression. This complex system involves various signaling pathways and developmental genes such as transcription factors as well as other molecular interactants that maintain cellular states, including several types of epigenetic marks. 5mC DNA methylation, the chemical modification of cytosines in eukaryotes, represents one such mark. By influencing the compaction of chromatin (a high-order DNA structure), DNA methylation can either repress or induce transcriptional activity. Mammals exhibit a reprogramming of DNA methylation from the parental genomes in the zygote following fertilization, and later in primordial germ cells (PGCs). Whether these periods of methylation reprogramming are evolutionarily conserved, or an innovation in mammals, is an emerging question. Looking into these processes in other vertebrate lineages is thus important, and teleost fish, with their extensive species richness, phenotypic diversity, and multiple rounds of whole genome duplication, provide the perfect research playground for answering such a question. This review aims to present a concise state of the art of DNA methylation reprogramming in early development in fish by summarizing findings from different research groups investigating methylation reprogramming patterns in teleosts, while keeping in mind the ramifications of the methodology used, then comparing those patterns to reprogramming patterns in mammals.
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Affiliation(s)
- Sébastien Matlosz
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Arnar Pálsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Zophonías O Jónsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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2
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Venney CJ, Bouchard R, April J, Normandeau E, Lecomte L, Côté G, Bernatchez L. Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: Sex-specificity and intergenerational stability. Mol Ecol Resour 2023. [PMID: 36760032 DOI: 10.1111/1755-0998.13766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/20/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
Captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even in the absence of genetic change. Evidence for hatchery-induced changes in DNA methylation is becoming abundant, though questions remain on the sex-specificity of these effects, their persistence until spawning and potential for transmission to future generations. Here we performed whole genome methylation sequencing of fin tissue for 16 hatchery and 16 wild Atlantic salmon (Salmo salar) returning to spawn in the Rimouski River, Québec, Canada. We identified two cohorts of hatchery-reared salmon through methylation analysis, one of which was epigenetically similar to wild fish, suggesting that supplementation efforts may be able to minimize the epigenetic effects of hatchery rearing. We found considerable sex-specific effects of hatchery rearing, with few genomic regions being affected in both males and females. We also analysed the methylome of 32 F1 offspring from four groups (pure wild, pure hatchery origin and reciprocal hybrids). We found that few epigenetic changes due to parental hatchery rearing persisted in the F1 offspring though the patterns of inheritance appear to be complex, involving nonadditive effects. Our results suggest that the epigenetic effects of hatchery rearing can be minimal in F0 . There may also be minimal epigenetic inheritance and rapid loss of epigenetic changes associated with hatchery rearing. However, due to sex-specificity and nonadditive patterns of inheritance, methylation changes due to captive rearing are rather complex and the field would benefit from further research on minimizing the epigenetic effects of captive rearing in conservation efforts.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Raphaël Bouchard
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Julien April
- Direction de l'expertise sur la faune aquatique, Ministère des Forêts, de la Faune et des Parcs du Québec, Québec, Quebec, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Laurie Lecomte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Guillaume Côté
- Direction de l'expertise sur la faune aquatique, Ministère des Forêts, de la Faune et des Parcs du Québec, Québec, Quebec, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
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3
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Population Epigenetics: The Extent of DNA Methylation Variation in Wild Animal Populations. EPIGENOMES 2022; 6:epigenomes6040031. [PMID: 36278677 PMCID: PMC9589984 DOI: 10.3390/epigenomes6040031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Population epigenetics explores the extent of epigenetic variation and its dynamics in natural populations encountering changing environmental conditions. In contrast to population genetics, the basic concepts of this field are still in their early stages, especially in animal populations. Epigenetic variation may play a crucial role in phenotypic plasticity and local adaptation as it can be affected by the environment, it is likely to have higher spontaneous mutation rate than nucleotide sequences do, and it may be inherited via non-mendelian processes. In this review, we aim to bring together natural animal population epigenetic studies to generate new insights into ecological epigenetics and its evolutionary implications. We first provide an overview of the extent of DNA methylation variation and its autonomy from genetic variation in wild animal population. Second, we discuss DNA methylation dynamics which create observed epigenetic population structures by including basic population genetics processes. Then, we highlight the relevance of DNA methylation variation as an evolutionary mechanism in the extended evolutionary synthesis. Finally, we suggest new research directions by highlighting gaps in the knowledge of the population epigenetics field. As for our results, DNA methylation diversity was found to reveal parameters that can be used to characterize natural animal populations. Some concepts of population genetics dynamics can be applied to explain the observed epigenetic structure in natural animal populations. The set of recent advancements in ecological epigenetics, especially in transgenerational epigenetic inheritance in wild animal population, might reshape the way ecologists generate predictive models of the capacity of organisms to adapt to changing environments.
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Snead AA, Earley RL. Predicting the in-between: Present and future habitat suitability of an intertidal euryhaline fish. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2021.101523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Robaire B, Delbes G, Head JA, Marlatt VL, Martyniuk CJ, Reynaud S, Trudeau VL, Mennigen JA. A cross-species comparative approach to assessing multi- and transgenerational effects of endocrine disrupting chemicals. ENVIRONMENTAL RESEARCH 2022; 204:112063. [PMID: 34562476 DOI: 10.1016/j.envres.2021.112063] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
A wide range of chemicals have been identified as endocrine disrupting chemicals (EDCs) in vertebrate species. Most studies of EDCs have focused on exposure of both male and female adults to these chemicals; however, there is clear evidence that EDCs have dramatic effects when mature or developing gametes are exposed, and consequently are associated with in multigenerational and transgenerational effects. Several publications have reviewed such actions of EDCs in subgroups of species, e.g., fish or rodents. In this review, we take a holistic approach synthesizing knowledge of the effects of EDCs across vertebrate species, including fish, anurans, birds, and mammals, and discuss the potential mechanism(s) mediating such multi- and transgenerational effects. We also propose a series of recommendations aimed at moving the field forward in a structured and coherent manner.
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Affiliation(s)
- Bernard Robaire
- Department of Pharmacology and Therapeutics and of Obstetrics and Gynecology, McGill University, Montreal, Canada.
| | - Geraldine Delbes
- Centre Armand Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique (INRS), Laval, QC, Canada
| | - Jessica A Head
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - Vicki L Marlatt
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Christopher J Martyniuk
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Stéphane Reynaud
- Univ. Grenoble-Alpes, Université. Savoie Mont Blanc, CNRS, LECA, Grenoble, 38000, France
| | - Vance L Trudeau
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
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6
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Fellous A, Wegner KM, John U, Mark FC, Shama LNS. Windows of opportunity: Ocean warming shapes temperature-sensitive epigenetic reprogramming and gene expression across gametogenesis and embryogenesis in marine stickleback. GLOBAL CHANGE BIOLOGY 2022; 28:54-71. [PMID: 34669228 DOI: 10.1111/gcb.15942] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/23/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Rapid climate change is placing many marine species at risk of local extinction. Recent studies show that epigenetic mechanisms (e.g. DNA methylation, histone modifications) can facilitate both within and transgenerational plasticity to cope with changing environments. However, epigenetic reprogramming (erasure and re-establishment of epigenetic marks) during gamete and early embryo development may hinder transgenerational epigenetic inheritance. Most of our knowledge about reprogramming stems from mammals and model organisms, whereas the prevalence and extent of reprogramming among non-model species from wild populations is rarely investigated. Moreover, whether reprogramming dynamics are sensitive to changing environmental conditions is not well known, representing a key knowledge gap in the pursuit to identify mechanisms underlying links between parental exposure to changing climate patterns and environmentally adapted offspring phenotypes. Here, we investigated epigenetic reprogramming (DNA methylation/hydroxymethylation) and gene expression across gametogenesis and embryogenesis of marine stickleback (Gasterosteus aculeatus) under three ocean warming scenarios (ambient, +1.5 and +4°C). We found that parental acclimation to ocean warming led to dynamic and temperature-sensitive reprogramming throughout offspring development. Both global methylation/hydroxymethylation and expression of genes involved in epigenetic modifications were strongly and differentially affected by the increased warming scenarios. Comparing transcriptomic profiles from gonads, mature gametes and early embryonic stages showed sex-specific accumulation and temperature sensitivity of several epigenetic actors. DNA methyltransferase induction was primarily maternally inherited (suggesting maternal control of remethylation), whereas induction of several histone-modifying enzymes was shaped by both parents. Importantly, massive, temperature-specific changes to the epigenetic landscape occurred in blastula, a critical stage for successful embryo development, which could, thus, translate to substantial consequences for offspring phenotype resilience in warming environments. In summary, our study identified key stages during gamete and embryo development with temperature-sensitive reprogramming and epigenetic gene regulation, reflecting potential 'windows of opportunity' for adaptive epigenetic responses under future climate change.
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Affiliation(s)
- Alexandre Fellous
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, List, Germany
| | - K Mathias Wegner
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, List, Germany
| | - Uwe John
- Ecological Chemistry Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Felix C Mark
- Integrative Ecophysiology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Lisa N S Shama
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, List, Germany
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Venney CJ, Sutherland BJG, Beacham TD, Heath DD. Population differences in Chinook salmon ( Oncorhynchus tshawytscha) DNA methylation: Genetic drift and environmental factors. Ecol Evol 2021; 11:6846-6861. [PMID: 34141260 PMCID: PMC8207424 DOI: 10.1002/ece3.7531] [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: 01/18/2021] [Revised: 03/10/2021] [Accepted: 03/17/2021] [Indexed: 12/18/2022] Open
Abstract
Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies have identified differences in methylation among populations of organisms, although most to date have been in plants and model animal species. Here we obtained eyed eggs from eight populations of Chinook salmon (Oncorhynchus tshawytscha) and assayed DNA methylation at 23 genes involved in development, immune function, stress response, and metabolism using a gene-targeted PCR-based assay for next-generation sequencing. Evidence for population differences in methylation was found at eight out of 23 gene loci after controlling for developmental timing in each individual. However, we found no correlation between freshwater environmental parameters and methylation variation among populations at those eight genes. A weak correlation was identified between pairwise DNA methylation dissimilarity among populations and pairwise F ST based on 15 microsatellite loci, indicating weak effects of genetic drift or geographic distance on methylation. The weak correlation was primarily driven by two genes, GTIIBS and Nkef. However, single-gene Mantel tests comparing methylation and pairwise F ST were not significant after Bonferroni correction. Thus, population differences in DNA methylation are more likely related to unmeasured oceanic environmental conditions, local adaptation, and/or genetic drift. DNA methylation is an additional mechanism that contributes to among population variation, with potential influences on organism phenotype, adaptive potential, and population resilience.
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Affiliation(s)
- Clare J. Venney
- Great Lakes Institute for Environmental ResearchUniversity of WindsorWindsorONCanada
| | | | - Terry D. Beacham
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Daniel D. Heath
- Great Lakes Institute for Environmental ResearchUniversity of WindsorWindsorONCanada
- Department of Integrative BiologyUniversity of WindsorWindsorONCanada
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8
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Brodie ED, Gregory B, Lisch D, Riddle NC. The epigenome and beyond: How does non-genetic inheritance change our view of evolution? Integr Comp Biol 2021; 61:2199-2207. [PMID: 34028538 DOI: 10.1093/icb/icab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evidence from across the tree of life suggests that epigenetic inheritance is more common than previously thought. If epigenetic inheritance is indeed as common as the data suggest, this finding has potentially important implications for evolutionary theory and our understanding of how evolution and adaptation progress. However, we currently lack an understanding of how common various epigenetic inheritance types are, and how they impact phenotypes. In this perspective, we review the open questions that need to be addressed to fully integrate epigenetic inheritance into evolutionary theory and to develop reliable predictive models for phenotypic evolution. We posit that addressing these challenges will require the collaboration of biologists from different disciplines and a focus on the exploration of data and phenomena without preconceived limits on potential mechanisms or outcomes.
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Affiliation(s)
- Edmund D Brodie
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Brian Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL
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9
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Voisin AS, Suarez Ulloa V, Stockwell P, Chatterjee A, Silvestre F. Genome-wide DNA methylation of the liver reveals delayed effects of early-life exposure to 17-α-ethinylestradiol in the self-fertilizing mangrove rivulus. Epigenetics 2021; 17:473-497. [PMID: 33892617 DOI: 10.1080/15592294.2021.1921337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Organisms exposed to endocrine disruptors in early life can show altered phenotype later in adulthood. Although the mechanisms underlying these long-term effects remain poorly understood, an increasing body of evidence points towards the potential role of epigenetic processes. In the present study, we exposed hatchlings of an isogenic lineage of the self-fertilizing fish mangrove rivulus for 28 days to 4 and 120 ng/L of 17-α-ethinylestradiol. After a recovery period of 140 days, reduced representation bisulphite sequencing (RRBS) was performed on the liver in order to assess the hepatic genome-wide methylation landscape. Across all treatment comparisons, a total of 146 differentially methylated fragments (DMFs) were reported, mostly for the group exposed to 4 ng/L, suggesting a non-monotonic effect of EE2 exposure. Gene ontology analysis revealed networks involved in lipid metabolism, cellular processes, connective tissue function, molecular transport and inflammation. The highest effect was reported for nipped-B-like protein B (NIPBL) promoter region after exposure to 4 ng/L EE2 (+ 21.9%), suggesting that NIPBL could be an important regulator for long-term effects of EE2. Our results also suggest a significant role of DNA methylation in intergenic regions and potentially in transposable elements. These results support the ability of early exposure to endocrine disruptors of inducing epigenetic alterations during adulthood, providing plausible mechanistic explanations for long-term phenotypic alteration. Additionally, this work demonstrates the usefulness of isogenic lineages of the self-fertilizing mangrove rivulus to better understand the biological significance of long-term alterations of DNA methylation by diminishing the confounding factor of genetic variability.
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Affiliation(s)
- Anne-Sophie Voisin
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Victoria Suarez Ulloa
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Peter Stockwell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Frédéric Silvestre
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
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Adrian-Kalchhauser I, Sultan SE, Shama LNS, Spence-Jones H, Tiso S, Keller Valsecchi CI, Weissing FJ. Understanding 'Non-genetic' Inheritance: Insights from Molecular-Evolutionary Crosstalk. Trends Ecol Evol 2020; 35:1078-1089. [PMID: 33036806 DOI: 10.1016/j.tree.2020.08.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022]
Abstract
Understanding the evolutionary and ecological roles of 'non-genetic' inheritance (NGI) is daunting due to the complexity and diversity of epigenetic mechanisms. We draw on insights from molecular and evolutionary biology perspectives to identify three general features of 'non-genetic' inheritance systems: (i) they are functionally interdependent with, rather than separate from, DNA sequence; (ii) precise mechanisms vary phylogenetically and operationally; and (iii) epigenetic elements are probabilistic, interactive regulatory factors and not deterministic 'epialleles' with defined genomic locations and effects. We discuss each of these features and offer recommendations for future empirical and theoretical research that implements a unifying inherited gene regulation (IGR) approach to studies of 'non-genetic' inheritance.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Centre for Fish and Wildlife Health, Department for Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland.
| | - Sonia E Sultan
- Biology Department, Wesleyan University, Middletown, CT 06459, USA
| | - Lisa N S Shama
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, Hafenstrasse 43, 25992 List, Germany
| | - Helen Spence-Jones
- Centre for Biological Diversity, School of Biology, University of St Andrews, St. Andrews, UK
| | - Stefano Tiso
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | | | - Franz J Weissing
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
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Navarro-Martín L, Martyniuk CJ, Mennigen JA. Comparative epigenetics in animal physiology: An emerging frontier. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100745. [PMID: 33126028 DOI: 10.1016/j.cbd.2020.100745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 12/19/2022]
Abstract
The unprecedented access to annotated genomes now facilitates the investigation of the molecular basis of epigenetic phenomena in phenotypically diverse animals. In this critical review, we describe the roles of molecular epigenetic mechanisms in regulating mitotically and meiotically stable spatiotemporal gene expression, phenomena that provide the molecular foundation for the intra-, inter-, and trans-generational emergence of physiological phenotypes. By focusing principally on emerging comparative epigenetic roles of DNA-level and transcriptome-level epigenetic mark dynamics in the emergence of phenotypes, we highlight the relationship between evolutionary conservation and innovation of specific epigenetic pathways, and their interplay as a priority for future study. This comparative approach is expected to significantly advance our understanding of epigenetic phenomena, as animals show a diverse array of strategies to epigenetically modify physiological responses. Additionally, we review recent technological advances in the field of molecular epigenetics (single-cell epigenomics and transcriptomics and editing of epigenetic marks) in order to (1) investigate environmental and endogenous factor dependent epigenetic mark dynamics in an integrative manner; (2) functionally test the contribution of specific epigenetic marks for animal phenotypes via genome and transcript-editing tools. Finally, we describe advantages and limitations of emerging animal models, which under the Krogh principle, may be particularly useful in the advancement of comparative epigenomics and its potential translational applications in animal science, ecotoxicology, ecophysiology, climate change science and wild-life conservation, as well as organismal health.
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Affiliation(s)
- Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON K1N6N5, Canada
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12
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Dalziel AC, Tirbhowan S, Drapeau HF, Power C, Jonah LS, Gbotsyo YA, Dion‐Côté A. Using asexual vertebrates to study genome evolution and animal physiology: Banded ( Fundulus diaphanus) x Common Killifish ( F. heteroclitus) hybrid lineages as a model system. Evol Appl 2020; 13:1214-1239. [PMID: 32684956 PMCID: PMC7359844 DOI: 10.1111/eva.12975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/27/2022] Open
Abstract
Wild, asexual, vertebrate hybrids have many characteristics that make them good model systems for studying how genomes evolve and epigenetic modifications influence animal physiology. In particular, the formation of asexual hybrid lineages is a form of reproductive incompatibility, but we know little about the genetic and genomic mechanisms by which this mode of reproductive isolation proceeds in animals. Asexual lineages also provide researchers with the ability to produce genetically identical individuals, enabling the study of autonomous epigenetic modifications without the confounds of genetic variation. Here, we briefly review the cellular and molecular mechanisms leading to asexual reproduction in vertebrates and the known genetic and epigenetic consequences of the loss of sex. We then specifically discuss what is known about asexual lineages of Fundulus diaphanus x F. heteroclitus to highlight gaps in our knowledge of the biology of these clones. Our preliminary studies of F. diaphanus and F. heteroclitus karyotypes from Porter's Lake (Nova Scotia, Canada) agree with data from other populations, suggesting a conserved interspecific chromosomal arrangement. In addition, genetic analyses suggest that: (a) the same major clonal lineage (Clone A) of F. diaphanus x F. heteroclitus has remained dominant over the past decade, (b) some minor clones have also persisted, (c) new clones may have recently formed, and iv) wild clones still mainly descend from F. diaphanus ♀ x F. heteroclitus ♂ crosses (96% in 2017-2018). These data suggest that clone formation may be a relatively rare, but continuous process, and there are persistent environmental or genetic factors causing a bias in cross direction. We end by describing our current research on the genomic causes and consequences of a transition to asexuality and the potential physiological consequences of epigenetic variation.
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Affiliation(s)
| | - Svetlana Tirbhowan
- Department of BiologySaint Mary's UniversityHalifaxNSCanada
- Département de biologieUniversité de MonctonMonctonNBCanada
| | | | - Claude Power
- Département de biologieUniversité de MonctonMonctonNBCanada
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13
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Berbel-Filho WM, Berry N, Rodríguez-Barreto D, Rodrigues Teixeira S, Garcia de Leaniz C, Consuegra S. Environmental enrichment induces intergenerational behavioural and epigenetic effects on fish. Mol Ecol 2020; 29:2288-2299. [PMID: 32434269 DOI: 10.1111/mec.15481] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/23/2020] [Accepted: 05/12/2020] [Indexed: 12/14/2022]
Abstract
Parental effects influence offspring phenotypes through pre- and post-natal routes but little is known about their molecular basis, and therefore their adaptive significance. Epigenetic modifications, which control gene expression without changes in the DNA sequence and are influenced by the environment, may contribute to parental effects. We investigated the effects of environmental enrichment on the behaviour, metabolic rate and brain DNA methylation patterns of parents and offspring of the highly inbreed mangrove killifish (Kryptolebias marmoratus). Parental fish reared in enriched environments had lower cortisol levels, lower metabolic rates and were more active and neophobic than those reared in barren environments. They also differed in 1,854 methylated cytosines (DMCs). Offspring activity and neophobia were determined by the parental environment. Among the DMCs of the parents, 98 followed the same methylation patterns in the offspring, three of which were significantly influenced by parental environments irrespective of their own rearing environment. Our results suggest that parental environment influences the behaviour and, to some extent, the brain DNA methylation patterns of the offspring.
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Affiliation(s)
- Waldir M Berbel-Filho
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, UK
| | - Nikita Berry
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, UK
| | - Deiene Rodríguez-Barreto
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, UK
| | | | - Carlos Garcia de Leaniz
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, UK
| | - Sofia Consuegra
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, UK
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14
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DNA methylation in the vertebrate germline: balancing memory and erasure. Essays Biochem 2020; 63:649-661. [PMID: 31755927 DOI: 10.1042/ebc20190038] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023]
Abstract
Cytosine methylation is a DNA modification that is critical for vertebrate development and provides a plastic yet stable information module in addition to the DNA code. DNA methylation memory establishment, maintenance and erasure is carefully balanced by molecular machinery highly conserved among vertebrates. In mammals, extensive erasure of epigenetic marks, including 5-methylcytosine (5mC), is a hallmark of early embryo and germline development. Conversely, global cytosine methylation patterns are preserved in at least some non-mammalian vertebrates over comparable developmental windows. The evolutionary mechanisms which drove this divergence are unknown, nevertheless a direct consequence of retaining epigenetic memory in the form of 5mC is the enhanced potential for transgenerational epigenetic inheritance (TEI). Given that DNA methylation dynamics remains underexplored in most vertebrate lineages, the extent of information transferred to offspring by epigenetic modification might be underestimated.
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15
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Biwer C, Kawam B, Chapelle V, Silvestre F. The Role of Stochasticity in the Origin of Epigenetic Variation in Animal Populations. Integr Comp Biol 2020; 60:1544-1557. [PMID: 32470118 DOI: 10.1093/icb/icaa047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epigenetic mechanisms such as DNA methylation modulate gene expression in a complex fashion are consequently recognized as among the most important contributors to phenotypic variation in natural populations of plants, animals, and microorganisms. Interactions between genetics and epigenetics are multifaceted and epigenetic variation stands at the crossroad between genetic and environmental variance, which make these mechanisms prominent in the processes of adaptive evolution. DNA methylation patterns depend on the genotype and can be reshaped by environmental conditions, while transgenerational epigenetic inheritance has been reported in various species. On the other hand, DNA methylation can influence the genetic mutation rate and directly affect the evolutionary potential of a population. The origin of epigenetic variance can be attributed to genetic, environmental, or stochastic factors. Generally less investigated than the first two components, variation lacking any predictable order is nevertheless present in natural populations and stochastic epigenetic variation, also referred to spontaneous epimutations, can sustain phenotypic diversity. Here, potential sources of such stochastic epigenetic variability in animals are explored, with a focus on DNA methylation. To this day, quantifying the importance of stochasticity in epigenetic variability remains a challenge. However, comparisons between the mutation and the epimutation rates showed a high level of the latter, suggesting a significant role of spontaneous epimutations in adaptation. The implications of stochastic epigenetic variability are multifold: by affecting development and subsequently phenotype, random changes in epigenetic marks may provide additional phenotypic diversity, which can help natural populations when facing fluctuating environments. In isogenic lineages and asexually reproducing organisms, poor or absent genetic diversity can hence be tolerated. Further implication of stochastic epigenetic variability in adaptation is found in bottlenecked invasive species populations and populations using a bet-hedging strategy.
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Affiliation(s)
| | | | | | - F Silvestre
- Institute of Earth, Life and Environment (ILEE), University of Namur, 61 rue de Bruxelles, Namur, 5000, Belgium
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16
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Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser JC, Wilson JY, Alm Rosenblad M, Burguera D, Gutnik S, Michiels N, Töpel M, Pankov K, Schloissnig S, Winkler S. The round goby genome provides insights into mechanisms that may facilitate biological invasions. BMC Biol 2020; 18:11. [PMID: 31992286 PMCID: PMC6988351 DOI: 10.1186/s12915-019-0731-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Background The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. Results We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby’s capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. Conclusions The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish. Electronic supplementary material The online version of this article (10.1186/s12915-019-0731-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland. .,University of Bern, Institute for Fish and Wildlife Health, Länggassstrasse 122, 3012, Bern, Austria.
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Tomas Larsson
- Department of Marine Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Zuzana Musilova
- Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Claire R Peart
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152 Planegg-, Martinsried, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Monica Hongroe Solbakken
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371, Oslo, Norway
| | - Jaanus Suurväli
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674, Köln, Germany
| | - Jean-Claude Walser
- Genetic Diversity Centre, ETH, Universitätsstrasse 16, 8092, Zurich, Switzerland
| | - Joanna Yvonne Wilson
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Magnus Alm Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden.,NBIS Bioinformatics Infrastructure for Life Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Demian Burguera
- Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Silvia Gutnik
- Biocenter, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Nico Michiels
- Institute of Evolution and Ecology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Mats Töpel
- University of Bern, Institute for Fish and Wildlife Health, Länggassstrasse 122, 3012, Bern, Austria
| | - Kirill Pankov
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Siegfried Schloissnig
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
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17
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Liu J, Hu H, Panserat S, Marandel L. Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications. Sci Rep 2020; 10:970. [PMID: 31969623 PMCID: PMC6976628 DOI: 10.1038/s41598-020-57753-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 12/20/2019] [Indexed: 01/11/2023] Open
Abstract
DNA methylation is an important epigenetic mechanism involved in many biological processes, i.e. gametogenesis and embryonic development. However, increased copy numbers of DNA methylation related genes (dnmt, tet and tdg) have been found during chordate evolution due to successive whole genome duplication (WGD) events. Their evolutionary history and phylogenetic relationships remain unclear. The present study is the first to clarify the evolutionary history of DNA methylation genes in chordates. In particular, our results highlight the fixation of several dnmt3-related genes following successive WGD throughout evolution. The rainbow trout genome offered a unique opportunity to study the early evolutionary fates of duplicated genes due to a recent round of WGD at the radiation of salmonids. Differences highlighted in transcriptional patterns of these genes during gametogenesis and ontogenesis in trout indicated that they might be subjected to sub- or neo-functionalisation after WDG. The fixation of multiple dnmt3 genes in genomes after WGD could contribute to the diversification and plastic adaptation of the teleost.
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Affiliation(s)
- Jingwei Liu
- INRAE, Univ Pau & Pays de l'Adour, E2S-UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France
| | - Huihua Hu
- INRAE, Univ Pau & Pays de l'Adour, E2S-UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Stéphane Panserat
- INRAE, Univ Pau & Pays de l'Adour, E2S-UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France
| | - Lucie Marandel
- INRAE, Univ Pau & Pays de l'Adour, E2S-UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France.
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18
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Zhao L, Li Y, Lou J, Yang Z, Liao H, Fu Q, Guo Z, Lian S, Hu X, Bao Z. Transcriptomic Profiling Provides Insights into Inbreeding Depression in Yesso Scallop Patinopecten yessoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:623-633. [PMID: 31300903 DOI: 10.1007/s10126-019-09907-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/30/2019] [Indexed: 06/10/2023]
Abstract
Inbreeding often causes a decline in biological fitness, known as inbreeding depression. In genetics study, inbreeding coefficient f gives the proportion by which the heterozygosity of an individual is reduced by inbreeding. With the development of high-throughput sequencing, researchers were able to perform deep approaches to investigate which genes are affected by inbreeding and reveal some molecular underpinnings of inbreeding depression. As one commercially important species, Yesso scallop Patinopecten yessoensis confront the same dilemma of inbreeding depression. To examine how inbreeding affects gene expression, we compared the transcriptome of two experimentally selfing families with inbreeding coefficient f reached 0.5 as well as one natural population (f ≈ 0) of P. yessoensis. A total of 24 RNA-Seq libraries were constructed using scallop adductor muscle, and eventually 676.56 M (96.85%) HQ reads were acquired. Based on differential gene analysis, we were able to identify nine common differentially expressed genes (DEGs) across the top-ranked 30 DEGs in both selfing families in comparation with the natural population. Remarkable, through weighted gene co-expression network analysis (WGCNA), five common DEGs were found enriched in the most significant inbreeding related functional module M14 (FDR = 1.64E-156), including SREBP1, G3BP2, SBK1, KIAA1161, and AATs-Glupro. These five genes showed significantly higher expression in self-bred progeny. Suggested by the genetic functional analysis, up-regulated SREBP1, G3BP2, and KIAA1161 may suggest a perturbing lipid metabolism, a severe inframammary reaction or immune response, and a stress-responsive behavior. Besides, the significant higher SBK1 and AATs-Glupro may reflect the abnormal cellular physiological situation. Together, these genetic aberrant transcriptomic performances may contribute to inbreeding depression in P. yessoensis, deteriorating the stress tolerance and survival phenotype in self-bred progeny. Our results would lay a foundation for further comprehensive understanding of bivalve inbreeding depression, which may potentially benefit the genetic breeding for scallop aquaculture.
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Affiliation(s)
- Liang Zhao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yangping Li
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Jiarun Lou
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Zhihui Yang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Huan Liao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Qiang Fu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Zhenyi Guo
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Shanshan Lian
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Xiaoli Hu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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19
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Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas. Genes (Basel) 2019; 10:genes10090695. [PMID: 31509985 PMCID: PMC6771004 DOI: 10.3390/genes10090695] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 12/20/2022] Open
Abstract
Histone methylation patterns are important epigenetic regulators of mammalian development, notably through stem cell identity maintenance by chromatin remodeling and transcriptional control of pluripotency genes. But, the implications of histone marks are poorly understood in distant groups outside vertebrates and ecdysozoan models. However, the development of the Pacific oyster Crassostrea gigas is under the strong epigenetic influence of DNA methylation, and Jumonji histone-demethylase orthologues are highly expressed during C. gigas early life. This suggests a physiological relevance of histone methylation regulation in oyster development, raising the question of functional conservation of this epigenetic pathway in lophotrochozoan. Quantification of histone methylation using fluorescent ELISAs during oyster early life indicated significant variations in monomethyl histone H3 lysine 4 (H3K4me), an overall decrease in H3K9 mono- and tri-methylations, and in H3K36 methylations, respectively, whereas no significant modification could be detected in H3K27 methylation. Early in vivo treatment with the JmjC-specific inhibitor Methylstat induced hypermethylation of all the examined histone H3 lysines and developmental alterations as revealed by scanning electronic microscopy. Using microarrays, we identified 376 genes that were differentially expressed under methylstat treatment, which expression patterns could discriminate between samples as indicated by principal component analysis. Furthermore, Gene Ontology revealed that these genes were related to processes potentially important for embryonic stages such as binding, cell differentiation and development. These results suggest an important physiological significance of histone methylation in the oyster embryonic and larval life, providing, to our knowledge, the first insights into epigenetic regulation by histone methylation in lophotrochozoan development.
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20
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Berbel-Filho WM, Rodríguez-Barreto D, Berry N, Garcia De Leaniz C, Consuegra S. Contrasting DNA methylation responses of inbred fish lines to different rearing environments. Epigenetics 2019; 14:939-948. [PMID: 31144573 DOI: 10.1080/15592294.2019.1625674] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Epigenetic mechanisms generate plastic phenotypes that can become locally adapted across environments. Disentangling genomic from epigenomic variation is challenging in sexual species due to genetic variation among individuals, but it is easier in self-fertilizing species. We analysed DNA methylation patterns of two highly inbred strains of a naturally self-fertilizing fish reared in two contrasting environments to investigate the obligatory (genotype-dependent), facilitated (partially depend on the genotype) or pure (genotype-independent) nature of the epigenetic variation. We found higher methylation differentiation between genotypes than between environments. Most methylation differences between environments common to both strains followed a pattern where the two genotypes (inbred lines) responded to the same environmental context with contrasting DNA methylation levels (facilitated epialleles). Our findings suggest that, at least in part, DNA methylation could depend on the dynamic interaction between the genotype and the environment, which could explain the plasticity of epigenetically mediated phenotypes.
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Affiliation(s)
| | | | - Nikita Berry
- a Department of Biosciences, Swansea University , Swansea , UK
| | | | - Sofia Consuegra
- a Department of Biosciences, Swansea University , Swansea , UK
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21
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Voisin AS, Kültz D, Silvestre F. Early-life exposure to the endocrine disruptor 17-α-ethinylestradiol induces delayed effects in adult brain, liver and ovotestis proteomes of a self-fertilizing fish. J Proteomics 2018; 194:112-124. [PMID: 30550985 DOI: 10.1016/j.jprot.2018.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 11/23/2018] [Accepted: 12/07/2018] [Indexed: 01/29/2023]
Abstract
Early-life represents a critically sensitive window to endocrine disrupting chemicals, potentially leading to long-term repercussions on the phenotype later in life. The mechanisms underlying this phenomenon, referred to as the Developmental Origins of Health and Disease (DOHaD), are still poorly understood. To gain molecular understanding of these effects, we exposed mangrove rivulus (Kryptolebias marmoratus) for 28 days post hatching (dph) to 4 and 120 ng/L 17-α-ethinylestradiol, a model xenoestrogen. After 28 days, fish were raised for 140 days in clean water and we performed quantitative label-free proteomics on brain, liver and ovotestis of 168 dph adults. A total of 820, 888 and 420 proteins were robustly identified in the brain, liver and ovotestis, respectively. Effects of 17-α-ethinylestradiol were tissue and dose-dependent: a total of 31, 51 and 18 proteins were differentially abundant at 4 ng/L in the brain, liver and ovotestis, respectively, compared to 20, 25 and 39 proteins at 120 ng/L. Our results suggest that estrogen-responsive pathways, such as lipid metabolism, inflammation, and the innate immune system were affected months after the exposure. In addition, the potential perturbation of S-adenosylmethionine metabolism encourages future studies to investigate the role of DNA methylation in mediating the long-term effects of early-life exposures. SIGNIFICANCE: The Developmental Origins of Health and Disease (DOHaD) states that early life stages of humans and animals are sensitive to environmental stressors and can develop health issues later in life, even if the stress has ceased. Molecular mechanisms supporting DOHaD are still unclear. The mangrove rivulus is a new fish model species naturally reproducing by self-fertilization, making it possible to use isogenic lineages in which all individuals are highly homozygous. This species therefore permits to strongly reduce the confounding factor of genetic variability in order to investigate the effects of environmental stress on the phenotype. After characterizing the molecular phenotype of brain, liver and ovotestis, we obtained true proteomic reaction norms of these three organs in adults after early life stages have been exposed to the common endocrine disruptor 17-α-ethinylestradiol (EE2). Our study demonstrates long-term effects of early-life endocrine disruption at the proteomic level in diverse estrogen-responsive pathways 5 months after the exposure. The lowest tested and environmentally relevant concentration of 4 ng/L had the highest impact on the proteome in brain and liver, highlighting the potency of endocrine disruptors at low concentrations.
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Affiliation(s)
- Anne-Sophie Voisin
- Laboratory of Evolutionary and Adaptive Physiology - Institute of Life, Earth and Environment - University of Namur, 61 Rue de Bruxelles, B5000 Namur, Belgium.
| | - Dietmar Kültz
- Department of Animal Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Frédéric Silvestre
- Laboratory of Evolutionary and Adaptive Physiology - Institute of Life, Earth and Environment - University of Namur, 61 Rue de Bruxelles, B5000 Namur, Belgium
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22
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Falisse E, Ducos B, Stockwell PA, Morison IM, Chatterjee A, Silvestre F. DNA methylation and gene expression alterations in zebrafish early-life stages exposed to the antibacterial agent triclosan. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:1867-1877. [PMID: 30408875 DOI: 10.1016/j.envpol.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/07/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
There is increasing evidence that toxicant exposure can alter DNA methylation profile, one of the main epigenetic mechanisms, particularly during embryogenesis when DNA methylation patterns are being established. In order to investigate the effects of the antibacterial agent Triclosan on DNA methylation and its correlation with gene expression, zebrafish embryos were exposed during 7 days post-fertilization (starting at maximum 8-cells stage) to 50 and 100 μg/l, two conditions for which increased sensitivity and acclimation have been respectively reported. Although global DNA methylation was not significantly affected, a total of 171 differentially methylated fragments were identified by Reduced Representation Bisulfite Sequencing. The majority of these fragments were found between the two exposed groups, reflecting dose-dependant specific responses. Gene ontology analysis revealed that pathways involved in TGF-β signaling were enriched in larvae exposed to 50 μg/l, while de novo pyrimidine biosynthesis functions were overrepresented in fish exposed to 100 μg/l. In addition, gene expression analysis revealed a positive correlation between mRNA levels and DNA methylation patterns in introns, together with significant alterations of the transcription of genes involved in nervous system development, transcriptional factors and histone methyltransferases. Overall this work provides evidence that Triclosan alters DNA methylation in zebrafish exposed during embryogenesis as well as related genes expression and proposes concentration specific modes of action. Further studies will investigate the possible long-term consequences of these alterations, i.e. latent defects associated with developmental exposure and transgenerational effects, and the possible implications in terms of fitness and adaptation to environmental pollutants.
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Affiliation(s)
- Elodie Falisse
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment - University of Namur, 61 rue de Bruxelles, 5000, Namur, Belgium
| | - Bertrand Ducos
- High Throughput qPCR Facility of ENS, IBENS, 46 rue d'Ulm, 75005, PARIS, France
| | - Peter A Stockwell
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin, 9016, New Zealand
| | - Ian M Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin, 9054, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin, 9054, New Zealand
| | - Frédéric Silvestre
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment - University of Namur, 61 rue de Bruxelles, 5000, Namur, Belgium.
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23
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Carion A, Hétru J, Markey A, Suarez-Ulloa V, Frédéric S. Behavioral effects of the neurotoxin -N-methylamino- L-alanine on the mangrove rivulus ( Kryptolebias marmoratus) larvae. J Xenobiot 2018; 8:7820. [PMID: 30701065 PMCID: PMC6343106 DOI: 10.4081/xeno.2018.7820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/17/2018] [Indexed: 11/23/2022] Open
Abstract
Mangrove rivulus, Kryptolebias marmoratus, is a hermaphrodite fish capable of self-fertilization. This particularity allows to naturally produce highly homozygous and isogenic individuals. Despite the low genetic diversity, rivulus can live in extremely variable environments and adjust its phenotype accordingly. This species represents a unique opportunity to clearly distinguish the genetic and non-genetic factors implicated in adaptation and evolution, such as epigenetic mechanisms. It is thus a great model in aquatic ecotoxicology to investigate the effects of xenobiotics on the epigenome, and their potential long-term impacts. In the present study, we used the mangrove rivulus to investigate the effects of the neurotoxin b-N-methylamino-L-alanine (BMAA) on larvae behaviors after 7 days exposure to two sub-lethal concentrations. Results show that BMAA can affect the maximal speed and prey capture (trials and failures), suggesting potential impacts on the organism’s fitness.
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Affiliation(s)
- Alessandra Carion
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Julie Hétru
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Angèle Markey
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Victoria Suarez-Ulloa
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Silvestre Frédéric
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
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24
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Legradi JB, Di Paolo C, Kraak MHS, van der Geest HG, Schymanski EL, Williams AJ, Dingemans MML, Massei R, Brack W, Cousin X, Begout ML, van der Oost R, Carion A, Suarez-Ulloa V, Silvestre F, Escher BI, Engwall M, Nilén G, Keiter SH, Pollet D, Waldmann P, Kienle C, Werner I, Haigis AC, Knapen D, Vergauwen L, Spehr M, Schulz W, Busch W, Leuthold D, Scholz S, vom Berg CM, Basu N, Murphy CA, Lampert A, Kuckelkorn J, Grummt T, Hollert H. An ecotoxicological view on neurotoxicity assessment. ENVIRONMENTAL SCIENCES EUROPE 2018; 30:46. [PMID: 30595996 PMCID: PMC6292971 DOI: 10.1186/s12302-018-0173-x] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/31/2018] [Indexed: 05/04/2023]
Abstract
The numbers of potential neurotoxicants in the environment are raising and pose a great risk for humans and the environment. Currently neurotoxicity assessment is mostly performed to predict and prevent harm to human populations. Despite all the efforts invested in the last years in developing novel in vitro or in silico test systems, in vivo tests with rodents are still the only accepted test for neurotoxicity risk assessment in Europe. Despite an increasing number of reports of species showing altered behaviour, neurotoxicity assessment for species in the environment is not required and therefore mostly not performed. Considering the increasing numbers of environmental contaminants with potential neurotoxic potential, eco-neurotoxicity should be also considered in risk assessment. In order to do so novel test systems are needed that can cope with species differences within ecosystems. In the field, online-biomonitoring systems using behavioural information could be used to detect neurotoxic effects and effect-directed analyses could be applied to identify the neurotoxicants causing the effect. Additionally, toxic pressure calculations in combination with mixture modelling could use environmental chemical monitoring data to predict adverse effects and prioritize pollutants for laboratory testing. Cheminformatics based on computational toxicological data from in vitro and in vivo studies could help to identify potential neurotoxicants. An array of in vitro assays covering different modes of action could be applied to screen compounds for neurotoxicity. The selection of in vitro assays could be guided by AOPs relevant for eco-neurotoxicity. In order to be able to perform risk assessment for eco-neurotoxicity, methods need to focus on the most sensitive species in an ecosystem. A test battery using species from different trophic levels might be the best approach. To implement eco-neurotoxicity assessment into European risk assessment, cheminformatics and in vitro screening tests could be used as first approach to identify eco-neurotoxic pollutants. In a second step, a small species test battery could be applied to assess the risks of ecosystems.
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Affiliation(s)
- J. B. Legradi
- Institute for Environmental Research, Department of Ecosystem Analysis, ABBt–Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- Environment and Health, VU University, 1081 HV Amsterdam, The Netherlands
| | - C. Di Paolo
- Institute for Environmental Research, Department of Ecosystem Analysis, ABBt–Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - M. H. S. Kraak
- FAME-Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands
| | - H. G. van der Geest
- FAME-Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands
| | - E. L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
| | - A. J. Williams
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, 109 T.W. Alexander Dr., Research Triangle Park, NC 27711 USA
| | - M. M. L. Dingemans
- KWR Watercycle Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, The Netherlands
| | - R. Massei
- Department Effect-Directed Analysis, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig, Germany
| | - W. Brack
- Department Effect-Directed Analysis, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig, Germany
| | - X. Cousin
- Ifremer, UMR MARBEC, Laboratoire Adaptation et Adaptabilités des Animaux et des Systèmes, Route de Maguelone, 34250 Palavas-les-Flots, France
- INRA, UMR GABI, INRA, AgroParisTech, Domaine de Vilvert, Batiment 231, 78350 Jouy-en-Josas, France
| | - M.-L. Begout
- Ifremer, Laboratoire Ressources Halieutiques, Place Gaby Coll, 17137 L’Houmeau, France
| | - R. van der Oost
- Department of Technology, Research and Engineering, Waternet Institute for the Urban Water Cycle, Amsterdam, The Netherlands
| | - A. Carion
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium
| | - V. Suarez-Ulloa
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium
| | - F. Silvestre
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium
| | - B. I. Escher
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Eberhard Karls University Tübingen, Environmental Toxicology, Center for Applied Geosciences, 72074 Tübingen, Germany
| | - M. Engwall
- MTM Research Centre, School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | - G. Nilén
- MTM Research Centre, School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | - S. H. Keiter
- MTM Research Centre, School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | - D. Pollet
- Faculty of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295 Darmstadt, Germany
| | - P. Waldmann
- Faculty of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295 Darmstadt, Germany
| | - C. Kienle
- Swiss Centre for Applied Ecotoxicology Eawag-EPFL, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - I. Werner
- Swiss Centre for Applied Ecotoxicology Eawag-EPFL, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - A.-C. Haigis
- Institute for Environmental Research, Department of Ecosystem Analysis, ABBt–Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - D. Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, University of Antwerp, Wilrijk, Belgium
| | - L. Vergauwen
- Zebrafishlab, Veterinary Physiology and Biochemistry, University of Antwerp, Wilrijk, Belgium
| | - M. Spehr
- Institute for Biology II, Department of Chemosensation, RWTH Aachen University, Aachen, Germany
| | - W. Schulz
- Zweckverband Landeswasserversorgung, Langenau, Germany
| | - W. Busch
- Department of Bioanalytical Ecotoxicology, UFZ–Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - D. Leuthold
- Department of Bioanalytical Ecotoxicology, UFZ–Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - S. Scholz
- Department of Bioanalytical Ecotoxicology, UFZ–Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - C. M. vom Berg
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Dübendorf, 8600 Switzerland
| | - N. Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - C. A. Murphy
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, USA
| | - A. Lampert
- Institute of Physiology (Neurophysiology), Aachen, Germany
| | - J. Kuckelkorn
- Section Toxicology of Drinking Water and Swimming Pool Water, Federal Environment Agency (UBA), Heinrich-Heine-Str. 12, 08645 Bad Elster, Germany
| | - T. Grummt
- Section Toxicology of Drinking Water and Swimming Pool Water, Federal Environment Agency (UBA), Heinrich-Heine-Str. 12, 08645 Bad Elster, Germany
| | - H. Hollert
- Institute for Environmental Research, Department of Ecosystem Analysis, ABBt–Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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