1
|
Jeremias G, Muñiz-González AB, Mendes Gonçalves FJ, Martínez-Guitarte JL, Asselman J, Luísa Pereira J. History of exposure to copper influences transgenerational gene expression responses in Daphnia magna. Epigenetics 2024; 19:2296275. [PMID: 38154067 PMCID: PMC10761054 DOI: 10.1080/15592294.2023.2296275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/13/2023] [Indexed: 12/30/2023] Open
Abstract
The establishment of transgenerational effects following chemical exposure is a powerful phenomenon, capable of modulating ecosystem health beyond exposure periods. This study assessed the transgenerational effects occurring due to copper exposure in the invertebrate D. magna at the transcriptional level, while evaluating the role of exposure history on such responses. Thus, daphnids acclimated for several generations in a copper vs. clean medium were then exposed for one generation (F0) to this metal, and monitored for the following non-exposed generations (F1, F2 and F3). Organisms differing in exposure histories showed remarkably different transcriptional profiles at the F0, with naïve organisms being more profoundly affected. These trends were confirmed for F3 treatments, which presented different transcriptional patterns for genes involved in detoxification, oxidative stress, DNA damage repair, circadian clock functioning and epigenetic regulation. Furthermore, regardless of exposure history, a great number of histone modifier genes were always found transcriptionally altered, thus suggesting the involvement of histone modifications in the response of Daphnia to metal exposure. Lastly, remarkably distinct transgenerational transcriptional responses were found between naïve and non-naïve organisms, thereby highlighting the influence of exposure history on gene expression and confirming the capacity of metals to determine transgenerational transcriptional effects across non-exposed generations.
Collapse
Affiliation(s)
- Guilherme Jeremias
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Ana-Belén Muñiz-González
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
- Biology & Toxicology Group, Department of Mathematics, Physics, and Fluids, National Distance Education University (UNED), Madrid, Spain
| | | | - José-Luis Martínez-Guitarte
- Biology & Toxicology Group, Department of Mathematics, Physics, and Fluids, National Distance Education University (UNED), Madrid, Spain
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Ostend, Belgium
| | - Joana Luísa Pereira
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
| |
Collapse
|
2
|
Yoon K, Williams S, Duncan EJ. DNA methylation machinery is involved in development and reproduction in the viviparous pea aphid (Acyrthosiphon pisum). INSECT MOLECULAR BIOLOGY 2024. [PMID: 38923717 DOI: 10.1111/imb.12936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Epigenetic mechanisms, such as DNA methylation, have been proposed to mediate plastic responses in insects. The pea aphid (Acyrthosiphon pisum), like the majority of extant aphids, displays cyclical parthenogenesis - the ability of mothers to switch the reproductive mode of their offspring from reproducing parthenogenetically to sexually in response to environmental cues. The pea aphid genome encodes two paralogs of the de novo DNA methyltransferase gene, dnmt3a and dnmt3x. Here we show, using phylogenetic analysis, that this gene duplication event occurred at least 150 million years ago, likely after the divergence of the lineage leading to the Aphidomorpha (phylloxerans, adelgids and true aphids) from that leading to the scale insects (Coccomorpha) and that the two paralogs are maintained in the genomes of all aphids examined. We also show that the mRNA of both dnmt3 paralogs is maternally expressed in the viviparous aphid ovary. During development both paralogs are expressed in the germ cells of embryos beginning at stage 5 and persisting throughout development. Treatment with 5-azactyidine, a chemical that generally inhibits the DNA methylation machinery, leads to defects of oocytes and early-stage embryos and causes a proportion of later stage embryos to be born dead or die soon after birth. These phenotypes suggest a role for DNA methyltransferases in reproduction, consistent with that seen in other insects. Taking the vast evolutionary history of the dnmt3 paralogs, and the localisation of their mRNAs in the ovary, we suggest there is a role for dnmt3a and/or dnmt3x in early development, and a role for DNA methylation machinery in reproduction and development of the viviparous pea aphid.
Collapse
Affiliation(s)
- Kane Yoon
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Stephanie Williams
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Elizabeth J Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| |
Collapse
|
3
|
Swaegers J, De Cupere S, Gaens N, Lancaster LT, Carbonell JA, Sánchez Guillén RA, Stoks R. Plasticity and associated epigenetic mechanisms play a role in thermal evolution during range expansion. Evol Lett 2024; 8:76-88. [PMID: 38370551 PMCID: PMC10872138 DOI: 10.1093/evlett/qrac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/06/2022] [Accepted: 12/28/2022] [Indexed: 02/20/2024] Open
Abstract
Due to global change, many species are shifting their distribution and are thereby confronted with novel thermal conditions at the moving range edges. Especially during the initial phases of exposure to a new environment, it has been hypothesized that plasticity and associated epigenetic mechanisms enable species to cope with environmental change. We tested this idea by capitalizing on the well-documented southward range expansion of the damselfly Ischnura elegans from France into Spain where the species invaded warmer regions in the 1950s in eastern Spain (old edge region) and in the 2010s in central Spain (new edge region). Using a common garden experiment at rearing temperatures matching the ancestral and invaded thermal regimes, we tested for evolutionary changes in (thermal plasticity in) larval life history and heat tolerance in these expansion zones. Through the use of de- and hypermethylating agents, we tested whether epigenetic mechanisms play a role in enabling heat tolerance during expansion. We used the phenotype of the native sister species in Spain, I. graellsii, as proxy for the locally adapted phenotype. New edge populations converged toward the phenotype of the native species through plastic thermal responses in life history and heat tolerance while old edge populations (partly) constitutively evolved a faster life history and higher heat tolerance than the core populations, thereby matching the native species. Only the heat tolerance of new edge populations increased significantly when exposed to the hypermethylating agent. This suggests that the DNA methylation machinery is more amenable to perturbation at the new edge and shows it is able to play a role in achieving a higher heat tolerance. Our results show that both (evolved) plasticity as well as associated epigenetic mechanisms are initially important when facing new thermal regimes but that their importance diminishes with time.
Collapse
Affiliation(s)
- Janne Swaegers
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Leuven, Belgium
| | - Simon De Cupere
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Leuven, Belgium
| | - Noah Gaens
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Leuven, Belgium
| | - Lesley T Lancaster
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - José A Carbonell
- Department of Zoology, Faculty of Biology, University of Seville, Seville, Spain
| | | | - Robby Stoks
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Leuven, Belgium
| |
Collapse
|
4
|
Bogan SN, Strader ME, Hofmann GE. Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity. BMC Biol 2023; 21:149. [PMID: 37365578 DOI: 10.1186/s12915-023-01645-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Epigenetic processes are proposed to be a mechanism regulating gene expression during phenotypic plasticity. However, environmentally induced changes in DNA methylation exhibit little-to-no association with differential gene expression in metazoans at a transcriptome-wide level. It remains unexplored whether associations between environmentally induced differential methylation and expression are contingent upon other epigenomic processes such as chromatin accessibility. We quantified methylation and gene expression in larvae of the purple sea urchin Strongylocentrotus purpuratus exposed to different ecologically relevant conditions during gametogenesis (maternal conditioning) and modeled changes in gene expression and splicing resulting from maternal conditioning as functions of differential methylation, incorporating covariates for genomic features and chromatin accessibility. We detected significant interactions between differential methylation, chromatin accessibility, and genic feature type associated with differential expression and splicing. RESULTS Differential gene body methylation had significantly stronger effects on expression among genes with poorly accessible transcriptional start sites while baseline transcript abundance influenced the direction of this effect. Transcriptional responses to maternal conditioning were 4-13 × more likely when accounting for interactions between methylation and chromatin accessibility, demonstrating that the relationship between differential methylation and gene regulation is partially explained by chromatin state. CONCLUSIONS DNA methylation likely possesses multiple associations with gene regulation during transgenerational plasticity in S. purpuratus and potentially other metazoans, but its effects are dependent on chromatin accessibility and underlying genic features.
Collapse
Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA.
| | - Marie E Strader
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
- Department of Biology, Texas A&M University, College Station, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
| |
Collapse
|
5
|
Pham K, Ho L, D'Incal CP, De Cock A, Berghe WV, Goethals P. Epigenetic analytical approaches in ecotoxicological aquatic research. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 330:121737. [PMID: 37121302 DOI: 10.1016/j.envpol.2023.121737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/15/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Environmental epigenetics has become a key research focus in global climate change studies and environmental pollutant investigations impacting aquatic ecosystems. Specifically, triggered by environmental stress conditions, intergenerational DNA methylation changes contribute to biological adaptive responses and survival of organisms to increase their tolerance towards these conditions. To critically review epigenetic analytical approaches in ecotoxicological aquatic research, we evaluated 78 publications reported over the past five years (2016-2021) that applied these methods to investigate the responses of aquatic organisms to environmental changes and pollution. The results show that DNA methylation appears to be the most robust epigenetic regulatory mark studied in aquatic animals. As such, multiple DNA methylation analysis methods have been developed in aquatic organisms, including enzyme restriction digestion-based and methyl-specific immunoprecipitation methods, and bisulfite (in)dependent sequencing strategies. In contrast, only a handful of aquatic studies, i.e. about 15%, have been focusing on histone variants and post-translational modifications due to the lack of species-specific affinity based immunological reagents, such as specific antibodies for chromatin immunoprecipitation applications. Similarly, ncRNA regulation remains as the least popular method used in the field of environmental epigenetics. Insights into the opportunities and challenges of the DNA methylation and histone variant analysis methods as well as decreasing costs of next generation sequencing approaches suggest that large-scale epigenetic environmental studies in model and non-model organisms will soon become available in the near future. Moreover, antibody-dependent and independent methods, such as mass spectrometry-based methods, can be used as an alternative epigenetic approach to characterize global changes of chromatin histone modifications in future aquatic research. Finally, a systematic guide for DNA methylation and histone variant methods is offered for ecotoxicological aquatic researchers to select the most relevant epigenetic analytical approach in their research.
Collapse
Affiliation(s)
- Kim Pham
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium.
| | - Long Ho
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - Claudio Peter D'Incal
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Andrée De Cock
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Peter Goethals
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| |
Collapse
|
6
|
Wang X, Cong R, Li A, Wang W, Zhang G, Li L. Experimental DNA Demethylation Reduces Expression Plasticity and Thermal Tolerance in Pacific Oysters. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023:10.1007/s10126-023-10208-5. [PMID: 37079122 DOI: 10.1007/s10126-023-10208-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Increasing seawater temperatures pose a great threat to marine organisms, especially those settled in fluctuating intertidal areas. DNA methylation, which can be induced by environmental variation, can influence gene expression and mediate phenotypic plasticity. However, the regulatory mechanisms of DNA methylation in gene expression-mediated adaptation to environmental stress have rarely been elucidated. In this study, DNA demethylation experiments were conducted on a typical intertidal species, the Pacific oyster (Crassostrea gigas), to determine the direct role of DNA methylation in regulating gene expression and adaptability under thermal stress. The global methylation level and the expression level of DNA methyltransferases (DNMT1, DNMT3a) showed an accordant variation trend under high temperatures, supporting that the genomic methylation status was catalyzed by DNMTs. DNA methylation inhibitor 5-Azacytidine (5-Aza) effectively inhibited DNA methylation level and decreased methylation plasticity at the 6th hour in thermal conditions. In total, 88 genes were identified as candidate DNA methylation-regulated thermal response genes; they exhibited reduced expression plasticity in response to heat stress, possibly caused by the decreased methylation plasticity. Post-heat shock, the thermal tolerance indicated by the survival curve was reduced when oysters were pretreated with 5-Aza, meaning that DNA demethylation negatively affected thermal adaptation in oysters. This study provides direct evidence for the crucial role of DNA methylation in mediating stress adaptation in marine invertebrates and contributes to the theoretical foundations underlying marine resource conservation and aquaculture.
Collapse
Affiliation(s)
- Xinxing Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China
| | - Rihao Cong
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China
| | - Ao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China
| | - Wei Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China.
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China.
| |
Collapse
|
7
|
Cuiping H, Na Z, Limei H, Tang T, Yang Y, Xiangping N. Assessment of ecotoxicity effects of aspirin on non-target organism (Daphnia magna) via analysis of the responses of oxidative stress, DNA methylation-related genes expressions and life traits changes. ECOTOXICOLOGY (LONDON, ENGLAND) 2023; 32:137-149. [PMID: 36680667 DOI: 10.1007/s10646-023-02624-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Aspirin (acetylsalicylic acid, ASA), a widely used non-steroidal anti-inflammatory drug, was frequently detected in aquatic environments around the world. However, information on the potential toxic effects of aspirin on non-target aquatic invertebrates is limited. In the present study, we investigated the effects of ASA on the transcriptional expressions of antioxidant genes (Nrf2, Keap1, HO-1, GCLC, GPx, TRX, TrxR and Prx1) and DNA methylation genes (DNMT1, DNMT3 and TET2) in Daphnia magna (D. magna)for 24, 48 and 96 h and the changes of antioxidant enzymatic activity and GSH, MDA content for 48 h. The effects of ASA on the life traits of D. magna were also addressed via a 21-days chronic toxicity test. Results showed that the expressions of Nrf2 and its target genes (HO-1, GPx and TrxR, GCLC, TRX and Prx1) were induced to different degrees at 48 h and/or 96 h. The activity of antioxidant enzymes (SOD, CAT, GST and GPx) and MDA content increased but GSH content decreased, indicating that ASA caused oxidative stress in D. magna. ASA also changed the expression of DNA methylation genes, such as DNMT and TET2, in D. magna. We speculated that ASA may affect the antioxidant system responses through regulation of Nrf2/Keap1 signaling pathway, and/or through indirectly influencing DNA methylation levels by DNMT and TET gene expression, but the detailed mechanism needs further investigations. Chronic exposure to ASA for 21 days caused inhibitions on the growth, reproduction and behavior of D. magna (e.g., delaying days to the first brood and shortening the body length). In summary, ASA significantly affected the antioxidant responses of D. magna, and negatively disturbed its life traits in growth, development and reproduction.
Collapse
Affiliation(s)
- He Cuiping
- Department of Ecology, Jinan University, Guangzhou, 510632, China
| | - Zhao Na
- Department of Ecology, Jinan University, Guangzhou, 510632, China
| | - Hu Limei
- Department of Ecology, Jinan University, Guangzhou, 510632, China
| | - Tianli Tang
- Department of Ecology, Jinan University, Guangzhou, 510632, China
| | - Yufeng Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, 510632, China
| | - Nie Xiangping
- Department of Ecology, Jinan University, Guangzhou, 510632, China.
| |
Collapse
|
8
|
Jeremias G, Veloso T, Gonçalves FJM, Van Nieuwerburgh F, Pereira JL, Asselman J. Multigenerational DNA methylation responses to copper exposure in Daphnia: Potential targets for epigenetic biomarkers? CHEMOSPHERE 2022; 308:136231. [PMID: 36055596 DOI: 10.1016/j.chemosphere.2022.136231] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Epigenetic mechanisms are moving to the forefront of environmental sciences, as environmentally induced epigenetic changes shape biological responses to chemical contamination. This work focused on Daphnia as a representative of potentially threatened freshwater biota, aiming to gain an insight into the involvement of epigenetic mechanisms in their response and eventual adaptation to metal contamination. Copper-induced DNA methylation changes, their potential transgenerational inheritance, and life-history traits were assessed. Organisms with different histories of past exposure to copper were exposed to toxic levels of the element for one generation (F0) and then monitored for three subsequent unexposed generations (F1, F2, and F3). Overall, methylation changes targeted important genes for counteracting the effects of metals and oxidative stress, including dynein light chain, ribosomal kinase and nuclear fragile X mental retardation-interacting protein. Also, contrasting overall and gene-specific methylation responses were observed in organisms differing in their history of exposure to copper, with different transgenerational methylation responses being also identified among the two groups, without apparent life-history costs. Taken together, these results demonstrate the capacity of copper to promote epigenetic transgenerational inheritance in a manner related explicitly to history of exposure, thereby supporting the development and incorporation of epigenetic biomarkers in risk assessment frameworks.
Collapse
Affiliation(s)
- Guilherme Jeremias
- Department of Biology & CESAM - Centre for Environmental and Marine Studies, University of Aveiro, Portugal
| | - Telma Veloso
- Department of Biology & CESAM - Centre for Environmental and Marine Studies, University of Aveiro, Portugal; CICECO - Aveiro Institute of Materials & Department of Chemistry, University of Aveiro, Portugal
| | - Fernando J M Gonçalves
- Department of Biology & CESAM - Centre for Environmental and Marine Studies, University of Aveiro, Portugal
| | | | - Joana Luísa Pereira
- Department of Biology & CESAM - Centre for Environmental and Marine Studies, University of Aveiro, Portugal.
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Bluebridge Building, Ostend Science Park 1, 8400, Ostend, Belgium
| |
Collapse
|
9
|
Veronica CS, Ivan GM, Francisco GG. Evolutionary consequences of pesticide exposure include transgenerational plasticity and potential terminal investment transgenerational effects. Evolution 2022; 76:2649-2668. [PMID: 36117275 DOI: 10.1111/evo.14613] [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: 08/21/2021] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 01/22/2023]
Abstract
Transgenerational plasticity, the influence of the environment experienced by parents on the phenotype and fitness of subsequent generations, is being increasingly recognized. Human-altered environments, such as those resulting from the increasing use of pesticides, may be major drivers of such cross-generational influences, which in turn may have profound evolutionary and ecological repercussions. Most of these consequences are, however, unknown. Whether transgenerational plasticity elicited by pesticide exposure is common, and the consequences of its potential carryover effects on fitness and population dynamics, remains to be determined. Here, we investigate whether exposure of parents to a common pesticide elicits intra-, inter-, and transgenerational responses (in F0, F1, and F2 generations) in life history (fecundity, longevity, and lifetime reproductive success), in an insect model system, the seed beetle Callosobruchus maculatus. We also assessed sex specificity of the effects. We found sex-specific and hormetic intergenerational and transgenerational effects on longevity and lifetime reproductive success, manifested both in the form of maternal and paternal effects. In addition, the transgenerational effects via mothers detected in this study are consistent with a new concept: terminal investment transgenerational effects. Such effects could underlie cross-generational responses to environmental perturbation. Our results indicate that pesticide exposure leads to unanticipated effects on population dynamics and have far-reaching ecological and evolutionary implications.
Collapse
Affiliation(s)
- Castano-Sanz Veronica
- Department of Ecology and Evolution, Estación Biológica de Doñana-CSIC, Seville, 41092, Spain
| | - Gomez-Mestre Ivan
- Department of Ecology and Evolution, Estación Biológica de Doñana-CSIC, Seville, 41092, Spain
| | - Garcia-Gonzalez Francisco
- Department of Ecology and Evolution, Estación Biológica de Doñana-CSIC, Seville, 41092, Spain.,Centre for Evolutionary Biology, School of Biological Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| |
Collapse
|
10
|
Feiner N, Radersma R, Vasquez L, Ringnér M, Nystedt B, Raine A, Tobi EW, Heijmans BT, Uller T. Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species. iScience 2022; 25:104303. [PMID: 35573201 PMCID: PMC9097707 DOI: 10.1016/j.isci.2022.104303] [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: 01/15/2021] [Revised: 04/02/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
Transgenerational inheritance of environmentally induced epigenetic marks can have significant impacts on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. We used whole-genome bisulfite sequencing of individual water fleas (Daphnia magna) to assess whether environmentally induced DNA methylation is transgenerationally inherited. Genetically identical females were exposed to one of three natural stressors, or a de-methylating drug, and their offspring were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) in F1 individuals whose mothers were exposed to a natural stressor. Roughly half of these environmentally induced DMPs persisted until generation F4. In contrast, treatment with the drug demonstrated that pervasive hypomethylation upon exposure is reset almost completely after one generation. These results suggest that environmentally induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of freshwater communities. Naturally induced DNA-methylation persists until generation F4 in Daphnia Drug-induced de-methylation is reset after one generation Methylation is enriched in exons suggesting a gene regulatory function Epigenetic inheritance may influence eco-evolutionary dynamics
Collapse
Affiliation(s)
| | - Reinder Radersma
- Department of Biology, Lund University, Lund, Sweden
- Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
| | - Louella Vasquez
- Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Markus Ringnér
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elmar W Tobi
- Periconceptional Epidemiology, Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Division of Human Nutrition and Health, Department of Agrotechnology and Food Science, Wageningen University & Research, Wageningen, The Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|
11
|
Aluru N, Fields DM, Shema S, Skiftesvik AB, Browman HI. Gene expression and epigenetic responses of the marine Cladoceran, Evadne nordmanni, and the copepod, Acartia clausi, to elevated CO 2. Ecol Evol 2021; 11:16776-16785. [PMID: 34938472 PMCID: PMC8668794 DOI: 10.1002/ece3.8309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 11/10/2022] Open
Abstract
Characterizing the capacity of marine organisms to adapt to climate change related drivers (e.g., pCO2 and temperature), and the possible rate of this adaptation, is required to assess their resilience (or lack thereof) to these drivers. Several studies have hypothesized that epigenetic markers such as DNA methylation, histone modifications and noncoding RNAs, act as drivers of adaptation in marine organisms, especially corals. However, this hypothesis has not been tested in zooplankton, a keystone organism in marine food webs. The objective of this study is to test the hypothesis that acute ocean acidification (OA) exposure alters DNA methylation in two zooplanktonic species-copepods (Acartia clausii) and cladocerans (Evadne nordmanii). We exposed these two species to near-future OA conditions (400 and 900 ppm pCO2) for 24 h and assessed transcriptional and DNA methylation patterns using RNA sequencing and Reduced Representation Bisulfite Sequencing (RRBS). OA exposure caused differential expression of genes associated with energy metabolism, cytoskeletal and extracellular matrix functions, hypoxia and one-carbon metabolism. Similarly, OA exposure also caused altered DNA methylation patterns in both species but the effect of these changes on gene expression and physiological effects remains to be determined. The results from this study form the basis for studies investigating the potential role of epigenetic mechanisms in OA induced phenotypic plasticity and/or adaptive responses in zooplanktonic organisms.
Collapse
Affiliation(s)
- Neelakanteswar Aluru
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | | | - Steven Shema
- Institute of Marine ResearchAustevoll Research Station, Ecosystem Acoustics GroupStorebøNorway
| | - Anne Berit Skiftesvik
- Institute of Marine ResearchAustevoll Research Station, Ecosystem Acoustics GroupStorebøNorway
| | - Howard I. Browman
- Institute of Marine ResearchAustevoll Research Station, Ecosystem Acoustics GroupStorebøNorway
| |
Collapse
|
12
|
Han T, Jiang W, Wu H, Wei W, Lu J, Lu H, Xu J, Gu W, Guo X, Wang Y, Ruan J, Li Y, Wang Y, Jiang X, Zhao S, Li Y, Sun C. Fetal malnutrition is associated with impairment of endogenous melatonin synthesis in pineal via hypermethylation of promoters of protein kinase C alpha and cAMP response element-binding. J Pineal Res 2021; 71:e12764. [PMID: 34486775 DOI: 10.1111/jpi.12764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/26/2021] [Accepted: 08/20/2021] [Indexed: 11/29/2022]
Abstract
This study investigated whether and how fetal malnutrition would influence endogenous melatonin synthesis, and whether such effect of fetal malnutrition would transmit to the next generation. We enrolled 2466 participants and 1313 of their offspring. The urine 6-hydroxymelatonin sulfate and serum melatonin rhythm were measured. Methylation microarray detection and bioinformatics analysis were performed to identify hub methylated sites. Additionally, rat experiment was performed to elucidate mechanisms. The participants with fetal malnutrition had lower 6-hydroxymelatonin sulfate (16.59 ± 10.12 μg/24 hours vs 24.29 ± 11.99 μg/24 hours, P < .001) and arear under curve of melatonin rhythm (67.11 ± 8.16 pg/mL vs 77.11 ± 8.04 pg/mL, P < .001). We identified 961 differentially methylated sites, in which the hub methylated sites were locating on protein kinase C alpha (PRKCA) and cAMP response element-binding protein (CREB1) promoters, mediating the association of fetal malnutrition with impaired melatonin secretion. However, such effects were not observed in the offspring (all P > .05). Impaired histomorphology of pineal, decreased melatonin in serum, pineal, and pinealocyte were also found in the in vivo and in vitro experiments (P < .05 for the differences of the indicators). Hypermethylation of 10 CpG sites on the PRKCA promoter and 8 CpG sites on the CREB1 promoter were identified (all P < .05), which down-regulated PRKCA and CREB1 expressions, leading to decreased expression of AANAT, and then resulting in the impaired melatonin synthesis. Collectively, fetal malnutrition can impair melatonin synthesis through hypermethylation of PRKCA and CREB1 promoters, and such effects cannot be transmitted to the next generation.
Collapse
Affiliation(s)
- Tianshu Han
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Wenbo Jiang
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Huanyu Wu
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Wei Wei
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Jiang Lu
- National Center for Food Safety Risk Assessment, Beijing, China
| | - Huimin Lu
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Jiaxu Xu
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Wenbo Gu
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Xiaoyu Guo
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Yu Wang
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Jingqi Ruan
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Yunong Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuxin Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xitao Jiang
- College of Engineering, IT and Environment, Charles Darwin University, Darwin, NT, Australia
| | - Shengnan Zhao
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| | - Ying Li
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin Medical University, Harbin, China
- NHC Key Laboratory of Cell Translation, Harbin Medical University, Harbin, China
| | - Changhao Sun
- Department of Nutrition and Food Hygiene, School of Public Health, National Key Discipline, Harbin Medical University, Harbin, China
| |
Collapse
|
13
|
Šrut M. Ecotoxicological epigenetics in invertebrates: Emerging tool for the evaluation of present and past pollution burden. CHEMOSPHERE 2021; 282:131026. [PMID: 34111635 DOI: 10.1016/j.chemosphere.2021.131026] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
The effect of environmental pollution on epigenetic changes and their heredity in affected organisms is of major concern as such changes can play a significant role in adaptation to changing environmental conditions. Changes of epigenetic marks including DNA methylation, histone modifications, and non-coding RNA's can induce changes in gene transcription leading to physiological long-term changes or even transgenerational inheritance. Such mechanisms have until recently been scarcely studied in invertebrate organisms, mainly focusing on model species including Caenorhabditis elegans and Daphnia magna. However, more data are becoming available, particularly focused on DNA methylation changes caused by anthropogenic pollutants in a wide range of invertebrates. This review examines the literature from field and laboratory studies utilising invertebrate species exposed to environmental pollutants and their effect on DNA methylation. Possible mechanisms of epigenetic modifications and their role on physiology and adaptation as well as the incidence of intergenerational and transgenerational inheritance are discussed. Furthermore, critical research challenges are defined and the way forward is proposed. Future studies should focus on the use of next generation sequencing tools to define invertebrate methylomes under environmental stress in higher resolution, those data should further be linked to gene expression patterns and phenotypes and detailed studies focusing on transgenerational effects are encouraged. Moreover, studies of other epigenetic mechanisms in various invertebrate species, apart from DNA methylation would provide better understanding of interconnected cross-talk between epigenetic marks. Taken together incorporating epigenetic studies in ecotoxicology context presents a promising tool for development of sensitive biomarkers for environmental stress assessment.
Collapse
Affiliation(s)
- Maja Šrut
- University of Innsbruck, Institute of Zoology, Technikerstraße 25, 6020, Innsbruck, Austria.
| |
Collapse
|
14
|
Song Y, Kamstra JH, Cao Y, Asselman J, Anglès d'Auriac M, Friberg N. High-throughput analyses and Bayesian network modeling highlight novel epigenetic Adverse Outcome Pathway networks of DNA methyltransferase inhibitor mediated transgenerational effects. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124490. [PMID: 33199140 DOI: 10.1016/j.jhazmat.2020.124490] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/26/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
A number of epigenetic modulating chemicals are known to affect multiple generations of a population from a single ancestral exposure, thus posing transgenerational hazards. The present study aimed to establish a high-throughput (HT) analytical workflow for cost-efficient concentration-response analysis of epigenetic and phenotypic effects, and to support the development of novel Adverse Outcome Pathway (AOP) networks for DNA methyltransferase (DNMT) inhibitor-mediated transgenerational effects on aquatic organisms. The model DNMT inhibitor 5-azacytidine (5AC) and the model freshwater crustacean Daphnia magna were used to generate new experimental data and served as prototypes to construct AOPs for aquatic organisms. Targeted HT bioassays (DNMT ELISA, MS-HRM and qPCR) in combination with multigenerational ecotoxicity tests revealed concentration-dependent transgenerational (F0-F3) effects of 5AC on total DNMT activity, DNA promoter methylation, gene body methylation, gene transcription and reproduction. Top sensitive toxicity pathways related to 5AC exposure, such as apoptosis and DNA damage responses were identified in both F0 and F3 using Gaussian Bayesian network modeling. Two novel epigenetic AOP networks on DNMT inhibitor mediated one-generational and transgenerational effects were developed for aquatic organisms and assessed for the weight of evidence. The new HT analytical workflow and AOPs can facilitate future ecological hazard assessment of epigenetic modulating chemicals.
Collapse
Affiliation(s)
- You Song
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo, Norway.
| | - Jorke H Kamstra
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80177, NL-3508 TD Utrecht, The Netherlands
| | - Yang Cao
- Clinical Epidemiology and Biostatistics, School of Medical Sciences, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Bluebridge building, Ostend Science Park 1, 8400 Ostend, Belgium
| | - Marc Anglès d'Auriac
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo, Norway
| | - Nikolai Friberg
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo, Norway; University of Copenhagen, Freshwater Biological Section, Universitetsparken 4, 3rd floor, 2100 Copenhagen, Denmark; University of Leeds, water@leeds, School of Geography, Leeds LS2 9JT UK
| |
Collapse
|
15
|
DNMT3.1 controls trade-offs between growth, reproduction, and life span under starved conditions in Daphnia magna. Sci Rep 2021; 11:7326. [PMID: 33795753 PMCID: PMC8016896 DOI: 10.1038/s41598-021-86578-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/25/2021] [Indexed: 02/01/2023] Open
Abstract
The cladoceran crustacean Daphnia has long been a model of energy allocation studies due to its important position in the trophic cascade of freshwater ecosystems. However, the loci for controlling energy allocation between life history traits still remain unknown. Here, we report CRISPR/Cas-mediated target mutagenesis of DNA methyltransferase 3.1 (DNMT3.1) that is upregulated in response to caloric restriction in Daphnia magna. The resulting biallelic mutant is viable and did not show any change in growth rate, reproduction, and longevity under nutrient rich conditions. In contrast, under starved conditions, the growth rate of this DNMT3.1 mutant was increased but its reproduction was reciprocally reduced compared to the wild type when the growth and reproduction activities competed during a period from instar 4 to 8. The life span of this mutant was significantly shorter than that of the wild type. We also compared transcriptomes between DNMT3.1 mutant and wild type under nutrient-rich and starved conditions. Consistent with the DNMT3.1 mutant phenotypes, the starved condition led to changes in the transcriptomes of the mutant including differential expression of vitellogenin genes. In addition, we found upregulation of the I am not dead yet (INDY) ortholog, which has been known to shorten the life span in Drosophila, explaining the shorter life span of the DNMT3.1 mutant. These results establish DNMT3.1 as a key regulator for life span and energy allocation between growth and reproduction during caloric restriction. Our findings reveal how energy allocation is implemented by selective expression of a DNMT3 ortholog that is widely distributed among animals. We also infer a previously unidentified adaptation of Daphnia that invests more energy for reproduction than growth under starved conditions.
Collapse
|
16
|
Vogt G. Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance. J Biosci 2021. [DOI: 10.1007/s12038-021-00138-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
17
|
Hearn J, Plenderleith F, Little TJ. DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna. Epigenetics Chromatin 2021; 14:4. [PMID: 33407738 PMCID: PMC7789248 DOI: 10.1186/s13072-020-00379-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Patterns of methylation influence lifespan, but methylation and lifespan may also depend on diet, or differ between genotypes. Prior to this study, interactions between diet and genotype have not been explored together to determine their influence on methylation. The invertebrate Daphnia magna is an excellent choice for testing the epigenetic response to the environment: parthenogenetic offspring are identical to their siblings (making for powerful genetic comparisons), they are relatively short lived and have well-characterised inter-strain life-history trait differences. We performed a survival analysis in response to caloric restriction and then undertook a 47-replicate experiment testing the DNA methylation response to ageing and caloric restriction of two strains of D. magna. RESULTS Methylated cytosines (CpGs) were most prevalent in exons two to five of gene bodies. One strain exhibited a significantly increased lifespan in response to caloric restriction, but there was no effect of food-level CpG methylation status. Inter-strain differences dominated the methylation experiment with over 15,000 differently methylated CpGs. One gene, Me31b, was hypermethylated extensively in one strain and is a key regulator of embryonic expression. Sixty-one CpGs were differentially methylated between young and old individuals, including multiple CpGs within the histone H3 gene, which were hypermethylated in old individuals. Across all age-related CpGs, we identified a set that are highly correlated with chronological age. CONCLUSIONS Methylated cytosines are concentrated in early exons of gene sequences indicative of a directed, non-random, process despite the low overall DNA methylation percentage in this species. We identify no effect of caloric restriction on DNA methylation, contrary to our previous results, and established impacts of caloric restriction on phenotype and gene expression. We propose our approach here is more robust in invertebrates given genome-wide CpG distributions. For both strain and ageing, a single gene emerges as differentially methylated that for each factor could have widespread phenotypic effects. Our data showed the potential for an epigenetic clock at a subset of age positions, which is exciting but requires confirmation.
Collapse
Affiliation(s)
- Jack Hearn
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Fiona Plenderleith
- The James Hutton Institute, Craigiebuckler, Aberdeen, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Tom J. Little
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
18
|
Thaulow J, Song Y, Lindeman LC, Kamstra JH, Lee Y, Xie L, Aleström P, Salbu B, Tollefsen KE. Epigenetic, transcriptional and phenotypic responses in Daphnia magna exposed to low-level ionizing radiation. ENVIRONMENTAL RESEARCH 2020; 190:109930. [PMID: 32738623 DOI: 10.1016/j.envres.2020.109930] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/18/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Ionizing radiation is known to induce oxidative stress and DNA damage as well as epigenetic effects in aquatic organisms. Epigenetic changes can be part of the adaptive responses to protect organisms from radiation-induced damage, or act as drivers of toxicity pathways leading to adverse effects. To investigate the potential roles of epigenetic mechanisms in low-dose ionizing radiation-induced stress responses, an ecologically relevant crustacean, adult Daphnia magna were chronically exposed to low and medium level external 60Co gamma radiation ranging from 0.4, 1, 4, 10, and 40 mGy/h for seven days. Biological effects at the molecular (global DNA methylation, histone modification, gene expression), cellular (reactive oxygen species formation), tissue/organ (ovary, gut and epidermal histology) and organismal (fecundity) levels were investigated using a suite of effect assessment tools. The results showed an increase in global DNA methylation associated with loci-specific alterations of histone H3K9 methylation and acetylation, and downregulation of genes involved in DNA methylation, one-carbon metabolism, antioxidant defense, DNA repair, apoptosis, calcium signaling and endocrine regulation of development and reproduction. Temporal changes of reactive oxygen species (ROS) formation were also observed with an apparent transition from ROS suppression to induction from 2 to 7 days after gamma exposure. The cumulative fecundity, however, was not significantly changed by the gamma exposure. On the basis of the new experimental evidence and existing knowledge, a hypothetical model was proposed to provide in-depth mechanistic understanding of the roles of epigenetic mechanisms in low dose ionizing radiation induced stress responses in D. magna.
Collapse
Affiliation(s)
- Jens Thaulow
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - You Song
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway.
| | - Leif C Lindeman
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Jorke H Kamstra
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, PO Box 80177, NL-3508 TD, Utrecht, the Netherlands
| | - YeonKyeong Lee
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of BioSciences, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Li Xie
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| | - Peter Aleström
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Brit Salbu
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| |
Collapse
|
19
|
Genome-wide identification and transcriptional modulation of histone variants and modification related genes in the low pH-exposed marine rotifer Brachionus koreanus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100748. [PMID: 33032078 DOI: 10.1016/j.cbd.2020.100748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/05/2020] [Accepted: 09/18/2020] [Indexed: 11/22/2022]
Abstract
Histone modification is considered to be a major epigenetic control mechanism. These modifications (e.g. acetylation, phosphorylation, and methylation) may affect the interaction of histones with DNA and/or regulate DNA-based processes (e.g., recombination, repair, replication, and transcription) and chromatin remodeling complexes. Despite their significance in metazoan life and evolution, few studies have been conducted to identify genes undergoing epigenetic control modification in aquatic invertebrates. In this study, we identified whole core histones (70 total genes) and post-translational modification (PTM) histone genes (63 total genes) in the marine rotifer Brachionus koreanus through whole-genome analysis, and annotated them according to the human nomenclature. Notably, upon comparative analysis of cis-regulatory motif sequences, we found that B. koreanus core histone protein structures were similar to those of mammals. Furthermore, to examine the effect of parental low pH stress on the offspring's epigenetic regulation, we investigated the expression of PTM genes in two generations of B. koreanus exposed to low pH conditions. Given that the B. koreanus genome does not possess DNA methyltransferase 1 and 3 genes, we concluded that histone genes could be involved as an important epigenetic mechanism in B. koreanus. Therefore, the histone-associated genes identified in this study could be useful for ecotoxicological studies and facilitate the application of chromatin immunoprecipitation sequencing using high-throughput DNA sequencing based on the genome-wide identification of transcription factor binding sites in rotifers.
Collapse
|
20
|
den Broeder MJ, Ballangby J, Kamminga LM, Aleström P, Legler J, Lindeman LC, Kamstra JH. Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish. Epigenetics Chromatin 2020; 13:5. [PMID: 32051014 PMCID: PMC7014624 DOI: 10.1186/s13072-020-0329-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background Recent studies indicate that exposure to environmental chemicals may increase susceptibility to developing metabolic diseases. This susceptibility may in part be caused by changes to the epigenetic landscape which consequently affect gene expression and lead to changes in lipid metabolism. The epigenetic modifier enhancer of zeste 2 (Ezh2) is a histone H3K27 methyltransferase implicated to play a role in lipid metabolism and adipogenesis. In this study, we used the zebrafish (Danio rerio) to investigate the role of Ezh2 on lipid metabolism and chromatin status following developmental exposure to the Ezh1/2 inhibitor PF-06726304 acetate. We used the environmental chemical tributyltin (TBT) as a positive control, as this chemical is known to act on lipid metabolism via EZH-mediated pathways in mammals. Results Zebrafish embryos (0–5 days post-fertilization, dpf) exposed to non-toxic concentrations of PF-06726304 acetate (5 μM) and TBT (1 nM) exhibited increased lipid accumulation. Changes in chromatin were analyzed by the assay for transposase-accessible chromatin sequencing (ATAC-seq) at 50% epiboly (5.5 hpf). We observed 349 altered chromatin regions, predominantly located at H3K27me3 loci and mostly more open chromatin in the exposed samples. Genes associated to these loci were linked to metabolic pathways. In addition, a selection of genes involved in lipid homeostasis, adipogenesis and genes specifically targeted by PF-06726304 acetate via altered chromatin accessibility were differentially expressed after TBT and PF-06726304 acetate exposure at 5 dpf, but not at 50% epiboly stage. One gene, cebpa, did not show a change in chromatin, but did show a change in gene expression at 5 dpf. Interestingly, underlying H3K27me3 marks were significantly decreased at this locus at 50% epiboly. Conclusions Here, we show for the first time the applicability of ATAC-seq as a tool to investigate toxicological responses in zebrafish. Our analysis indicates that Ezh2 inhibition leads to a partial primed state of chromatin linked to metabolic pathways which results in gene expression changes later in development, leading to enhanced lipid accumulation. Although ATAC-seq seems promising, our in-depth assessment of the cebpa locus indicates that we need to consider underlying epigenetic marks as well.
Collapse
Affiliation(s)
- Marjo J den Broeder
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jarle Ballangby
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Leonie M Kamminga
- Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Wageningen University and Research Library, Wageningen, The Netherlands
| | - Peter Aleström
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Juliette Legler
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Leif C Lindeman
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Jorke H Kamstra
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands. .,Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway.
| |
Collapse
|