1
|
Ibragimova M, Kussainova A, Aripova A, Bersimbaev R, Bulgakova O. The Molecular Mechanisms in Senescent Cells Induced by Natural Aging and Ionizing Radiation. Cells 2024; 13:550. [PMID: 38534394 DOI: 10.3390/cells13060550] [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: 02/20/2024] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
This review discusses the relationship between cellular senescence and radiation exposure. Given the wide range of ionizing radiation sources encountered by people in professional and medical spheres, as well as the influence of natural background radiation, the question of the effect of radiation on biological processes, particularly on aging processes, remains highly relevant. The parallel relationship between natural and radiation-induced cellular senescence reveals the common aspects underlying these processes. Based on recent scientific data, the key points of the effects of ionizing radiation on cellular processes associated with aging, such as genome instability, mitochondrial dysfunction, altered expression of miRNAs, epigenetic profile, and manifestation of the senescence-associated secretory phenotype (SASP), are discussed. Unraveling the molecular mechanisms of cellular senescence can make a valuable contribution to the understanding of the molecular genetic basis of age-associated diseases in the context of environmental exposure.
Collapse
Affiliation(s)
- Milana Ibragimova
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
| | - Assiya Kussainova
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
- Department of Health Sciences, University of Genova, Via Pastore 1, 16132 Genoa, Italy
| | - Akmaral Aripova
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
| | - Rakhmetkazhi Bersimbaev
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
| | - Olga Bulgakova
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
| |
Collapse
|
2
|
Ruprecht NA, Singhal S, Schaefer K, Panda O, Sens D, Singhal SK. A Review: Multi-Omics Approach to Studying the Association between Ionizing Radiation Effects on Biological Aging. BIOLOGY 2024; 13:98. [PMID: 38392316 PMCID: PMC10886797 DOI: 10.3390/biology13020098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Multi-omics studies have emerged as powerful tools for tailoring individualized responses to various conditions, capitalizing on genome sequencing technologies' increasing affordability and efficiency. This paper delves into the potential of multi-omics in deepening our understanding of biological age, examining the techniques available in light of evolving technology and computational models. The primary objective is to review the relationship between ionizing radiation and biological age, exploring a wide array of functional, physiological, and psychological parameters. This comprehensive review draws upon an extensive range of sources, including peer-reviewed journal articles, government documents, and reputable websites. The literature review spans from fundamental insights into radiation effects to the latest developments in aging research. Ionizing radiation exerts its influence through direct mechanisms, notably single- and double-strand DNA breaks and cross links, along with other critical cellular events. The cumulative impact of DNA damage forms the foundation for the intricate process of natural aging, intersecting with numerous diseases and pivotal biomarkers. Furthermore, there is a resurgence of interest in ionizing radiation research from various organizations and countries, reinvigorating its importance as a key contributor to the study of biological age. Biological age serves as a vital reference point for the monitoring and mitigation of the effects of various stressors, including ionizing radiation. Ionizing radiation emerges as a potent candidate for modeling the separation of biological age from chronological age, offering a promising avenue for tailoring protocols across diverse fields, including the rigorous demands of space exploration.
Collapse
Affiliation(s)
- Nathan A Ruprecht
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND 58202, USA
| | - Sonalika Singhal
- Department of Pathology, University of North Dakota, Grand Forks, ND 58202, USA
| | - Kalli Schaefer
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND 58202, USA
| | - Om Panda
- Department of Public Health, University of California Irvine, Irvine, CA 92697, USA
| | - Donald Sens
- Department of Pathology, University of North Dakota, Grand Forks, ND 58202, USA
| | - Sandeep K Singhal
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND 58202, USA
- Department of Pathology, University of North Dakota, Grand Forks, ND 58202, USA
| |
Collapse
|
3
|
Guirandy N, Simon O, Geffroy B, Daffe G, Daramy F, Houdelet C, Gonzalez P, Pierron F. Gamma irradiation-induced offspring masculinization is associated with epigenetic changes in female zebrafish. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 269:115790. [PMID: 38086259 DOI: 10.1016/j.ecoenv.2023.115790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024]
Abstract
Sex ratio variation is a key topic in ecology, because of its direct effects on population dynamics and thus, on animal conservation strategies. Among factors affecting sex ratio, types of sex determination systems have a central role, since some species could have a sex determined by genetic factors, environmental factors or a mix of those two. Yet, most studies on the factors affecting sex determination have focused on temperature or endocrine-disrupting chemicals (EDCs), and much less is known regarding other factors. Exposure to gamma irradiation was found to trigger offspring masculinization in zebrafish. Here we aimed at deciphering the potential mechanisms involved, by focusing on stress (i.e. cortisol) and epigenetic regulation of key genes involved in sex differentiation in fish. Cortisol levels in exposed and control (F0) zebrafish females' gonads were similar. However, irradiation increased the DNA methylation level of foxl2a and cyp19a1a in females of the F0 and F1 generation, respectively, while no effects were detected in testis. Overall, our results suggest that parental exposure could alter offspring sex ratio, at least in part by inducing methylation changes in ovaries.
Collapse
Affiliation(s)
- Noëmie Guirandy
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache-B.P. 3 - Bat 183, 13115 St Paul Lez Durance, France.
| | - Olivier Simon
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache-B.P. 3 - Bat 183, 13115 St Paul Lez Durance, France
| | - Benjamin Geffroy
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Guillemine Daffe
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Flore Daramy
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Camille Houdelet
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Patrice Gonzalez
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Fabien Pierron
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| |
Collapse
|
4
|
He X, Cai L, Tang H, Chen W, Hu W. Epigenetic modifications in radiation-induced non-targeted effects and their clinical significance. Biochim Biophys Acta Gen Subj 2023; 1867:130386. [PMID: 37230420 DOI: 10.1016/j.bbagen.2023.130386] [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: 03/23/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Ionizing radiation (IR) plays an important role in the diagnosis and treatment of cancer. Besides the targeted effects, the non-targeted effects, which cause damage to non-irradiated cells and genomic instability in normal tissues, also play a role in the side effects of radiotherapy and have been shown to involve both alterations in DNA sequence and regulation of epigenetic modifications. SCOPE OF REVIEW We summarize the recent findings regarding epigenetic modifications that are involved in radiation-induced non-targeted effects as well as their clinical significance in radiotherapy and radioprotection. MAJOR CONCLUSIONS Epigenetic modifications play an important role in both the realization and modulation of radiobiological effects. However, the molecular mechanisms underlying non-targeted effects still need to be clarified. GENERAL SIGNIFICANCE A better understanding of the epigenetic mechanisms related to radiation-induced non-targeted effects will guide both individualized clinical radiotherapy and individualized precise radioprotection.
Collapse
Affiliation(s)
- Xiangyang He
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Luwei Cai
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Haoyi Tang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Weibo Chen
- Nuclear and Radiation Incident Medical Emergency Office, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.
| | - Wentao Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| |
Collapse
|
5
|
Fallet M, Blanc M, Di Criscio M, Antczak P, Engwall M, Guerrero Bosagna C, Rüegg J, Keiter SH. Present and future challenges for the investigation of transgenerational epigenetic inheritance. ENVIRONMENT INTERNATIONAL 2023; 172:107776. [PMID: 36731188 DOI: 10.1016/j.envint.2023.107776] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic pathways are essential in different biological processes and in phenotype-environment interactions in response to different stressors and they can induce phenotypic plasticity. They encompass several processes that are mitotically and, in some cases, meiotically heritable, so they can be transferred to subsequent generations via the germline. Transgenerational Epigenetic Inheritance (TEI) describes the phenomenon that phenotypic traits, such as changes in fertility, metabolic function, or behavior, induced by environmental factors (e.g., parental care, pathogens, pollutants, climate change), can be transferred to offspring generations via epigenetic mechanisms. Investigations on TEI contribute to deciphering the role of epigenetic mechanisms in adaptation, adversity, and evolution. However, molecular mechanisms underlying the transmission of epigenetic changes between generations, and the downstream chain of events leading to persistent phenotypic changes, remain unclear. Therefore, inter-, (transmission of information between parental and offspring generation via direct exposure) and transgenerational (transmission of information through several generations with disappearance of the triggering factor) consequences of epigenetic modifications remain major issues in the field of modern biology. In this article, we review and describe the major gaps and issues still encountered in the TEI field: the general challenges faced in epigenetic research; deciphering the key epigenetic mechanisms in inheritance processes; identifying the relevant drivers for TEI and implement a collaborative and multi-disciplinary approach to study TEI. Finally, we provide suggestions on how to overcome these challenges and ultimately be able to identify the specific contribution of epigenetics in transgenerational inheritance and use the correct tools for environmental science investigation and biomarkers identification.
Collapse
Affiliation(s)
- Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden; Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd, Oxford OX1 3QU, United Kingdom.
| | - Mélanie Blanc
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, Palavas, France
| | - Michela Di Criscio
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Philipp Antczak
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Center for Molecular Medicine Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, Germany
| | - Magnus Engwall
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | | | - Joëlle Rüegg
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| |
Collapse
|
6
|
Lu K, Liang XF, Liu T, Cai W, Zhuang W, Zhang Y, Bibi A. DNA methylation of pck1 might contribute to the programming effects of early high-carbohydrate diets feeding to the glucose metabolism across two generations in zebrafish (Danio rerio). FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:1619-1633. [PMID: 36481836 DOI: 10.1007/s10695-022-01149-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
The purpose of this study is to assess the effects of early high-carbohydrate stimulus on glucose metabolism in zebrafish (Danio rerio) over two generations and explore the mechanisms that explain those nutritional programming effects via epigenetic modifications. The larvae were delivered a high-carbohydrate diet (53.66%) that was used as an early nutritional stimulus from the first feeding to the end of the yolk sac (FF) and 5 days after yolk-sac exhaustion (YE). The larvae (F0) and their offspring (F1) were then both fed the control diet (22.69%) until adulthood (15 weeks), and they were challenged with a high-carbohydrate diet (35.36%) at the 16th week. The results indicated that early stimulus immediately raised the mRNA levels of genes involved in glycolysis and gluconeogenesis. At the end of F0 challenge, both treatment groups decreased the plasma glucose levels, increased the expression levels of glucokinase (gck), and inhibited the mRNA during gluconeogenesis. When challenged in F1, the glucose levels were lower in FF (F1), and the mRNA levels of phosphoenolpyruvate carboxykinase 1 (pck1) were decreased in FF (F1) and YE (F1). Besides, in both experimental groups (F0 and F1), the CpG island of pck1 maintained lower levels of hypermethylated expression from F0 adult, 24 h post-fertilization embryo, to F1 adult. In conclusion, these results indicated that an early high-carbohydrate stimulus could significantly reprogram glucose metabolism in adult zebrafish, that those modifications could be partially transmitted to the next generation, and that the DNA methylation of pck1 might work as a stable epigenetic marker to contribute to those processes.
Collapse
Affiliation(s)
- Ke Lu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China.
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
| | - Tong Liu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Wenjing Cai
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Wuyuan Zhuang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Yanpeng Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Asima Bibi
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| |
Collapse
|
7
|
Lowe D, Roy L, Tabocchini MA, Rühm W, Wakeford R, Woloschak GE, Laurier D. Radiation dose rate effects: what is new and what is needed? RADIATION AND ENVIRONMENTAL BIOPHYSICS 2022; 61:507-543. [PMID: 36241855 PMCID: PMC9630203 DOI: 10.1007/s00411-022-00996-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/13/2022] [Indexed: 05/04/2023]
Abstract
Despite decades of research to understand the biological effects of ionising radiation, there is still much uncertainty over the role of dose rate. Motivated by a virtual workshop on the "Effects of spatial and temporal variation in dose delivery" organised in November 2020 by the Multidisciplinary Low Dose Initiative (MELODI), here, we review studies to date exploring dose rate effects, highlighting significant findings, recent advances and to provide perspective and recommendations for requirements and direction of future work. A comprehensive range of studies is considered, including molecular, cellular, animal, and human studies, with a focus on low linear-energy-transfer radiation exposure. Limits and advantages of each type of study are discussed, and a focus is made on future research needs.
Collapse
Affiliation(s)
- Donna Lowe
- UK Health Security Agency, CRCE Chilton, Didcot, OX11 0RQ, Oxfordshire, UK
| | - Laurence Roy
- Institut de Radioprotection Et de Sûreté Nucléaire, Fontenay-Aux-Roses, France
| | - Maria Antonella Tabocchini
- Istituto Nazionale i Fisica Nucleare, Sezione i Roma, Rome, Italy
- Istituto Superiore Di Sanità, Rome, Italy
| | - Werner Rühm
- Institute of Radiation Medicine, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Richard Wakeford
- Centre for Occupational and Environmental Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Gayle E Woloschak
- Department of Radiation Oncology, Northwestern University School of Medicine, Chicago, IL, USA.
| | - Dominique Laurier
- Institut de Radioprotection Et de Sûreté Nucléaire, Fontenay-Aux-Roses, France
| |
Collapse
|
8
|
Zhou R, Lu G, Yan Z, Jiang R, Sun Y, Zhang P. Epigenetic mechanisms of DNA methylation in the transgenerational effect of ethylhexyl salicylate on zebrafish. CHEMOSPHERE 2022; 295:133926. [PMID: 35150701 DOI: 10.1016/j.chemosphere.2022.133926] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/24/2022] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
In this study, a 120-day whole-life cycle exposure and oviposition experiment on zebrafish with maternal and paternal mixed mating strategy was conducted to investigate the epigenetic mechanism of DNA methylation in ethylhexyl salicylate (EHS, 1, 10, 100 μg/L)-induced transgenerational effects. Results showed that EHS could induce the decrease of DNA methyltransferase 1 (DNMT1) activity and average global DNA methylation level in maternal parents and the increase of the above indexes in paternal parents, while the change of glycine N-methyltransferase activity was opposite to DNMT1. The average global DNA methylation levels were significantly increased in the offsprings of both parents exposed and father-only exposed to EHS, suggesting that EHS-induced epigenetic modifications may be stable and heritable. Hierarchical clustering analysis of promoter at different methylation sites showed that the DNA methylation pattern of offsprings were similar to that of the paternal parents, meaning that the offsprings may have inherited paternal DNA methylation pattern with eya2, pcdh2g5 and pcdh2g1 as key genes and lead to high locomotor activity in offsprings. KEGG pathway analysis showed that parental exposure to EHS may interfere with the central nervous system, insulin function system, melanogenesis system and the normal development of somatic axis of offsprings.
Collapse
Affiliation(s)
- Ranran Zhou
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China; School of Environmental Science & Engineering, Nanjing Tech University, 30 Puzhu Southern Road, Nanjing, 211816, China
| | - Guanghua Lu
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Zhenhua Yan
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Runren Jiang
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yu Sun
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Peng Zhang
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| |
Collapse
|
9
|
Abstract
Organisms mount the cellular stress response whenever environmental parameters exceed the range that is conducive to maintaining homeostasis. This response is critical for survival in emergency situations because it protects macromolecular integrity and, therefore, cell/organismal function. From an evolutionary perspective, the cellular stress response counteracts severe stress by accelerating adaptation via a process called stress-induced evolution. In this Review, we summarize five key physiological mechanisms of stress-induced evolution. Namely, these are stress-induced changes in: (1) mutation rates, (2) histone post-translational modifications, (3) DNA methylation, (4) chromoanagenesis and (5) transposable element activity. Through each of these mechanisms, organisms rapidly generate heritable phenotypes that may be adaptive, maladaptive or neutral in specific contexts. Regardless of their consequences to individual fitness, these mechanisms produce phenotypic variation at the population level. Because variation fuels natural selection, the physiological mechanisms of stress-induced evolution increase the likelihood that populations can avoid extirpation and instead adapt under the stress of new environmental conditions.
Collapse
Affiliation(s)
- Elizabeth A Mojica
- Department of Animal Science, University of California, Davis, One Shields Avenue, Meyer Hall, Davis, CA 95616, USA
| | - Dietmar Kültz
- Department of Animal Science, University of California, Davis, One Shields Avenue, Meyer Hall, Davis, CA 95616, USA
| |
Collapse
|
10
|
Noëmie G, Béatrice G, Virginie C, Isabelle C, Fabien P, Patrice G, Olivier S. Multigenerational exposure to gamma radiation affects offspring differently over generations in zebrafish. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 244:106101. [PMID: 35123208 DOI: 10.1016/j.aquatox.2022.106101] [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: 05/10/2021] [Revised: 01/16/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Mutigenerational studies are now of great interest in ecotoxicology and previous studies have shown the importance of conducting multigenerational studies when assessing radiation toxicity in fish. In our study, the first objective was to study the early life stages (embryo-larval stages) and critical functions such as reproduction (which are generally studied in the context of ecological risk assessment (ERA)), in order to assess the sensitivity of zebrafish to ionizing radiation. The second objective was to assess acquisition of phenotypic effects at select life stages over generations. To our knowledge, this was the first time that irradiation of zebrafish (0.05 and 5 mGy.h-1) up to generation F2 was maintained with the following two exposure conditions: (1) recovery, only F0 genitors were irradiated and the progeny were placed in control condition, (2) irradiated condition, all generations were exposed. Multigenerational irradiation affected F1 parental reproductive capacity (reproductive success) mainly over the first reproductive cycle (104d) and larval survival rate. Unexpected yet significant effects on sex ratio were observed in F1 progeny after parental irradiation (mainly at 5 mGy.h-1). These effects were observed for both conditions -irradiated and recovery- suggesting transmitted effects from F0 genitors to offspring. All studied life stages were affected by ionizing radiation (IR), suggesting an alteration of vital physiological functions (reproduction and sexual determination). Such results highlight the hypothesis that IR affects population dynamics. In addition, the clear evidence of transmitted effects suggests worsening of effects at the population scale over generations. This approach is closer to environmental conditions to assess wild population fate, and thus highlights the importance of multigenerational studies to support ERA of ionizing radiation in fish.
Collapse
Affiliation(s)
- Guirandy Noëmie
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache, B.P. 3 - Bat 183, St Paul Lez Durance 13115, France.
| | - Gagnaire Béatrice
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache, B.P. 3 - Bat 183, St Paul Lez Durance 13115, France
| | - Camilleri Virginie
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache, B.P. 3 - Bat 183, St Paul Lez Durance 13115, France
| | - Cavalié Isabelle
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache, B.P. 3 - Bat 183, St Paul Lez Durance 13115, France
| | - Pierron Fabien
- UMR EPOC CNRS 5805, Place du Docteur Bertrand Peyneau, Arcachon 33120, France
| | - Gonzalez Patrice
- UMR EPOC CNRS 5805, Place du Docteur Bertrand Peyneau, Arcachon 33120, France
| | - Simon Olivier
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache, B.P. 3 - Bat 183, St Paul Lez Durance 13115, France
| |
Collapse
|
11
|
Terrazas-Salgado L, García-Gasca A, Betancourt-Lozano M, Llera-Herrera R, Alvarado-Cruz I, Yáñez-Rivera B. Epigenetic Transgenerational Modifications Induced by Xenobiotic Exposure in Zebrafish. Front Cell Dev Biol 2022; 10:832982. [PMID: 35281093 PMCID: PMC8914061 DOI: 10.3389/fcell.2022.832982] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Zebrafish (Danio rerio) is a well-established vertebrate model in ecotoxicology research that responds to a wide range of xenobiotics such as pesticides, drugs, and endocrine-disrupting compounds. The epigenome can interact with the environment and transform internal and/or external signals into phenotypic responses through changes in gene transcription. Environmental exposures can also generate epigenetic variations in offspring even by indirect exposure. In this review, we address the advantages of using zebrafish as an experimental animal model to study transgenerational epigenetic processes upon exposure to xenobiotics. We focused mostly on DNA methylation, although studies on post-translational modifications of histones, and non-coding RNAs related to xenobiotic exposure in zebrafish are also discussed. A revision of the methods used to study epigenetic changes in zebrafish revealed the relevance and reproducibility for epigenetics-related research. PubMed and Google Scholar databases were consulted for original research articles published from 2013 to date, by using six keywords: zebrafish, epigenetics, exposure, parental, transgenerational, and F2. From 499 articles identified, 92 were considered, of which 14 were selected as included F2 and epigenetic mechanisms. Current knowledge regarding the effect of xenobiotics on DNA methylation, histone modifications, and changes in non-coding RNAs expressed in F2 is summarized, along with key experimental design considerations to characterize transgenerational effects.
Collapse
Affiliation(s)
| | | | | | - Raúl Llera-Herrera
- Instituto de Ciencias del Mar y Limnología—Unidad Académica Mazatlán, Universidad Nacional Autónoma de México, Mazatlán, Mexico
| | - Isabel Alvarado-Cruz
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, AZ, United States
| | - Beatriz Yáñez-Rivera
- Centro de Investigación en Alimentación y Desarrollo, A. C., Mazatlán, Mexico
- Consejo Nacional de Ciencia y Tecnología, México, Mexico
- *Correspondence: Beatriz Yáñez-Rivera,
| |
Collapse
|
12
|
Harney E, Paterson S, Collin H, Chan BH, Bennett D, Plaistow SJ. Pollution induces epigenetic effects that are stably transmitted across multiple generations. Evol Lett 2022; 6:118-135. [PMID: 35386832 PMCID: PMC8966472 DOI: 10.1002/evl3.273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
It has been hypothesized that the effects of pollutants on phenotypes can be passed to subsequent generations through epigenetic inheritance, affecting populations long after the removal of a pollutant. But there is still little evidence that pollutants can induce persistent epigenetic effects in animals. Here, we show that low doses of commonly used pollutants induce genome‐wide differences in cytosine methylation in the freshwater crustacean Daphnia pulex. Uniclonal populations were either continually exposed to pollutants or switched to clean water, and methylation was compared to control populations that did not experience pollutant exposure. Although some direct changes to methylation were only present in the continually exposed populations, others were present in both the continually exposed and switched to clean water treatments, suggesting that these modifications had persisted for 7 months (>15 generations). We also identified modifications that were only present in the populations that had switched to clean water, indicating a long‐term legacy of pollutant exposure distinct from the persistent effects. Pollutant‐induced differential methylation tended to occur at sites that were highly methylated in controls. Modifications that were observed in both continually and switched treatments were highly methylated in controls and showed reduced methylation in the treatments. On the other hand, modifications found just in the switched treatment tended to have lower levels of methylation in the controls and showed increase methylation in the switched treatment. In a second experiment, we confirmed that sublethal doses of the same pollutants generate effects on life histories for at least three generations following the removal of the pollutant. Our results demonstrate that even low doses of pollutants can induce transgenerational epigenetic effects that are stably transmitted over many generations. Persistent effects are likely to influence phenotypic development, which could contribute to the rapid adaptation, or extinction, of populations confronted by anthropogenic stressors.
Collapse
Affiliation(s)
- Ewan Harney
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
- Current address: Institute of Evolutionary Biology (CSIC‐UPF) CMIMA Building Barcelona 08003 Spain
| | - Steve Paterson
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Hélène Collin
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Brian H.K. Chan
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
- Current address: Faculty of Biology, Medicine and Health The University of Manchester Manchester M13 9PT United Kingdom
| | - Daimark Bennett
- Molecular and Physiology Cell Signalling, Institute of Systems, Molecular and Integrative Biology University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Stewart J. Plaistow
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
| |
Collapse
|
13
|
de Sena Brandine G, Smith AD. Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet. NAR Genom Bioinform 2022; 3:lqab115. [PMID: 34988438 PMCID: PMC8693577 DOI: 10.1093/nargab/lqab115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/25/2021] [Accepted: 11/29/2021] [Indexed: 01/03/2023] Open
Abstract
DNA cytosine methylation is an important epigenomic mark with a wide range of functions in many organisms. Whole genome bisulfite sequencing is the gold standard to interrogate cytosine methylation genome-wide. Algorithms used to map bisulfite-converted reads often encode the four-base DNA alphabet with three letters by reducing two bases to a common letter. This encoding substantially reduces the entropy of nucleotide frequencies in the resulting reference genome. Within the paradigm of read mapping by first filtering possible candidate alignments, reduced entropy in the sequence space can increase the required computing effort. We introduce another bisulfite mapping algorithm (abismal), based on the idea of encoding a four-letter DNA sequence as only two letters, one for purines and one for pyrimidines. We show that this encoding can lead to greater specificity compared to existing encodings used to map bisulfite sequencing reads. Through the two-letter encoding, the abismal software tool maps reads in less time and using less memory than most bisulfite sequencing read mapping software tools, while attaining similar accuracy. This allows in silico methylation analysis to be performed in a wider range of computing machines with limited hardware settings.
Collapse
Affiliation(s)
- Guilherme de Sena Brandine
- Quantitative and Computational Biology, University of Southern California. 1050 Child's way, Los Angeles, CA 90007, USA
| | - Andrew D Smith
- Quantitative and Computational Biology, University of Southern California. 1050 Child's way, Los Angeles, CA 90007, USA
| |
Collapse
|
14
|
Becker BV, Kaatsch HL, Nestler K, Jakobi J, Schäfer B, Hantke T, Brockmann MA, Waldeck S, Port M, Ullmann R. Impact of medical imaging on the epigenome - low-dose exposure in the course of computed tomography does not induce detectable changes of DNA-methylation profiles in peripheral blood cells. Int J Radiat Biol 2021; 98:980-985. [PMID: 34779695 DOI: 10.1080/09553002.2021.2004329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND Computed tomography (CT) is a main contributor to artificial low-dose exposure. Understanding the biological effects induced by CT exposure and their dependency on the characteristics of photon spectra is essential for knowledge-driven risk assessment. In a previous gene expression study, we have identified upregulation of AEN, BAX, DDB2, EDA2R and FDXR after ex vivo exposure with single-energy CT and dual-energy CT (DECT). In this study, we focused on CT-induced changes of DNA methylation. This epigenetic modification of DNA is a central regulator of gene expression and instrumental in preserving genome integrity. Previous studies reported focal hypermethylation and global hypomethylation after exposure with doses above 100 mSv, however, the effect of low dose exposure on DNA methylation is hardly explored. MATERIALS AND METHODS DNA was isolated from peripheral blood of three healthy individuals 6 h after ex vivo exposition to single-energy (80 kV and 150 kV) and DECT (80 kV/Sn150 kV) with a calculated effective dose of 7.0 ± 0.08 mSv. The experimental setting was identical to the one used in our previous gene expression study enabling a direct comparison of gene expression results with changes of DNA methylation identified in this study. DNA methylation was analyzed by high-throughput sequencing of bisulfite-treated DNA targeted methylation sequencing. RESULTS Unsupervised hierarchical clustering based on DNA methylation profiles of all samples created three distinct clusters. Formation of these three clusters was solely determined by the origin of samples, indicating the absence of prominent irradiation-associated changes of DNA methylation. In line with this observation, inter-individual comparison of non-irradiated samples revealed 1163, 1224 and 4550 significant differentially methylated regions (DMRs), respectively, whereas the pairwise comparison of irradiated and non-irradiated samples failed to identify irradiation-induced DMRs in any of the three probands. This even applied to the genomic regions harboring AEN, BAX, DDB2, EDA2R and FDXR, the five genes known to be upregulated by CT exposure. CONCLUSIONS CT exposure with various photon spectra did not result in detectable changes of DNA methylation. However, minor effects in a subpopulation of irradiated cells cannot be ruled out. Thus, future studies with extended observation intervals are needed to investigate DNA methylation changes that are induced by indirect effects at later points of time or become detectable by clonal expansion of affected cells. Moreover, our data suggest that DNA methylation analysis is less sensitive in detecting immediate effects of low-dose irradiation when compared to gene expression analysis.
Collapse
Affiliation(s)
| | | | - Kai Nestler
- Department of Radiology and Neuroradiology, Bundeswehr Central Hospital, Koblenz, Germany
| | - Julia Jakobi
- Bundeswehr Institute of Radiobiology Affiliated to Ulm University, Munich, Germany
| | - Barbara Schäfer
- Bundeswehr Institute of Radiobiology Affiliated to Ulm University, Munich, Germany
| | - Thomas Hantke
- Bundeswehr Institute of Radiobiology Affiliated to Ulm University, Munich, Germany
| | - Marc A Brockmann
- Department of Neuroradiology, University Medical Center Mainz, Mainz, Germany
| | - Stephan Waldeck
- Department of Radiology and Neuroradiology, Bundeswehr Central Hospital, Koblenz, Germany
| | - Matthias Port
- Bundeswehr Institute of Radiobiology Affiliated to Ulm University, Munich, Germany
| | - Reinhard Ullmann
- Bundeswehr Institute of Radiobiology Affiliated to Ulm University, Munich, Germany
| |
Collapse
|
15
|
Sayed AEDH, Nagata K, Nakazawa T, Mitani H, Kobayashi J, Oda S. Low Dose-Rate Irradiation of Gamma-Rays-Induced Cytotoxic and Genotoxic Alterations in Peripheral Erythrocytes of p53-Deficient Medaka (Oryzias latipes). FRONTIERS IN MARINE SCIENCE 2021. [DOI: 10.3389/fmars.2021.773481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Morphological alterations and nuclear abnormalities in fish erythrocytes have been used in many studies as bioindicators of environmental mutagens including ionizing radiation. In this study, adult Japanese medaka (Oryzias latipes) were irradiated with gamma rays at a low dose rate (9.92 μGy/min) for 7 days, giving a total dose of 100 mGy; and morphological alterations, nuclear abnormalities, and apoptotic cell death induced in peripheral erythrocytes were investigated 8 h and 7 days after the end of the irradiation. A variety of abnormalities, such as tear-drop cell, crenated cell, acanthocyte, sickled cell, micronucleated cell, eccentric nucleus, notched nucleus, and schistocyte, were induced in the peripheral erythrocytes of the wild-type fish, and a less number of abnormalities and apoptotic cell death were induced in the p53-deficient fish. These results indicate that low dose-rate chronic irradiation of gamma rays can induce cytotoxic and genotoxic effects in the peripheral erythrocytes of medaka, and p53-deficient medaka are tolerant to the gamma-ray irradiation than the wild type on the surface.
Collapse
|
16
|
Pucci G, Forte GI, Cavalieri V. Evaluation of Epigenetic and Radiomodifying Effects during Radiotherapy Treatments in Zebrafish. Int J Mol Sci 2021; 22:ijms22169053. [PMID: 34445758 PMCID: PMC8396651 DOI: 10.3390/ijms22169053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 01/03/2023] Open
Abstract
Radiotherapy is still a long way from personalizing cancer treatment plans, and its effectiveness depends on the radiosensitivity of tumor cells. Indeed, therapies that are efficient and successful for some patients may be relatively ineffective for others. Based on this, radiobiological research is focusing on the ability of some reagents to make cancer cells more responsive to ionizing radiation, as well as to protect the surrounding healthy tissues from possible side effects. In this scenario, zebrafish emerged as an effective model system to test for radiation modifiers that can potentially be used for radiotherapeutic purposes in humans. The adoption of this experimental organism is fully justified and supported by the high similarity between fish and humans in both their genome sequences and the effects provoked in them by ionizing radiation. This review aims to provide the literature state of the art of zebrafish in vivo model for radiobiological studies, particularly focusing on the epigenetic and radiomodifying effects produced during fish embryos’ and larvae’s exposure to radiotherapy treatments.
Collapse
Affiliation(s)
- Gaia Pucci
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STeBiCeF), University of Palermo, 90128 Palermo, Italy;
| | - Giusi Irma Forte
- Institute of Molecular Bioimaging and Physiology, National Research Council, 90015 Cefalù, Italy
- Correspondence: (G.I.F.); (V.C.)
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STeBiCeF), University of Palermo, 90128 Palermo, Italy;
- Zebrafish Laboratory, Advanced Technologies Network (ATeN) Center, University of Palermo, 90128 Palermo, Italy
- Correspondence: (G.I.F.); (V.C.)
| |
Collapse
|
17
|
Leung CT, Yang Y, Yu KN, Tam N, Chan TF, Lin X, Kong RYC, Chiu JMY, Wong AST, Lui WY, Yuen KWY, Lai KP, Wu RSS. Low-Dose Radiation Can Cause Epigenetic Alterations Associated With Impairments in Both Male and Female Reproductive Cells. Front Genet 2021; 12:710143. [PMID: 34408775 PMCID: PMC8365519 DOI: 10.3389/fgene.2021.710143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Humans are regularly and continuously exposed to ionizing radiation from both natural and artificial sources. Cumulating evidence shows adverse effects of ionizing radiation on both male and female reproductive systems, including reduction of testis weight and sperm count and reduction of female germ cells and premature ovarian failure. While most of the observed effects were caused by DNA damage and disturbance of DNA repairment, ionizing radiation may also alter DNA methylation, histone, and chromatin modification, leading to epigenetic changes and transgenerational effects. However, the molecular mechanisms underlying the epigenetic changes and transgenerational reproductive impairment induced by low-dose radiation remain largely unknown. In this study, two different types of human ovarian cells and two different types of testicular cells were exposed to low dose of ionizing radiation, followed by bioinformatics analysis (including gene ontology functional analysis and Ingenuity Pathway Analysis), to unravel and compare epigenetic effects and pathway changes in male and female reproductive cells induced by ionizing radiation. Our findings showed that the radiation could alter the expression of gene cluster related to DNA damage responses through the control of MYC. Furthermore, ionizing radiation could lead to gender-specific reproductive impairment through deregulation of different gene networks. More importantly, the observed epigenetic modifications induced by ionizing radiation are mediated through the alteration of chromatin remodeling and telomere function. This study, for the first time, demonstrated that ionizing radiation may alter the epigenome of germ cells, leading to transgenerational reproductive impairments, and correspondingly call for research in this new emerging area which remains almost unknown.
Collapse
Affiliation(s)
- Chi Tim Leung
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Yi Yang
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kwan Ngok Yu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong.,Department of Physics, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Nathan Tam
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Ting Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xiao Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Richard Yuen Chong Kong
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Jill Man Ying Chiu
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,Department of Biology, Hong Kong Baptist University, Kowloon Tsai, Hong Kong
| | - Alice Sze Tsai Wong
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Wing Yee Lui
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Keng Po Lai
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong.,Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
| | - Rudolf Shiu Sun Wu
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Hong Kong, China.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong.,Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong
| |
Collapse
|
18
|
Blanc M, Antczak P, Cousin X, Grunau C, Scherbak N, Rüegg J, Keiter SH. The insecticide permethrin induces transgenerational behavioral changes linked to transcriptomic and epigenetic alterations in zebrafish (Danio rerio). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146404. [PMID: 33752003 DOI: 10.1016/j.scitotenv.2021.146404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 06/12/2023]
Abstract
The pyrethroid insecticide permethrin is widely used for agricultural and domestic purposes. Previous data indicated that it acts as a developmental neurotoxicant and can induce transgenerational effects in non-target organisms. However, associated underlying mechanisms remain unclear. The aim of this study was to investigate permethrin-related transgenerational effects in the zebrafish model, and to identify possible molecular mechanisms underlying inheritance. Zebrafish (F0) were exposed to permethrin during early-life (2 h post-fertilization up to 28 days). The F1 and F2 offspring generations were obtained by pairing exposed F0 males and females, and were bred unexposed. Locomotor and anxiety behavior were investigated, together with transcriptomic and epigenomic (DNA methylation) changes in brains. Permethrin exposed F0 fish were hypoactive at adulthood, while males from the F1 and F2 generations showed a specific decrease in anxiety-like behavior. In F0, transcriptomic data showed enrichment in pathways related to glutamatergic synapse activity, which may partly underlie the behavioral effects. In F1 and F2 males, dysregulation of similar pathways was observed, including a subset of differentially methylated regions that were inherited from the F0 to the F2 generation and indicated stable dysregulation of glutamatergic signaling. Altogether, the present results provide novel evidence on the transgenerational neurotoxic effects of permethrin, as well as mechanistic insight: a transient exposure induces persistent transcriptional and DNA methylation changes that may translate into transgenerational alteration of glutamatergic signaling and, thus, into behavioral alterations.
Collapse
Affiliation(s)
- Mélanie Blanc
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82 Örebro, Sweden; MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Palavas, France; Université Paris-Saclay, AgroParisTech, INRAE, GABI, Domaine de Vilvert, F-78350 Jouy-en-Josas, France.
| | - Philipp Antczak
- Centre for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Xavier Cousin
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Palavas, France; Université Paris-Saclay, AgroParisTech, INRAE, GABI, Domaine de Vilvert, F-78350 Jouy-en-Josas, France
| | - Christoph Grunau
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Nikolai Scherbak
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82 Örebro, Sweden; Örebro Life Science Centre, School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82 Örebro, Sweden
| | - Joëlle Rüegg
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82 Örebro, Sweden
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Pierron F, Lorioux S, Héroin D, Daffe G, Etcheverria B, Cachot J, Morin B, Dufour S, Gonzalez P. Transgenerational epigenetic sex determination: Environment experienced by female fish affects offspring sex ratio. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116864. [PMID: 33714788 DOI: 10.1016/j.envpol.2021.116864] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/22/2021] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
Sex determination is a complex process that can be influenced by environment in various taxa. Disturbed environments can affect population sex ratios and thus threaten their viability. Emerging evidences support a role of epigenetic mechanisms, notably DNA methylation, in environmental sex determination (ESD). In this work, using zebrafish as model and a transgenerational experiment comprising 4 successive generations, we report a strength link between the promotor methylation level of three genes in female gonads and population sex ratio. One generation of zebrafish was exposed throughout its lifetime to cadmium (Cd), a non-essential metal, at an environmentally relevant concentration. The subsequent generations were not exposed. At the first and the third generation a subset of individuals was exposed to an elevated temperature, a well-known masculinizing factor in zebrafish. While heat was associated to an increase in the methylation level of cyp19a1a gene and population masculinization, foxl2a/dmrt1 methylation levels appeared to be influenced by Cd and fish density leading to offspring feminization. Ancestral Cd exposure indeed led to a progressive feminization of the population over generations and affected the sex plastic response of zebrafish in response to heat. The effect of Cd on the methylation level of foxl2a was observed until the third generation, supporting potential transgenerational inheritance. Our results support (i) a key role of cyp19a1a methylation in SD in zebrafish in response to environmental cues and (ii) the fact that the environment experienced by parents, namely mothers in the present case, can affect their offspring sex ratio via environment-induced DNA methylation changes in gonads.
Collapse
Affiliation(s)
- Fabien Pierron
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, F-33600, Pessac, France.
| | - Sophie Lorioux
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, F-33600, Pessac, France
| | - Débora Héroin
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, F-33600, Pessac, France
| | - Guillemine Daffe
- Univ. Bordeaux, CNRS, INRAE, La Rochelle Univ., UMS 2567 POREA, F-33615, Pessac, France
| | | | - Jérôme Cachot
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, F-33600, Pessac, France
| | - Bénédicte Morin
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, F-33600, Pessac, France
| | - Sylvie Dufour
- Laboratory Biology of Aquatic Organisms and Ecosystems (BOREA), Muséum National D'Histoire Naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, 75231, Paris Cedex, 05, France
| | - Patrice Gonzalez
- Univ. Bordeaux, CNRS, EPOC, EPHE, UMR 5805, F-33600, Pessac, France
| |
Collapse
|
21
|
Martín L, Kamstra JH, Hurem S, Lindeman LC, Brede DA, Aanes H, Babiak I, Arenal A, Oughton D, Salbu B, Lyche JL, Aleström P. Altered non-coding RNA expression profile in F 1 progeny 1 year after parental irradiation is linked to adverse effects in zebrafish. Sci Rep 2021; 11:4142. [PMID: 33602989 PMCID: PMC7893006 DOI: 10.1038/s41598-021-83345-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Gamma radiation produces DNA instability and impaired phenotype. Previously, we observed negative effects on phenotype, DNA methylation, and gene expression profiles, in offspring of zebrafish exposed to gamma radiation during gametogenesis. We hypothesize that previously observed effects are accompanied with changes in the expression profile of non-coding RNAs, inherited by next generations. Non-coding RNA expression profile was analysed in F1 offspring (5.5 h post-fertilization) by high-throughput sequencing 1 year after parental irradiation (8.7 mGy/h, 5.2 Gy total dose). Using our previous F1-γ genome-wide gene expression data (GSE98539), hundreds of mRNAs were predicted as targets of differentially expressed (DE) miRNAs, involved in pathways such as insulin receptor, NFkB and PTEN signalling, linking to apoptosis and cancer. snRNAs belonging to the five major spliceosomal snRNAs were down-regulated in the F1-γ group, Indicating transcriptional and post-transcriptional alterations. In addition, DEpiRNA clusters were associated to 9 transposable elements (TEs) (LTR, LINE, and TIR) (p = 0.0024), probable as a response to the activation of these TEs. Moreover, the expression of the lincRNAs malat-1, and several others was altered in the offspring F1, in concordance with previously observed phenotypical alterations. In conclusion, our results demonstrate diverse gamma radiation-induced alterations in the ncRNA profiles of F1 offspring observable 1 year after parental irradiation.
Collapse
Affiliation(s)
- Leonardo Martín
- grid.441252.40000 0000 9526 034XMorphophysiology Department, Faculty of Agricultural Sciences, University of Camagüey Ignacio Agramonte y Loynaz, 74 650 Camagüey, Cuba ,grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Jorke H. Kamstra
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.5477.10000000120346234Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Selma Hurem
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Paraclinical Sciences, Norwegian University of Life Sciences, 0454 Oslo, Norway
| | - Leif C. Lindeman
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, 0454 Oslo, Norway
| | - Dag A. Brede
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Environmental Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Håvard Aanes
- grid.458778.1PatoGen AS, P.O.box 548, 6001 Ålesund, Norway
| | - Igor Babiak
- grid.465487.cFaculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Amilcar Arenal
- grid.441252.40000 0000 9526 034XMorphophysiology Department, Faculty of Agricultural Sciences, University of Camagüey Ignacio Agramonte y Loynaz, 74 650 Camagüey, Cuba
| | - Deborah Oughton
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Environmental Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Brit Salbu
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Environmental Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Jan Ludvig Lyche
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Paraclinical Sciences, Norwegian University of Life Sciences, 0454 Oslo, Norway
| | - Peter Aleström
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, 0454 Oslo, Norway
| |
Collapse
|
22
|
Swati, Chadha VD. Role of epigenetic mechanisms in propagating off-targeted effects following radiation based therapies - A review. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2021; 787:108370. [PMID: 34083045 DOI: 10.1016/j.mrrev.2021.108370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/17/2022]
Abstract
Despite being an important diagnostic and treatment modality, ionizing radiation (IR) is also known to cause genotoxicity and multiple side effects leading to secondary carcinogenesis. While modern cancer radiation therapy has improved patient recovery and enhanced survival rates, the risk of radiation-related adverse effects has become a growing challenge. It is now well-accepted that IR-induced side effects are not exclusively restricted to exposed cells but also spread to distant 'bystander' cells and even to the unexposed progeny of the irradiated cells. These 'off-targeted' effects involve a plethora of molecular events depending on the type of radiation and tumor tissue background. While the mechanisms by which off-targeted effects arise remain obscure, emerging evidence based on the non-mendelian inheritance of various manifestations of them as well as their persistence for longer periods supports a contribution of epigenetic factors. This review focuses on the major epigenetic phenomena including DNA methylation, histone modifications, and small RNA mediated silencing and their versatile role in the manifestation of IR induced off-targeted effects. As short- and long-range communication vehicles respectively, the role of gap junctions and exosomes in spreading these epigenetic-alteration driven off-targeted effects is also discussed. Furthermore, this review emphasizes the possible therapeutic potentials of these epigenetic mechanisms and how beneficial outcomes could potentially be achieved by targeting various signaling molecules involved in these mechanisms.
Collapse
Affiliation(s)
- Swati
- Centre for Nuclear Medicine (U.I.E.A.S.T), South Campus, Panjab University, Sector 25, Chandigarh, 160014, India.
| | - Vijayta D Chadha
- Centre for Nuclear Medicine (U.I.E.A.S.T), South Campus, Panjab University, Sector 25, Chandigarh, 160014, India.
| |
Collapse
|
23
|
Vo NTK. Environmental radiobiology of amphibians - knowledge gaps to be filled using cell lines. Int J Radiat Biol 2021; 98:1034-1046. [PMID: 33428858 DOI: 10.1080/09553002.2021.1872815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Amphibians are facing an unprecedented level of population declines worldwide. The causes run the gamut from habitat loss and succumbing to opportunistic pathogen infections to vulnerability to toxic pollutants and ultraviolet (UV)-B radiation exposure. Anthropogenic activities including Chernobyl and Fukushima nuclear disasters and radioactive waste leakage into the environment raise the background radiation levels. Their immediate and chronic effects on amphibian populations are still being studied. However, the literature on environmental radiation effects on amphibian health still requires a lot more work. Laboratory and field works need to be conducted hand in hand in order to make informative and conclusive analyses to distinguish bad from good and harm from risk or to argue for or against the linear no-threshold model in radioprotection programs. Amphibian cell lines can help seek answers to important questions pertaining environmental radiobiology and amphibian health wherever they can suitably and effectively. The purpose of this work is to show that amphibian cell lines can 'rescue' important knowledge gaps in the literature, especially in the low-dose radiation mechanisms. Presently, there are 142 amphibian cell lines developed from six urodelans and 17 anurans. Amphibian cell lines can help expand and enrich the limited literature on environmental radiation effects on amphibians. They can be used to study mechanisms of radiation actions and discover reliable biomarkers for low-dose exposure. They can be used in environmental radiation monitoring and radioprotection programs. They can be used to determine the effects of co-exposure of IR and other stressors in the environment on amphibian health. They represent an ethical choice for amphibian conservation efforts in the current global amphibian declines. Lessons learned from cellular data can be useful guides to gain a better picture of effects occurring at the amphibian population and ecosystem levels.
Collapse
Affiliation(s)
- Nguyen T K Vo
- Department of Biology, McMaster University, Hamilton, Canada.,School of Interdisciplinary Science, McMaster University, Hamilton, Canada
| |
Collapse
|
24
|
Paunesku T, Stevanović A, Popović J, Woloschak GE. Effects of low dose and low dose rate low linear energy transfer radiation on animals - review of recent studies relevant for carcinogenesis. Int J Radiat Biol 2021; 97:757-768. [PMID: 33289582 PMCID: PMC9216178 DOI: 10.1080/09553002.2020.1859155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/20/2020] [Accepted: 11/29/2020] [Indexed: 02/06/2023]
Abstract
Purpose: Carcinogenic effects of radiation are often assumed to be universally understood, more often than, for example, carcinogenic effects of many different chemicals. This in turn leads to an assumption that any dose of radiation, delivered at any dose rate, poses a serious health challenge. This remains an issue of dispute and low dose radiation research is focused on understanding whether these exposures contribute to cancer incidence. This review is focused on the low linear energy transfer (low LET) radiation exposures for which the data is the most abundant in recent years. Materials and methods: Review of the literature between 2008 and today, highlighting some of the most diverse studies in low dose research. Results: Low dose and low dose rate, low LET ionizing radiation animal studies suggest that the effects of exposure very much depend on animal genotype and health status.Conclusions: Only the integration of all of the data from different models and studies will lead to a fuller understanding of low dose radiation effects. Therefore, we hope to see an increase in international archival efforts and exchange of raw data information opening the possibilities for new types of meta analyses.
Collapse
Affiliation(s)
- Tatjana Paunesku
- Department of Radiation Oncology, Northwestern University, Chicago, IL, USA
| | - Aleksandra Stevanović
- Multidisciplinary Studies of History and Philosophy of Natural Sciences and Technology, University of Belgrade, Belgrade, Serbia
| | - Jelena Popović
- Department of Radiation Oncology, Northwestern University, Chicago, IL, USA
| | - Gayle E Woloschak
- Department of Radiation Oncology, Northwestern University, Chicago, IL, USA
| |
Collapse
|
25
|
Venney CJ, Wellband KW, Heath DD. Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon. Heredity (Edinb) 2021; 126:38-49. [PMID: 32699390 PMCID: PMC7852867 DOI: 10.1038/s41437-020-0346-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhelming evidence for environmental effects on phenotype, the underlying mechanisms are less clear. Variation in DNA methylation is a potential mechanism mediating environmental effects on phenotype due to its sensitivity to environmental stimuli, transgenerational inheritance, and influences on transcription. To characterize the effect of environment on methylation, we created two 6 × 6 (North Carolina II) Chinook salmon breeding crosses and reared the offspring in two environments: uniform hatchery tanks and seminatural stream channels. We sampled the fish twice during development, at the alevin (larval) and fry (juvenile) stages. We measured DNA methylation at 13 genes using a PCR-based bisulfite sequencing protocol. The genetic architecture of DNA methylation differed between rearing environments, with greater additive and nonadditive genetic variance in hatchery fish and greater maternal effects in seminatural channel fish, though gene-specific variation was evident. We observed plasticity in methylation across all assayed genes, as well as gene-specific effects at two genes in alevin and six genes in fry, indicating developmental stage-specific effects of rearing environment on methylation. Characterizing genetic and environmental influences on methylation is critical for future studies on DNA methylation as a potential mechanism for acclimation and adaptation.
Collapse
Affiliation(s)
- Clare J Venney
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada
| | - Kyle W Wellband
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, G1V 0A6, Québec City, QC, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, 401 Sunset Ave, Windsor, ON, N9B 3P4, Canada.
| |
Collapse
|
26
|
Anastasiadi D, Shao C, Chen S, Piferrer F. Footprints of global change in marine life: Inferring past environment based on DNA methylation and gene expression marks. Mol Ecol 2020; 30:747-760. [PMID: 33372368 DOI: 10.1111/mec.15764] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/17/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022]
Abstract
Ocean global warming affects the distribution, life history and physiology of marine life. Extreme events, like marine heatwaves, are increasing in frequency and intensity. During sensitive stages of early fish development, the consequences may be long-lasting and mediated by epigenetic mechanisms. Here, we used European sea bass as a model to study the possible long-lasting effects of a marine heatwave during early development. We measured DNA methylation and gene expression in four tissues (brain, muscle, liver and testis) and detected differentially methylated regions (DMRs). Six genes were differentially expressed and contained DMRs three years after exposure to increased temperature, indicating direct phenotypic consequences and representing persistent changes. Interestingly, nine genes contained DMRs around the same genomic regions across tissues, therefore consisting of common footprints of developmental temperature in environmentally responsive loci. These loci are, to our knowledge, the first metastable epialleles (MEs) described in fish. MEs may serve as biomarkers to infer past life history events linked with persistent consequences. These results highlight the importance of subtle phenotypic changes mediated by epigenetics to extreme weather events during sensitive life stages. Also, to our knowledge, it is the first time the molecular effects of a marine heatwave during the lifetime of individuals are assessed. MEs could be used in surveillance programs aimed at determining the footprints of climate change on marine life. Our study paves the way for the identification of conserved MEs that respond equally to environmental perturbations across species. Conserved MEs would constitute a tool of assessment of global change effects in marine life at a large scale.
Collapse
Affiliation(s)
- Dafni Anastasiadi
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Songlin Chen
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| |
Collapse
|
27
|
Gombeau K, Bonzom JM, Cavalié I, Camilleri V, Orjollet D, Dubourg N, Beaugelin-Seiller K, Bourdineaud JP, Lengagne T, Armant O, Ravanat JL, Adam-Guillermin C. Dose-dependent genomic DNA hypermethylation and mitochondrial DNA damage in Japanese tree frogs sampled in the Fukushima Daiichi area. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2020; 225:106429. [PMID: 33059178 DOI: 10.1016/j.jenvrad.2020.106429] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
The long-term consequences of the nuclear disaster at the Fukushima Daiichi Nuclear Power Plant (FDNPP) that occurred on March 2011, have been scarcely studied on wildlife. We sampled Japanese tree frogs (Dryophytes japonicus), in a 50 -km area around the FDNPP to test for an increase of DNA damages and variation of DNA methylation level. The ambient dose rate ranged between 0.4 and 2.8 μGy h-1 and the total estimated dose rate absorbed by frogs ranged between 0.3 and 7.7 μGy h-1. Frogs from contaminated sites exhibited a dose-dependent increase of global genomic DNA methylation level (5-mdC and 5-hmdC) and of mitochondrial DNA damages. Such DNA damages may indicate a genomic instability, which may induce physiological adaptations governed by DNA methylation changes. This study stresses the need for biological data combining targeted molecular methods and classic ecotoxicology, in order to better understand the impacts on wildlife of long term exposure to low ionizing radiation levels.
Collapse
Affiliation(s)
- Kewin Gombeau
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France; University of Bordeaux, CNRS, UMR5095 CNRS, Institute for Cellular Biochemistry and Genetics, 1 Rue Camille Saint Saëns, CS 61390, 33077, Bordeaux Cedex, France
| | - Jean-Marc Bonzom
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Isabelle Cavalié
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Virginie Camilleri
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Daniel Orjollet
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LR2T, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Nicolas Dubourg
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Karine Beaugelin-Seiller
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Jean-Paul Bourdineaud
- University of Bordeaux, CNRS, UMR MFP 5234, European Institute of Chemistry and Biology, 2 Rue Robert Escarpit, 33607, Pessac, France
| | - Thierry Lengagne
- Université de Lyon, UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, ENTPE, CNRS, 6 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Olivier Armant
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance, 13115, France
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes, INAC-SCIB, 38000, Grenoble, France; CEA, INAC-SCIB Laboratoire des Lésions des Acides Nucléiques, 38000, Grenoble, France
| | | |
Collapse
|
28
|
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
|
29
|
Venney CJ, Love OP, Drown EJ, Heath DD. DNA Methylation Profiles Suggest Intergenerational Transfer of Maternal Effects. Mol Biol Evol 2020; 37:540-548. [PMID: 31651942 DOI: 10.1093/molbev/msz244] [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] [Indexed: 12/13/2022] Open
Abstract
The view of maternal effects (nongenetic maternal environmental influence on offspring phenotype) has changed from one of distracting complications in evolutionary genetics to an important evolutionary mechanism for improving offspring fitness. Recent studies have shown that maternal effects act as an adaptive mechanism to prepare offspring for stressful environments. Although research into the magnitude of maternal effects is abundant, the molecular mechanisms of maternal influences on offspring phenotypic variation are not fully understood. Despite recent work identifying DNA methylation as a potential mechanism of nongenetic inheritance, currently proposed links between DNA methylation and parental effects are indirect and primarily involve genomic imprinting. We combined a factorial breeding design and gene-targeted sequencing methods to assess inheritance of methylation during early life stages at 14 genes involved in growth, development, metabolism, stress response, and immune function of Chinook salmon (Oncorhynchus tshawytscha). We found little evidence for additive or nonadditive genetic effects acting on methylation levels during early development; however, we detected significant maternal effects. Consistent with conventional maternal effect data, maternal effects on methylation declined through development and were replaced with nonadditive effects when offspring began exogenous feeding. We mapped methylation at individual CpG sites across the selected candidate genes to test for variation in site-specific methylation profiles and found significant maternal effects at selected CpG sites that also declined with development stage. While intergenerational inheritance of methylated DNA is controversial, we show that CpG-specific methylation may function as an underlying molecular mechanism for maternal effects, with important implications for offspring fitness.
Collapse
Affiliation(s)
- Clare J Venney
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Oliver P Love
- Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| | - Ellen Jane Drown
- Yellow Island Aquaculture Ltd., Campbell River, British Columbia, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada.,Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| |
Collapse
|
30
|
Vo NTK. The sine qua non of the fish invitrome today and tomorrow in environmental radiobiology. Int J Radiat Biol 2020; 98:1025-1033. [PMID: 32816609 DOI: 10.1080/09553002.2020.1812761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Fish cell lines, collectively referred to as the fish invitrome, are useful diagnostic tools to study radiation impacts on aquatic health and elucidate radiation mechanisms in fish. This paper will highlight the advantages, discuss the challenges, and propose possible future directions for uses of the fish invitrome in the field of environmental radiobiology. The fish invitrome contains at least 714 fish cell lines. However, only a few of these cell lines have been used to study radiation biology in fish and they represent only 10 fish species. The fish invitrome is clearly not yet explored for its full potential in radiation biology. Evidence suggests that they are useful and, in some cases, irreplaceable in making underlying theories and fundamental concepts in radiation responses in fish. The debate of whether environmental radiation is harmful, presents risks, has no effect on health, or is beneficial is on-going and is one that fish cell lines can help address in a time-effective fashion. Any information obtained with fish cell lines is useful in the framework of environment radiation risk assessments. Radiation threats to aquatic health will continue due to the very likely rise of nuclear energy and medicine in the future. The fish invitrome, in theory, lives forever and can meet new challenges at any given time to provide diagnostic risk analyses pertaining to aquatic health and environmental radiation protection.
Collapse
Affiliation(s)
- Nguyen T K Vo
- Department of Biology, McMaster University, Hamilton, ON, Canada
| |
Collapse
|
31
|
Ionizing Radiation-Induced Epigenetic Modifications and Their Relevance to Radiation Protection. Int J Mol Sci 2020; 21:ijms21175993. [PMID: 32825382 PMCID: PMC7503247 DOI: 10.3390/ijms21175993] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
The present system of radiation protection assumes that exposure at low doses and/or low dose-rates leads to health risks linearly related to the dose. They are evaluated by a combination of epidemiological data and radiobiological models. The latter imply that radiation induces deleterious effects via genetic mutation caused by DNA damage with a linear dose-dependence. This picture is challenged by the observation of radiation-induced epigenetic effects (changes in gene expression without altering the DNA sequence) and of non-linear responses, such as non-targeted and adaptive responses, that in turn can be controlled by gene expression networks. Here, we review important aspects of the biological response to ionizing radiation in which epigenetic mechanisms are, or could be, involved, focusing on the possible implications to the low dose issue in radiation protection. We examine in particular radiation-induced cancer, non-cancer diseases and transgenerational (hereditary) effects. We conclude that more realistic models of radiation-induced cancer should include epigenetic contribution, particularly in the initiation and progression phases, while the impact on hereditary risk evaluation is expected to be low. Epigenetic effects are also relevant in the dispute about possible "beneficial" effects at low dose and/or low dose-rate exposures, including those given by the natural background radiation.
Collapse
|
32
|
Valdivieso A, Ribas L, Monleón-Getino A, Orbán L, Piferrer F. Exposure of zebrafish to elevated temperature induces sex ratio shifts and alterations in the testicular epigenome of unexposed offspring. ENVIRONMENTAL RESEARCH 2020; 186:109601. [PMID: 32371278 DOI: 10.1016/j.envres.2020.109601] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
Accumulating evidence shows that environmental changes can affect population sex ratios through epigenetic regulation of gene expression in species where sex depends on both genetic and environmental cues. Sometimes, altered sex ratios persist in the next generation even when the environmental cue is no longer present (a multigenerational effect). However, evidence of transgenerational effects (i.e., beyond the first non-exposed generation), which tend to be paternally transmitted, is scarce and a matter of debate. Here, we used the AB strain of zebrafish, where sex depends on both genetic and environmental influences, to study possible multi- (to the F1) and transgenerational (to the F2) effects of elevated temperature during the critical period of sex differentiation. From eight initial different families, five were selected in order to capture sufficient variation between the sex ratio of the control group (28 °C) and the group exposed to elevated (35 °C) temperature only at the parental (P) generation. Results showed a consistent increase in the proportion of males in the P generation in all five families as a result of heat treatment. Sex ratios were then determined in the F1 and F2 offspring derived from both above groups, which were all raised at 28 °C. A persisting male-skewed sex ratio in the 35°C-derived, unexposed offspring of the F1 generation was observed in three families, denoting family-dependent multigenerational effects. However, no transgenerational effects were observed in the F2 generation of any family. DNA methylation was also assessed in the testis of P, F1 and F2 males derived from exposed and non-exposed fathers and grandfathers. DNA methylation was significantly decreased only in the testis of the 35°C-derived males in the F1 generation but not of the F2 generation and, surprisingly, neither in the 35°C-exposed males of the P generation. Taken together, our results show great interfamily variation, not only in sex ratio response to elevated temperature, but also on its multigenerational effects, denoting a strong influence of genetics. Alterations in the testicular epigenome in F1 males calls for attention to possible, previously unnoticed, effects of temperature in the unexposed offspring of heat-exposed parents in a global warming scenario.
Collapse
Affiliation(s)
- Alejandro Valdivieso
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Antonio Monleón-Getino
- Group of Research in Biostatistics and Bioinformatics (GRBIO), BIOST(3), Department of Genetics, Microbiology and Statistics: Section of Statistics. University of Barcelona (UB), Barcelona, Spain
| | - László Orbán
- Frontline Fish Genomics Research Group, Department of Animal Sciences, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.
| |
Collapse
|
33
|
Fan X, Hou T, Guan Y, Li X, Zhang S, Wang Z. Genomic responses of DNA methylation and transcript profiles in zebrafish cells upon nutrient deprivation stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137980. [PMID: 32208287 DOI: 10.1016/j.scitotenv.2020.137980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/14/2020] [Accepted: 03/15/2020] [Indexed: 06/10/2023]
Abstract
Environmental stress such as nutrient deprivation across multiple fields in nature causes physiological and biochemical changes in organism. Understanding the potential epigenetic modulations to phenotypic variation upon nutrient deprivation stress is crucial for environmental assessments. Here, the methyl-cytosine at single-base resolution was mapped across the whole genome and the methylation patterns and methylation levels coordinated with transcript analysis were systemically elaborated in zebrafish embryonic fibroblast cells under serum starvation stress. The down-regulated genes mainly annotated to the pathways of DNA replication and cell cycle that were consistent with cell physiological changes. Vast differentially methylated regions were identified in genomic chromosome and showed enrichment in the intron and intergenic regions. In an integrated transcriptome and DNA methylation analyses, 135 negatively correlated genes were determined, wherein the hub genes of gins2, cdca5, fbxo5, slc29a2, suv39h1b, and zgc:174160 were predominant responsive to the nutrient condition changes. Besides, nutrient recovery and DNA methyltransferases inhibitor supplements partly rescued cell proliferation with decrease of DNA methylation and reactivation of several depressed genes, implying the possible intrinsic relationships among cell physiological state, mRNA expression, and DNA methylation. Collectively, current study proved the broad role of DNA methylation in governing cellular responses to nutrient deprivation and revealed the epigenetic risk of starvation stress in zebrafish.
Collapse
Affiliation(s)
- Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tingting Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangju Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuai Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
34
|
Murat El Houdigui S, Adam-Guillermin C, Armant O. Ionising Radiation Induces Promoter DNA Hypomethylation and Perturbs Transcriptional Activity of Genes Involved in Morphogenesis during Gastrulation in Zebrafish. Int J Mol Sci 2020; 21:ijms21114014. [PMID: 32512748 PMCID: PMC7312202 DOI: 10.3390/ijms21114014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
Embryonic development is particularly vulnerable to stress and DNA damage, as mutations can accumulate through cell proliferation in a wide number of cells and organs. However, the biological effects of chronic exposure to ionising radiation (IR) at low and moderate dose rates (< 6 mGy/h) remain largely controversial, raising concerns for environmental protection. The present study focuses on the molecular effects of IR (0.005 to 50 mGy/h) on zebrafish embryos at the gastrula stage (6 hpf), at both the transcriptomics and epigenetics levels. Our results show that exposure to IR modifies the expression of genes involved in mitochondrial activity from 0.5 to 50 mGy/h. In addition, important developmental pathways, namely, the Notch, retinoic acid, BMP and Wnt signalling pathways, were altered at 5 and 50 mGy/h. Transcriptional changes of genes involved in the morphogenesis of the ectoderm and mesoderm were detected at all dose rates, but were prominent from 0.5 to 50 mGy/h. At the epigenetic level, exposure to IR induced a hypomethylation of DNA in the promoter of genes that colocalised with both H3K27me3 and H3Kme4 histone marks and correlated with changes in transcriptional activity. Finally, pathway enrichment analysis demonstrated that the DNA methylation changes occurred in the promoter of important developmental genes, including morphogenesis of the ectoderm and mesoderm. Together, these results show that the transcriptional program regulating morphogenesis in gastrulating embryos was modified at dose rates greater than or equal to 0.5 mGy/h, which might predict potential neurogenesis and somitogenesis defects observed at similar dose rates later in development.
Collapse
Affiliation(s)
- Sophia Murat El Houdigui
- PSE-ENV/SRTE/LECO, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Cadarache, 13115 Saint-Paul-Lez-Durance, France;
| | - Christelle Adam-Guillermin
- PSE-SANTE/SDOS/LMDN, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Cadarache, 13115 Saint-Paul-Lez-Durance, France;
| | - Olivier Armant
- PSE-ENV/SRTE/LECO, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Cadarache, 13115 Saint-Paul-Lez-Durance, France;
- Correspondence:
| |
Collapse
|
35
|
Haanes H, Hansen EL, Hevrøy TH, Jensen LK, Gjelsvik R, Jaworska A, Bradshaw C. Realism and usefulness of multispecies experiment designs with regard to application in radioecology: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:134485. [PMID: 31839283 DOI: 10.1016/j.scitotenv.2019.134485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
Multispecies experiments like microcosms and mesocosms are widely used in many fields of research but not in radioecology. In radioecology, size limitations are important as large experimental volumes involve problems with waste (radionuclides), or shielding, absorption and available space in gamma fields (often within a climate chamber). We have therefore performed a literature review (ISI Web of Science, n = 406) of the design and properties of multispecies effect studies <100 L in size and with three or more mentioned taxa in other research fields to assess their suitability to radioecology. Studies with more mentioned taxa assess structural ecosystem parameters more often than studies with fewer mentioned taxa, while the opposite trend is seen for indirect effects/interactions. Studies of indirect effects benefit from more replicates and longer experiments. Almost all studies assess some ecosystem level parameter but only a quarter take a holistic approach assessing both structural and functional as well as indirect effects. We find that most cosms are custom-made systems, rather than standardised designs. Unmanipulated cosms consist of excised portions of the natural environment with a higher number of mentioned taxa, high ecological complexity and high realism, but have a relatively low replicability. In contrast, standardised cosms with fewer mentioned taxa have less ecological complexity but much higher replicability. This literature review shows that smaller cosm sizes have similar ecological complexity (e.g. number of taxa and trophic levels) and experimental duration as larger sized cosms, allowing for ecologically-relevant investigations, despite their small size. We encourage multispecies radioecology studies, preferably with environmental relevant doses and sufficient detail on dosimetry.
Collapse
Affiliation(s)
- Hallvard Haanes
- Norwegian Radiation and Nuclear Safety Authority, P.O. Box 329 Skøyen, NO-0213 Oslo, Norway; Centre for Environmental Radioactivity (CERAD CoE), P.O. Box 5003, NO-1432 Ås, Norway.
| | - Elisabeth Lindbo Hansen
- Norwegian Radiation and Nuclear Safety Authority, P.O. Box 329 Skøyen, NO-0213 Oslo, Norway; Centre for Environmental Radioactivity (CERAD CoE), P.O. Box 5003, NO-1432 Ås, Norway.
| | - Tanya Helena Hevrøy
- Norwegian Radiation and Nuclear Safety Authority, P.O. Box 329 Skøyen, NO-0213 Oslo, Norway; Centre for Environmental Radioactivity (CERAD CoE), P.O. Box 5003, NO-1432 Ås, Norway.
| | - Louise Kiel Jensen
- Centre for Environmental Radioactivity (CERAD CoE), P.O. Box 5003, NO-1432 Ås, Norway; Norwegian Radiation and Nuclear Safety Authority, The Fram Centre, P.O. Box 6606 Langnes, 9296 Tromsø, Norway.
| | - Runhild Gjelsvik
- Norwegian Radiation and Nuclear Safety Authority, P.O. Box 329 Skøyen, NO-0213 Oslo, Norway; Centre for Environmental Radioactivity (CERAD CoE), P.O. Box 5003, NO-1432 Ås, Norway.
| | - Alicja Jaworska
- Norwegian Radiation and Nuclear Safety Authority, P.O. Box 329 Skøyen, NO-0213 Oslo, Norway; Centre for Environmental Radioactivity (CERAD CoE), P.O. Box 5003, NO-1432 Ås, Norway.
| | - Clare Bradshaw
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden.
| |
Collapse
|
36
|
Combined neurodevelopmental exposure to deltamethrin and corticosterone is associated with Nr3c1 hypermethylation in the midbrain of male mice. Neurotoxicol Teratol 2020; 80:106887. [PMID: 32348866 DOI: 10.1016/j.ntt.2020.106887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/10/2020] [Accepted: 04/21/2020] [Indexed: 12/21/2022]
Abstract
Attention-Deficit Hyperactivity Disorder (ADHD) is one of the most common neurodevelopmental disorders and manifests inattention, hyperactivity, and impulsivity symptoms in childhood that can last throughout life. Genetic and environmental studies implicate the dopamine system in ADHD pathogenesis. Work from our group and that of others indicates that deltamethrin insecticide and stress exposure during neurodevelopment leads to alterations in dopamine function, and we hypothesized that exposure to both of these factors together would lead to synergistic effects on DNA methylation of key genes within the midbrain, a highly dopaminergic region, that could contribute to these findings. Through targeted next-generation sequencing of a panel of cortisol and dopamine pathway genes, we observed hypermethylation of the glucocorticoid receptor gene, Nr3c1, in the midbrain of C57/BL6N males in response to dual deltamethrin and corticosterone exposures during development. This is the first description of DNA methylation studies of Nr3c1 and key dopaminergic genes within the midbrain in response to a pyrethroid insecticide, corticosterone, and these two exposures together. Our results provide possible connections between environmental exposures that impact the dopamine system and the hypothalamic-pituitary-adrenal axis via changes in DNA methylation and provides new information about the presence of epigenetic effects in adulthood after exposure during neurodevelopment.
Collapse
|
37
|
Jeremias G, Gonçalves FJM, Pereira JL, Asselman J. Prospects for incorporation of epigenetic biomarkers in human health and environmental risk assessment of chemicals. Biol Rev Camb Philos Soc 2020; 95:822-846. [PMID: 32045110 DOI: 10.1111/brv.12589] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 12/18/2022]
Abstract
Epigenetic mechanisms have gained relevance in human health and environmental studies, due to their pivotal role in disease, gene × environment interactions and adaptation to environmental change and/or contamination. Epigenetic mechanisms are highly responsive to external stimuli and a wide range of chemicals has been shown to determine specific epigenetic patterns in several organisms. Furthermore, the mitotic/meiotic inheritance of such epigenetic marks as well as the resulting changes in gene expression and cell/organismal phenotypes has now been demonstrated. Therefore, epigenetic signatures are interesting candidates for linking environmental exposures to disease as well as informing on past exposures to stressors. Accordingly, epigenetic biomarkers could be useful tools in both prospective and retrospective risk assessment but epigenetic endpoints are currently not yet incorporated into risk assessments. Achieving a better understanding on this apparent impasse, as well as identifying routes to promote the application of epigenetic biomarkers within environmental risk assessment frameworks are the objectives of this review. We first compile evidence from human health studies supporting the use of epigenetic exposure-associated changes as reliable biomarkers of exposure. Then, specifically focusing on environmental science, we examine the potential and challenges of developing epigenetic biomarkers for environmental fields, and discuss useful organisms and appropriate sequencing techniques to foster their development in this context. Finally, we discuss the practical incorporation of epigenetic biomarkers in the environmental risk assessment of chemicals, highlighting critical data gaps and making key recommendations for future research within a regulatory context.
Collapse
Affiliation(s)
- Guilherme Jeremias
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Fernando J M Gonçalves
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Joana L Pereira
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jana Asselman
- Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit - GhEnToxLab, Ghent University, 9000, Gent, Belgium
| |
Collapse
|
38
|
Anastasiadi D, Piferrer F. Epimutations in Developmental Genes Underlie the Onset of Domestication in Farmed European Sea Bass. Mol Biol Evol 2020; 36:2252-2264. [PMID: 31289822 PMCID: PMC6759067 DOI: 10.1093/molbev/msz153] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Domestication of wild animals induces a set of phenotypic characteristics collectively known as the domestication syndrome. However, how this syndrome emerges is still not clear. Recently, the neural crest cell deficit hypothesis proposed that it is generated by a mildly disrupted neural crest cell developmental program, but clear support is lacking due to the difficulties of distinguishing pure domestication effects from preexisting genetic differences between farmed and wild mammals and birds. Here, we use a farmed fish as model to investigate the role of persistent changes in DNA methylation (epimutations) in the process of domestication. We show that early domesticates of sea bass, with no genetic differences with wild counterparts, contain epimutations in tissues with different embryonic origins. About one fifth of epimutations that persist into adulthood are established by the time of gastrulation and affect genes involved in developmental processes that are expressed in embryonic structures, including the neural crest. Some of these genes are differentially expressed in sea bass with lower jaw malformations, a key feature of domestication syndrome. Interestingly, these epimutations significantly overlap with cytosine-to-thymine polymorphisms after 25 years of selective breeding. Furthermore, epimutated genes coincide with genes under positive selection in other domesticates. We argue that the initial stages of domestication include dynamic alterations in DNA methylation of developmental genes that affect the neural crest. Our results indicate a role for epimutations during the beginning of domestication that could be fixed as genetic variants and suggest a conserved molecular process to explain Darwin’s domestication syndrome across vertebrates.
Collapse
Affiliation(s)
- Dafni Anastasiadi
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Barcelona, Spain.,The New Zealand Institute for Plant & Food Research, Nelson, New Zealand
| | - Francesc Piferrer
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Barcelona, Spain
| |
Collapse
|
39
|
Guirandy N, Gagnaire B, Frelon S, Munch T, Dubourg N, Camilleri V, Cavalié I, Floriani M, Arcanjo C, Murat El Houdigui S, Armant O, Adam-Guillermin C, Gonzalez P, Simon O. Adverse effects induced by chronic gamma irradiation in progeny of adult fish not affecting parental reproductive performance. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2019; 38:2556-2567. [PMID: 31393625 DOI: 10.1002/etc.4562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/11/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Multigenerational studies have become of great interest in ecotoxicology since the consequence of parental exposure to contaminants on offspring generations was established in situ or in laboratory conditions. The present study mainly examined the chronic effects of external Cs-137 gamma irradiation exposure at 4 dose rates (control, 0.5, 5, and 50 mGy h-1 ) on adult zebrafish (F0) exposed for 10 d and their progeny (F1) exposed or unexposed for 4 to 5 d. The main endpoints investigated included parental reproductive performance, embryo-larval survival, DNA alterations, and reactive oxygen species (ROS) production in F0 and F1. No effects on reproductive success, fecundity, or egg fertilization rate were observed. However, drastic effects were observed on F1 exposed to 50 mGy h-1 , resulting in a mortality rate of 100%. The drastic effects were also observed when the progeny was not irradiated. It was demonstrated that the sensitivity of the embryos was mainly attributable to parental irradiation. Moreover, these drastic effects induced by adult irradiation disappeared over time when 10 d-irradiated adults were placed in a nonirradiated condition. Alterations in larval DNA were observed for the 3 dose rates, and an increase of ROS production was also shown for the 2 lowest dose rates. The present study improves our understanding of the consequences of parental exposure conditions to the progeny. Furthermore, it provides an incentive to take transmitted generational effects into account in ecological risk assessments. Environ Toxicol Chem 2019;38:2556-2567. © 2019 SETAC.
Collapse
Affiliation(s)
- Noémie Guirandy
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Béatrice Gagnaire
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Sandrine Frelon
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Thomas Munch
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Nicolas Dubourg
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Virginie Camilleri
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Isabelle Cavalié
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Magali Floriani
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Caroline Arcanjo
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Sophia Murat El Houdigui
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Olivier Armant
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | - Christelle Adam-Guillermin
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| | | | - Olivier Simon
- Institut de Radioprotection et de Surêté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul-lez-Durance, France
| |
Collapse
|
40
|
Horemans N, Spurgeon DJ, Lecomte-Pradines C, Saenen E, Bradshaw C, Oughton D, Rasnaca I, Kamstra JH, Adam-Guillermin C. Current evidence for a role of epigenetic mechanisms in response to ionizing radiation in an ecotoxicological context. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 251:469-483. [PMID: 31103007 DOI: 10.1016/j.envpol.2019.04.125] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/14/2019] [Accepted: 04/27/2019] [Indexed: 05/22/2023]
Abstract
The issue of potential long-term or hereditary effects for both humans and wildlife exposed to low doses (or dose rates) of ionising radiation is a major concern. Chronic exposure to ionising radiation, defined as an exposure over a large fraction of the organism's lifespan or even over several generations, can possibly have consequences in the progeny. Recent work has begun to show that epigenetics plays an important role in adaptation of organisms challenged to environmental stimulae. Changes to so-called epigenetic marks such as histone modifications, DNA methylation and non-coding RNAs result in altered transcriptomes and proteomes, without directly changing the DNA sequence. Moreover, some of these environmentally-induced epigenetic changes tend to persist over generations, and thus, epigenetic modifications are regarded as the conduits for environmental influence on the genome. Here, we review the current knowledge of possible involvement of epigenetics in the cascade of responses resulting from environmental exposure to ionising radiation. In addition, from a comparison of lab and field obtained data, we investigate evidence on radiation-induced changes in the epigenome and in particular the total or locus specific levels of DNA methylation. The challenges for future research and possible use of changes as an early warning (biomarker) of radiosensitivity and individual exposure is discussed. Such a biomarker could be used to detect and better understand the mechanisms of toxic action and inter/intra-species susceptibility to radiation within an environmental risk assessment and management context.
Collapse
Affiliation(s)
- Nele Horemans
- Belgian Nuclear Research Centre, Boeretang 200, B-2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Agoralaan, 3590, Diepenbeek, Belgium.
| | - David J Spurgeon
- Centre for Ecology and Hydrology, MacLean Building, Benson Lane, Wallingford, Oxon, OX10 8BB, UK
| | - Catherine Lecomte-Pradines
- Institut de Radioprotection et de Sûreté Nucléaire, PSE-ENV/SRTE/LECO, Cadarache, Saint Paul Lez Durance, France
| | - Eline Saenen
- Belgian Nuclear Research Centre, Boeretang 200, B-2400, Mol, Belgium
| | - Clare Bradshaw
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Deborah Oughton
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences, 1430, Aas, Norway
| | - Ilze Rasnaca
- Centre for Ecology and Hydrology, MacLean Building, Benson Lane, Wallingford, Oxon, OX10 8BB, UK
| | - Jorke H Kamstra
- Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Christelle Adam-Guillermin
- Institut de Radioprotection et de Sûreté Nucléaire, PSE-SANTE, Cadarache, Saint Paul Lez Durance, France
| |
Collapse
|
41
|
Bell AM, Hellmann JK. An Integrative Framework for Understanding the Mechanisms and Multigenerational Consequences of Transgenerational Plasticity. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2019; 50:97-118. [PMID: 36046014 PMCID: PMC9427003 DOI: 10.1146/annurev-ecolsys-110218-024613] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Transgenerational plasticity (TGP) occurs when the environment experienced by a parent influences the development of their offspring. In this article, we develop a framework for understanding the mechanisms and multi-generational consequences of TGP. First, we conceptualize the mechanisms of TGP in the context of communication between parents (senders) and offspring (receivers) by dissecting the steps between an environmental cue received by a parent and its resulting effects on the phenotype of one or more future generations. Breaking down the problem in this way highlights the diversity of mechanisms likely to be involved in the process. Second, we review the literature on multigenerational effects and find that the documented patterns across generations are diverse. We categorize different multigenerational patterns and explore the proximate and ultimate mechanisms that can generate them. Throughout, we highlight opportunities for future work in this dynamic and integrative area of study.
Collapse
Affiliation(s)
- Alison M Bell
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Program in Neuroscience and Program in Ecology, Evolution and Conservation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jennifer K Hellmann
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
42
|
de Vocht F, Suderman M, Ruano-Ravina A, Thomas R, Wakeford R, Relton C, Tilling K, Boyd A. Residential exposure to radon and DNA methylation across the lifecourse: an exploratory study in the ALSPAC birth cohort. Wellcome Open Res 2019; 4:3. [PMID: 30906879 PMCID: PMC6426102 DOI: 10.12688/wellcomeopenres.14991.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Radon (and its decay products) is a known human carcinogen and the leading cause of lung cancer in never-smokers and the second in ever-smokers. The carcinogenic mechanism from radiation is a combination of genetic and epigenetic processes, but compared to the genetic mechanisms, epigenetic processes remain understudied in humans. This study aimed to explore associations between residential radon exposure and DNA methylation in the general population. Methods: Potential residential radon exposure for 75-metre area buffers was linked to genome-wide DNA methylation measured in peripheral blood from children and mothers of the Accessible Resource for Integrated Epigenomic Studies subsample of the ALSPAC birth cohort. Associations with DNA methylation were tested at over 450,000 CpG sites at ages 0, 7 and 17 years (children) and antenatally and during middle-age (mothers). Analyses were adjusted for potential residential and lifestyle confounding factors and were determined for participants with complete data (n = 786 to 980). Results: Average potential exposure to radon was associated in an exposure-dependent manner with methylation at cg25422346 in mothers during pregnancy, with no associations at middle age. For children, radon potential exposure was associated in an exposure-dependent manner with methylation of cg16451995 at birth, cg01864468 at age 7, and cg04912984, cg16105117, cg23988964, cg04945076, cg08601898, cg16260355 and cg26056703 in adolescence. Conclusions: Residential radon exposure was associated with DNA methylation in an exposure-dependent manner. Although chance and residual confounding cannot be excluded, the identified associations may show biological mechanisms involved in early biological effects from radon exposure.
Collapse
Affiliation(s)
- Frank de Vocht
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - Richard Thomas
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Avon Longitudinal Study of Parents and Children, University of Bristol, Bristol, UK
| | - Richard Wakeford
- Centre for Occupational and Environmental Health, University of Manchester, Manchester, UK
| | - Caroline Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kate Tilling
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Andy Boyd
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Avon Longitudinal Study of Parents and Children, University of Bristol, Bristol, UK
| |
Collapse
|
43
|
Lindeman LC, Kamstra JH, Ballangby J, Hurem S, Martín LM, Brede DA, Teien HC, Oughton DH, Salbu B, Lyche JL, Aleström P. Gamma radiation induces locus specific changes to histone modification enrichment in zebrafish and Atlantic salmon. PLoS One 2019; 14:e0212123. [PMID: 30759148 PMCID: PMC6373941 DOI: 10.1371/journal.pone.0212123] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/28/2019] [Indexed: 12/14/2022] Open
Abstract
Ionizing radiation is a recognized genotoxic agent, however, little is known about the role of the functional form of DNA in these processes. Post translational modifications on histone proteins control the organization of chromatin and hence control transcriptional responses that ultimately affect the phenotype. The purpose of this study was to investigate effects on chromatin caused by ionizing radiation in fish. Direct exposure of zebrafish (Danio rerio) embryos to gamma radiation (10.9 mGy/h for 3h) induced hyper-enrichment of H3K4me3 at the genes hnf4a, gmnn and vegfab. A similar relative hyper-enrichment was seen at the hnf4a loci of irradiated Atlantic salmon (Salmo salar) embryos (30 mGy/h for 10 days). At the selected genes in ovaries of adult zebrafish irradiated during gametogenesis (8.7 and 53 mGy/h for 27 days), a reduced enrichment of H3K4me3 was observed, which was correlated with reduced levels of histone H3 was observed. F1 embryos of the exposed parents showed hyper-methylation of H3K4me3, H3K9me3 and H3K27me3 on the same three loci, while these differences were almost negligible in F2 embryos. Our results from three selected loci suggest that ionizing radiation can affect chromatin structure and organization, and that these changes can be detected in F1 offspring, but not in subsequent generations.
Collapse
Affiliation(s)
- Leif Christopher Lindeman
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Jorke Harmen Kamstra
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Jarle Ballangby
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Selma Hurem
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Leonardo Martín Martín
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
- Faculty of Agropecuary Sciences, University of Camagüey (UC) Ignacio Agramonte Loynaz, Camagüey, Cuba
| | - Dag Anders Brede
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Hans Christian Teien
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Deborah H. Oughton
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Brit Salbu
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Jan Ludvig Lyche
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Peter Aleström
- Centre for Environmental Radioactivity (CERAD CoE), Norwegian University of Life Sciences, Ås, Norway
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| |
Collapse
|
44
|
de Vocht F, Suderman M, Ruano-Ravina A, Thomas R, Wakeford R, Relton C, Tilling K, Boyd A. Residential exposure to radon and DNA methylation across the lifecourse: an exploratory study in the ALSPAC birth cohort. Wellcome Open Res 2019; 4:3. [PMID: 30906879 PMCID: PMC6426102 DOI: 10.12688/wellcomeopenres.14991.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2018] [Indexed: 10/12/2023] Open
Abstract
Background: Radon (and its decay products) is a known human carcinogen and the leading cause of lung cancer in never-smokers and the second in ever-smokers. The carcinogenic mechanism from radiation is a combination of genetic and epigenetic processes, but compared to the genetic mechanisms, epigenetic processes remain understudied in humans. This study aimed to explore associations between residential radon exposure and DNA methylation in the general population. Methods: Potential residential radon exposure for 75-metre area buffers was linked to genome-wide DNA methylation measured in peripheral blood from children and mothers of the Accessible Resource for Integrated Epigenomic Studies subsample of the ALSPAC birth cohort. Associations with DNA methylation were tested at over 450,000 CpG sites at ages 0, 7 and 17 years (children) and antenatally and during middle-age (mothers). Analyses were adjusted for potential residential and lifestyle confounding factors and were determined for participants with complete data (n = 786-980). Results: Average potential exposure to radon was associated in an exposure-dependent manner with methylation at cg25422346 in mothers during pregnancy, with no associations at middle age. For children, radon potential exposure was associated in an exposure-dependent manner with methylation of cg16451995 at birth, cg01864468 at age 7, and cg04912984, cg16105117, cg23988964, cg04945076, cg08601898, cg16260355 and cg26056703 in adolescence. Conclusions: Residential radon exposure was associated with DNA methylation in an exposure-dependent manner. Although residual confounding cannot be excluded, the identified associations may show biological mechanisms involved in early biological effects from radon exposure.
Collapse
Affiliation(s)
- Frank de Vocht
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - Richard Thomas
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Avon Longitudinal Study of Parents and Children, University of Bristol, Bristol, UK
| | - Richard Wakeford
- Centre for Occupational and Environmental Health, University of Manchester, Manchester, UK
| | - Caroline Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kate Tilling
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Andy Boyd
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Avon Longitudinal Study of Parents and Children, University of Bristol, Bristol, UK
| |
Collapse
|