151
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Pathak R, Feil R. Environmental effects on chromatin repression at imprinted genes and endogenous retroviruses. Curr Opin Chem Biol 2018; 45:139-147. [DOI: 10.1016/j.cbpa.2018.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/05/2018] [Accepted: 04/24/2018] [Indexed: 12/26/2022]
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152
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A critical view on transgenerational epigenetic inheritance in humans. Nat Commun 2018; 9:2973. [PMID: 30061690 PMCID: PMC6065375 DOI: 10.1038/s41467-018-05445-5] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 07/06/2018] [Indexed: 02/07/2023] Open
Abstract
Transgenerational epigenetic inheritance refers to the transmission of epigenetic information through the germline. While it has been observed in plants, nematodes and fruit flies, its occurrence in mammals-and humans in particular-is the matter of controversial debate, mostly because the study of transgenerational epigenetic inheritance is confounded by genetic, ecological and cultural inheritance. In this comment, I discuss the phenomenon of transgenerational epigenetic inheritance and the difficulty of providing conclusive proof for it in experimental and observational studies.
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153
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Liu Y. Darwin's Pangenesis and the Lamarckian Inheritance of Acquired Characters. ADVANCES IN GENETICS 2018; 101:115-144. [PMID: 30037391 DOI: 10.1016/bs.adgen.2018.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Since the earliest days of evolutionary thought, the problem of the inheritance of acquired characters has been a central debate. Darwin accepted the inheritance of acquired characters as an established fact and gave many instances. His Pangenesis was more than anything else an attempt to provide a theory for its explanation. Over the past several decades, there has been increasing evidence for the inheritance of acquired habit and immunity, and for heritable changes induced by food and fertilizer, stress, chemicals, temperature, light and other environmental factors. Many studies also suggest that parental age has certain influences on the characters of offspring. The current explanations include environmentally induced DNA changes (mainly DNA rearrangements and DNA methylation), RNA-mediated inheritance, and horizontal gene transfer. These mechanistic explanations are consistent with Darwin's Pangenesis.
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Affiliation(s)
- Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China; Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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154
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Paternal sepsis induces alterations of the sperm methylome and dampens offspring immune responses-an animal study. Clin Epigenetics 2018; 10:89. [PMID: 29988283 PMCID: PMC6022485 DOI: 10.1186/s13148-018-0522-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/19/2018] [Indexed: 12/29/2022] Open
Abstract
Background Sepsis represents the utmost severe consequence of infection, involving a dysregulated and self-damaging immune response of the host. While different environmental exposures like chronic stress or malnutrition have been well described to reprogram the germline and subsequently offspring attributes, the intergenerational impact of sepsis as a tremendous immunological stressor has not been examined yet. Methods Polymicrobial sepsis in 12-week-old male C57BL/6 mice was induced by cecal ligation and puncture (CLP), followed by a mating of the male survivors (or appropriate sham control animals) 6 weeks later with healthy females. Alveolar macrophages of offspring animals were isolated and stimulated with either LPS or Zymosan, and supernatant levels of TNF-α were quantified by ELISA. Furthermore, systemic cytokine response to intraperitoneally injected LPS was assessed after 24 h. Also, morphology, motility, and global DNA methylation of the sepsis survivors’ sperm was examined. Results Comparative reduced reduction bisulfite sequencing (RRBS) of sperm revealed changes of DNA methylation (n = 381), most pronounced in the intergenic genome as well as within introns of developmentally relevant genes. Offspring of sepsis fathers exhibited a slight decrease in body weight, with a more pronounced weight difference in male animals (CLP vs. sham). Male descendants of sepsis fathers, but not female descendants, exhibited lower plasma concentrations of IL-6, TNF-alpha, and IL-10 24 h after injection of LPS. In line, only alveolar macrophages of male descendants of sepsis fathers produced less TNF-alpha upon Zymosan stimulation compared to sham descendants, while LPS responses kept unchanged. Conclusion We can prove that male—but surprisingly not female—descendants of post-sepsis fathers show a dampened systemic as well as pulmonary immune response. Based on this observation of an immune hypo-responsivity, we propose that male descendants of sepsis fathers are at risk to develop fungal and bacterial infections and might benefit from therapeutic immune modulation. Electronic supplementary material The online version of this article (10.1186/s13148-018-0522-z) contains supplementary material, which is available to authorized users.
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155
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Western PS. Epigenomic drugs and the germline: Collateral damage in the home of heritability? Mol Cell Endocrinol 2018; 468:121-133. [PMID: 29471014 DOI: 10.1016/j.mce.2018.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 02/07/2023]
Abstract
The testis and ovary provide specialised environments that nurture germ cells and facilitate their maturation, culminating in the production of mature gametes that can found the following generation. The sperm and egg not only transmit genetic information, but also epigenetic modifications that affect the development and physiology of offspring. Importantly, the epigenetic information contained in mature sperm and oocytes can be influenced by a range of environmental factors, such as diet, chemicals and drugs. An increasing range of studies are revealing how gene-environment interactions are mediated through the germline. Outside the germline, altered epigenetic state is common in a range of diseases, including many cancers. As epigenetic modifications are reversible, pharmaceuticals that directly target epigenetic modifying proteins have been developed and are delivering substantial benefits to patients, particularly in oncology. While providing the most effective patient treatment is clearly the primary concern, some patients will want to conceive children after treatment. However, the impacts of epigenomic drugs on the male and female gametes are poorly understood and whether these drugs will have lasting effects on patients' germline epigenome and subsequent offspring remains largely undetermined. Currently, evidence based clinical guidelines for use of epigenomic drugs in patients of reproductive age are limited in this context. Developing a deeper understanding of the epigenetic mechanisms regulating the germline epigenome and its impact on inherited traits and disease susceptibility is required to determine how specific epigenomic drugs might affect the germline and inheritance. Understanding these potential effects will facilitate the development of informed clinical guidelines appropriate for the use of epigenomic drugs in patients of reproductive age, ultimately improving the safety of these therapies in the clinic.
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Affiliation(s)
- Patrick S Western
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia.
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156
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Abstract
Environmental factors, particularly during early life, are important for the later metabolic health of the individual. In our obesogenic environment, it is of major socio-economic importance to investigate the mechanisms that contribute to the risk of metabolic ill health. Increasing evidence from a variety of model organisms suggests that non-genetically determined phenotypes, including metabolic effects such as glucose intolerance and obesity, can be passed between generations, which encourages us to revisit heredity. Inheritance of altered epigenetic information through the germ line has been proposed as one plausible mechanism. Whether the germline epigenome can be altered by environmental conditions such as diet and the extent to which this occurs in humans are the subject of intense current interest and debate, especially given that extensive germline epigenetic reprogramming is known to occur. As epigenetic mechanisms are often highly conserved between organisms, studying epigenetic inheritance in plants and lower metazoans has the potential to inform our investigation in mammals. This Review explores the extent to which epigenetic inheritance contributes to heredity in these different organisms, whether the environment can affect epigenetic inheritance and whether there is any evidence for the inheritance of acquired phenotypes.
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Affiliation(s)
- Elizabeth J Radford
- Department of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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157
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Zhang Y, Zhang X, Shi J, Tuorto F, Li X, Liu Y, Liebers R, Zhang L, Qu Y, Qian J, Pahima M, Liu Y, Yan M, Cao Z, Lei X, Cao Y, Peng H, Liu S, Wang Y, Zheng H, Woolsey R, Quilici D, Zhai Q, Li L, Zhou T, Yan W, Lyko F, Zhang Y, Zhou Q, Duan E, Chen Q. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nat Cell Biol 2018; 20:535-540. [PMID: 29695786 PMCID: PMC5926820 DOI: 10.1038/s41556-018-0087-2] [Citation(s) in RCA: 309] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 03/19/2018] [Indexed: 12/29/2022]
Abstract
The discovery of RNAs (for example, messenger RNAs, non-coding RNAs) in sperm has opened the possibility that sperm may function by delivering additional paternal information aside from solely providing the DNA 1 . Increasing evidence now suggests that sperm small non-coding RNAs (sncRNAs) can mediate intergenerational transmission of paternally acquired phenotypes, including mental stress2,3 and metabolic disorders4-6. How sperm sncRNAs encode paternal information remains unclear, but the mechanism may involve RNA modifications. Here we show that deletion of a mouse tRNA methyltransferase, DNMT2, abolished sperm sncRNA-mediated transmission of high-fat-diet-induced metabolic disorders to offspring. Dnmt2 deletion prevented the elevation of RNA modifications (m5C, m2G) in sperm 30-40 nt RNA fractions that are induced by a high-fat diet. Also, Dnmt2 deletion altered the sperm small RNA expression profile, including levels of tRNA-derived small RNAs and rRNA-derived small RNAs, which might be essential in composing a sperm RNA 'coding signature' that is needed for paternal epigenetic memory. Finally, we show that Dnmt2-mediated m5C contributes to the secondary structure and biological properties of sncRNAs, implicating sperm RNA modifications as an additional layer of paternal hereditary information.
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Affiliation(s)
- Yunfang Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
- University of Chinese Academy of Sciences, Beijing, China
| | - Xudong Zhang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Junchao Shi
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Xin Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yusheng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Reinhard Liebers
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Liwen Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongcun Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingjing Qian
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Maya Pahima
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Ying Liu
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Menghong Yan
- Key Laboratory of Nutrition and Metabolism, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhonghong Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Shandong University of Technology, Zibo, China
| | - Xiaohua Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yujing Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongying Peng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Shichao Liu
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Yue Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Rebekah Woolsey
- Nevada Proteomics Center, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - David Quilici
- Nevada Proteomics Center, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Qiwei Zhai
- Key Laboratory of Nutrition and Metabolism, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Enkui Duan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
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158
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Zhang Y, Zhang X, Shi J, Tuorto F, Li X, Liu Y, Liebers R, Zhang L, Qu Y, Qian J, Pahima M, Liu Y, Yan M, Cao Z, Lei X, Cao Y, Peng H, Liu S, Wang Y, Zheng H, Woolsey R, Quilici D, Zhai Q, Li L, Zhou T, Yan W, Lyko F, Zhang Y, Zhou Q, Duan E, Chen Q. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nat Cell Biol 2018. [DOI: doi.org/10.1038/s41556-018-0087-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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159
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Abstract
Fusion of sperm and egg generates a totipotent zygote that develops into a whole organism. Accordingly, the "immortal" germline transmits genetic and epigenetic information to subsequent generations with consequences for human health and disease. In mammals, primordial germ cells (PGCs) originate from peri-gastrulation embryos. While early human embryos are inaccessible for research, in vitro model systems using pluripotent stem cells have provided critical insights into human PGC specification, which differs from that in mice. This might stem from significant differences in early embryogenesis at the morphological and molecular levels, including pluripotency networks. Here, we discuss recent advances and experimental systems used to study mammalian germ cell development. We also highlight key aspects of germ cell disorders, as well as mitochondrial and potentially epigenetic inheritance in humans.
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Affiliation(s)
- Naoko Irie
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; University of Cambridge, Cambridge, United Kingdom.
| | - Anastasiya Sybirna
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; University of Cambridge, Cambridge, United Kingdom; Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; University of Cambridge, Cambridge, United Kingdom.
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160
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Guerrero-Bosagna C, Morisson M, Liaubet L, Rodenburg TB, de Haas EN, Košťál Ľ, Pitel F. Transgenerational epigenetic inheritance in birds. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy008. [PMID: 29732172 PMCID: PMC5920295 DOI: 10.1093/eep/dvy008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 05/04/2023]
Abstract
While it has been shown that epigenetics accounts for a portion of the variability of complex traits linked to interactions with the environment, the real contribution of epigenetics to phenotypic variation remains to be assessed. In recent years, a growing number of studies have revealed that epigenetic modifications can be transmitted across generations in several animal species. Numerous studies have demonstrated inter- or multi-generational effects of changing environment in birds, but very few studies have been published showing epigenetic transgenerational inheritance in these species. In this review, we mention work conducted in parent-to-offspring transmission analyses in bird species, with a focus on the impact of early stressors on behaviour. We then present recent advances in transgenerational epigenetics in birds, which involve germline linked non-Mendelian inheritance, underline the advantages and drawbacks of working on birds in this field and comment on future directions of transgenerational studies in bird species.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58 183, Sweden
| | - Mireille Morisson
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - Laurence Liaubet
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - T Bas Rodenburg
- Behavioural Ecology Group, Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Elske N de Haas
- Behavioural Ecology Group, Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Ľubor Košťál
- Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
- Correspondence address. GenPhySE, INRA, 31326 Castanet-Tolosan, France. Tel:+33 561 28 54 35. E-mail:
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161
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Herrera CM, Alonso C, Medrano M, Pérez R, Bazaga P. Transgenerational epigenetics: Inheritance of global cytosine methylation and methylation-related epigenetic markers in the shrub Lavandula latifolia. AMERICAN JOURNAL OF BOTANY 2018; 105:741-748. [PMID: 29727470 DOI: 10.1002/ajb2.1074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/22/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The ecological and evolutionary significance of natural epigenetic variation (i.e., not based on DNA sequence variants) variation will depend critically on whether epigenetic states are transmitted from parents to offspring, but little is known on epigenetic inheritance in nonmodel plants. METHODS We present a quantitative analysis of transgenerational transmission of global DNA cytosine methylation (= proportion of all genomic cytosines that are methylated) and individual epigenetic markers (= methylation status of anonymous MSAP markers) in the shrub Lavandula latifolia. Methods based on parent-offspring correlations and parental variance component estimation were applied to epigenetic features of field-growing plants ('maternal parents') and greenhouse-grown progenies. Transmission of genetic markers (AFLP) was also assessed for reference. KEY RESULTS Maternal parents differed significantly in global DNA cytosine methylation (range = 21.7-36.7%). Greenhouse-grown maternal families differed significantly in global methylation, and their differences were significantly related to maternal origin. Methylation-sensitive amplified polymorphism (MSAP) markers exhibited significant transgenerational transmission, as denoted by significant maternal variance component of marker scores in greenhouse families and significant mother-offspring correlations of marker scores. CONCLUSIONS Although transmission-related measurements for global methylation and MSAP markers were quantitatively lower than those for AFLP markers taken as reference, this study has revealed extensive transgenerational transmission of genome-wide global cytosine methylation and anonymous epigenetic markers in L. latifolia. Similarity of results for global cytosine methylation and epigenetic markers lends robustness to this conclusion, and stresses the value of considering both types of information in epigenetic studies of nonmodel plants.
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Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de, Sevilla, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
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162
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Adrian-Kalchhauser I, Walser JC, Schwaiger M, Burkhardt-Holm P. RNA sequencing of early round goby embryos reveals that maternal experiences can shape the maternal RNA contribution in a wild vertebrate. BMC Evol Biol 2018; 18:34. [PMID: 29566669 PMCID: PMC5863367 DOI: 10.1186/s12862-018-1132-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/29/2018] [Indexed: 01/01/2023] Open
Abstract
Background It has been proposed that non-genetic inheritance could promote species fitness. Non-genetic inheritance could allow offspring to benefit from the experience of their parents, and could advocate pre-adaptation to prevailing and potentially selective conditions. Indeed, adaptive parental effects have been modeled and observed, but the molecular mechanisms behind them are far from understood. Results In the present study, we investigated whether maternal RNA can carry information about environmental conditions experienced by the mother in a wild vertebrate. Maternal RNA directs the development of the early embryo in many non-mammalian vertebrates and invertebrates. However, it is not known whether vertebrate maternal RNA integrates information about the parental environment. We sequenced the maternal RNA contribution from a model that we expected to rely on parental effects: the invasive benthic fish species Neogobius melanostomus (Round Goby). We found that maternal RNA expression levels correlated with the water temperature experienced by the mother before oviposition, and identified temperature-responsive gene groups such as core nucleosome components or the microtubule cytoskeleton. Conclusions Our findings suggest that the maternal RNA contribution may incorporate environmental information. Maternal RNA should therefore be considered a potentially relevant pathway for non-genetic inheritance. Also, the ability of a species to integrate environmental information in the maternal RNA contribution could potentially contribute to species fitness and may also play a role in extraordinary adaptive success stories of invasive species such as the round goby. Electronic supplementary material The online version of this article (10.1186/s12862-018-1132-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
| | - Jean-Claude Walser
- Department of Environmental Systems Science, Genetic Diversity Centre Zurich, ETH Zurich, Universitätstrasse 16, CH-8092, Zurich, Switzerland
| | - Michaela Schwaiger
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Patricia Burkhardt-Holm
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
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163
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Mashoodh R, Habrylo IB, Gudsnuk KM, Pelle G, Champagne FA. Maternal modulation of paternal effects on offspring development. Proc Biol Sci 2018; 285:20180118. [PMID: 29514964 PMCID: PMC5879637 DOI: 10.1098/rspb.2018.0118] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/12/2018] [Indexed: 01/22/2023] Open
Abstract
The paternal transmission of environmentally induced phenotypes across generations has been reported to occur following a number of qualitatively different exposures and appear to be driven, at least in part, by epigenetic factors that are inherited via the sperm. However, previous studies of paternal germline transmission have not addressed the role of mothers in the propagation of paternal effects to offspring. We hypothesized that paternal exposure to nutritional restriction would impact male mate quality and subsequent maternal reproductive investment with consequences for the transmission of paternal germline effects. In the current report, using embryo transfer in mice, we demonstrate that sperm factors in adult food restricted males can influence growth rate, hypothalamic gene expression and behaviour in female offspring. However, under natural mating conditions females mated with food restricted males show increased pre- and postnatal care, and phenotypic outcomes observed during embryo transfer conditions are absent or reversed. We demonstrate that these compensatory changes in maternal investment are associated with a reduced mate preference for food restricted males and elevated gene expression within the maternal hypothalamus. Therefore, paternal experience can influence offspring development via germline inheritance, but mothers can serve as a modulating factor in determining the impact of paternal influences on offspring development.
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Affiliation(s)
- Rahia Mashoodh
- Department of Psychology, Columbia University, 1190 Amsterdam Avenue, Room 406 Schermerhorn Hall, New York, NY 10027, USA
- Department of Zoology, University of Cambridge, Downing St, Cambridge, CB2 3EJ, UK
| | - Ireneusz B Habrylo
- Department of Psychology, Columbia University, 1190 Amsterdam Avenue, Room 406 Schermerhorn Hall, New York, NY 10027, USA
| | - Kathryn M Gudsnuk
- Department of Psychology, Columbia University, 1190 Amsterdam Avenue, Room 406 Schermerhorn Hall, New York, NY 10027, USA
| | - Geralyn Pelle
- Columbia University Medical Center, 650 W 168 St, New York, NY 10032, USA
| | - Frances A Champagne
- Department of Psychology, Columbia University, 1190 Amsterdam Avenue, Room 406 Schermerhorn Hall, New York, NY 10027, USA
- Department of Psychology, University of Texas at Austin, 108 E Dean Keeton St, Austin, TX 78712, USA
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164
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Cipriano A, Ballarino M. The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions. Front Mol Biosci 2018; 5:20. [PMID: 29560353 PMCID: PMC5845540 DOI: 10.3389/fmolb.2018.00020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/20/2018] [Indexed: 12/12/2022] Open
Abstract
The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as “junk” DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs), which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins) endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.
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Affiliation(s)
- Andrea Cipriano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
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165
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Widschwendter M, Jones A, Evans I, Reisel D, Dillner J, Sundström K, Steyerberg EW, Vergouwe Y, Wegwarth O, Rebitschek FG, Siebert U, Sroczynski G, de Beaufort ID, Bolt I, Cibula D, Zikan M, Bjørge L, Colombo N, Harbeck N, Dudbridge F, Tasse AM, Knoppers BM, Joly Y, Teschendorff AE, Pashayan N. Epigenome-based cancer risk prediction: rationale, opportunities and challenges. Nat Rev Clin Oncol 2018; 15:292-309. [PMID: 29485132 DOI: 10.1038/nrclinonc.2018.30] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The incidence of cancer is continuing to rise and risk-tailored early diagnostic and/or primary prevention strategies are urgently required. The ideal risk-predictive test should: integrate the effects of both genetic and nongenetic factors and aim to capture these effects using an approach that is both biologically stable and technically reproducible; derive a score from easily accessible biological samples that acts as a surrogate for the organ in question; and enable the effectiveness of risk-reducing measures to be monitored. Substantial evidence has accumulated suggesting that the epigenome and, in particular, DNA methylation-based tests meet all of these requirements. However, the development and implementation of DNA methylation-based risk-prediction tests poses considerable challenges. In particular, the cell type specificity of DNA methylation and the extensive cellular heterogeneity of the easily accessible surrogate cells that might contain information relevant to less accessible tissues necessitates the use of novel methods in order to account for these confounding issues. Furthermore, the engagement of the scientific community with health-care professionals, policymakers and the public is required in order to identify and address the organizational, ethical, legal, social and economic challenges associated with the routine use of epigenetic testing.
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Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Allison Jones
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Iona Evans
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Daniel Reisel
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Sundström
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ewout W Steyerberg
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands.,Department of Biomedical Data Sciences, LUMC, Leiden, Netherlands
| | - Yvonne Vergouwe
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands
| | - Odette Wegwarth
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany.,Max Planck Institute for Human Development, Center for Adaptive Rationality, Berlin, Germany
| | - Felix G Rebitschek
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany
| | - Uwe Siebert
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria.,Harvard T. C. Chan School of Public Health, Center for Health Decision Science, Department of Health Policy and Management, Boston, MA, USA.,Oncotyrol: Center for Personalized Medicine, Innsbruck, Austria
| | - Gaby Sroczynski
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria
| | - Inez D de Beaufort
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ineke Bolt
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - David Cibula
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Michal Zikan
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Line Bjørge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, and Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nicoletta Colombo
- European Institute of Oncology and University Milan-Bicocca, Milan, Italy
| | - Nadia Harbeck
- Breast Center, Department of Gynaecology and Obstetrics, University of Munich (LMU), Munich, Germany
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anne-Marie Tasse
- Public Population Project in Genomics and Society, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | | | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Andrew E Teschendorff
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Nora Pashayan
- Department of Applied Health Research, Institute of Epidemiology and Healthcare, University College London, UK
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166
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Puttabyatappa M, Padmanabhan V. Developmental Programming of Ovarian Functions and Dysfunctions. VITAMINS AND HORMONES 2018; 107:377-422. [PMID: 29544638 PMCID: PMC6119353 DOI: 10.1016/bs.vh.2018.01.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The pathophysiological mechanisms underlying the origin of several ovarian pathologies remain unclear. In addition to the genetic basis, developmental insults are gaining attention as a basis for the origin of these pathologies. Such early insults include maternal over or under nutrition, stress, and exposure to environmental chemicals. This chapter reviews the development and physiological function of the ovary, the known ovarian pathologies, the developmental check points of ovarian differentiation impacted by developmental insults, the role played by steroidal and metabolic factors as mediaries, the epigenetic mechanisms via which these mediaries induce their effects, and the knowledge gaps for targeting future studies to ultimately aid in the development of improved treatments.
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167
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Leonova K, Safina A, Nesher E, Sandlesh P, Pratt R, Burkhart C, Lipchick B, Gitlin I, Frangou C, Koman I, Wang J, Kirsanov K, Yakubovskaya MG, Gudkov AV, Gurova K. TRAIN (Transcription of Repeats Activates INterferon) in response to chromatin destabilization induced by small molecules in mammalian cells. eLife 2018; 7:e30842. [PMID: 29400649 PMCID: PMC5815852 DOI: 10.7554/elife.30842] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/04/2018] [Indexed: 12/13/2022] Open
Abstract
Cellular responses to the loss of genomic stability are well-established, while how mammalian cells respond to chromatin destabilization is largely unknown. We previously found that DNA demethylation on p53-deficient background leads to transcription of repetitive heterochromatin elements, followed by an interferon response, a phenomenon we named TRAIN (Transcription of Repeats Activates INterferon). Here, we report that curaxin, an anticancer small molecule, destabilizing nucleosomes via disruption of histone/DNA interactions, also induces TRAIN. Furthermore, curaxin inhibits oncogene-induced transformation and tumor growth in mice in an interferon-dependent manner, suggesting that anticancer activity of curaxin, previously attributed to p53-activation and NF-kappaB-inhibition, may also involve induction of interferon response to epigenetic derepression of the cellular 'repeatome'. Moreover, we observed that another type of drugs decondensing chromatin, HDAC inhibitor, also induces TRAIN. Thus, we proposed that TRAIN may be one of the mechanisms ensuring epigenetic integrity of mammalian cells via elimination of cells with desilenced chromatin.
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Affiliation(s)
- Katerina Leonova
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Alfiya Safina
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Elimelech Nesher
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
- Department of Molecular BiologyAriel UniversityArielIsrael
| | - Poorva Sandlesh
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Rachel Pratt
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | | | - Brittany Lipchick
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Ilya Gitlin
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Costakis Frangou
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Igor Koman
- Department of Molecular BiologyAriel UniversityArielIsrael
| | - Jianmin Wang
- Department of BioinformaticsRoswell Park Cancer InstituteBuffaloUnited States
| | - Kirill Kirsanov
- Department of Chemical CarcinogenesisInstitute of Carcinogenesis, Blokhin Cancer Research Center RAMSMoscowRussia
| | - Marianna G Yakubovskaya
- Department of Chemical CarcinogenesisInstitute of Carcinogenesis, Blokhin Cancer Research Center RAMSMoscowRussia
| | - Andrei V Gudkov
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Katerina Gurova
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
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168
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Schmid MW, Giraldo-Fonseca A, Rövekamp M, Smetanin D, Bowman JL, Grossniklaus U. Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha. Genome Biol 2018; 19:9. [PMID: 29368664 PMCID: PMC5784723 DOI: 10.1186/s13059-017-1383-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/21/2017] [Indexed: 12/19/2022] Open
Abstract
Background In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur during land plant reproduction, but there is little consensus on the generality and extent of epigenetic reprogramming in plants. We studied DNA methylation dynamics during the life cycle of the liverwort Marchantia polymorpha. We isolated thalli and meristems from male and female gametophytes, archegonia, antherozoids, as well as sporophytes at early and late developmental stages, and compared their DNA methylation profiles. Results Of all cytosines tested for differential DNA methylation, 42% vary significantly in their methylation pattern throughout the life cycle. However, the differences are limited to few comparisons between specific stages of the life cycle and suggest four major epigenetic states specific to sporophytes, vegetative gametophytes, antherozoids, and archegonia. Further analyses indicated clear differences in the mechanisms underlying reprogramming in the gametophytic and sporophytic generations, which are paralleled by differences in the expression of genes involved in DNA methylation. Differentially methylated cytosines with a gain in methylation in antherozoids and archegonia are enriched in the CG and CHG contexts, as well as in gene bodies and gene flanking regions. In contrast, gain of DNA methylation during sporophyte development is mostly limited to the CHH context, LTR retrotransposons, DNA transposons, and repeats. Conclusion We conclude that epigenetic reprogramming occurs at least twice during the life cycle of M. polymorpha and that the underlying mechanisms are likely different between the two events. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1383-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc W Schmid
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alejandro Giraldo-Fonseca
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Moritz Rövekamp
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Dmitry Smetanin
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - John L Bowman
- Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
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169
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Yehuda R, Meaney MJ. Relevance of Psychological Symptoms in Pregnancy to Intergenerational Effects of Preconception Trauma. Biol Psychiatry 2018; 83:94-96. [PMID: 29223220 DOI: 10.1016/j.biopsych.2017.10.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Rachel Yehuda
- James J. Peters Veterans Affairs Medical Center, Bronx, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Michael J Meaney
- Sackler Program for Epigenetics and Psychobiology at McGill University, Montreal, Quebec, Canada; Douglas Hospital Research Centre, McGill University, Montreal, Quebec, Canada; Singapore Institute for Clinical Sciences, Singapore
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170
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Jones MJ, Moore SR, Kobor MS. Principles and Challenges of Applying Epigenetic Epidemiology to Psychology. Annu Rev Psychol 2018; 69:459-485. [DOI: 10.1146/annurev-psych-122414-033653] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Meaghan J. Jones
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Sarah R. Moore
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
- Human Early Learning Partnership, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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171
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Schofield PN, Kondratowicz M. Evolving paradigms for the biological response to low dose ionizing radiation; the role of epigenetics. Int J Radiat Biol 2017; 94:769-781. [PMID: 29157078 DOI: 10.1080/09553002.2017.1388548] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE In the late 1990s, it had become clear that the long-standing paradigm for the action of radiation on living cells and organisms did not have sufficient power to explain the observed effects of low dose ionizing radiation. The purpose of this commentary is to examine the experiments that lead up to the modification of the classic paradigm consequent on these observations, their historical precedents, and the development of our understanding of the role of epigenetics in low dose radiation effects. RESULTS AND CONCLUSIONS We discuss how parallel advances in epigenetics from developmental biology and cancer studies, and the discovery of epigenetic modifications of chromatin, such as DNA methylation, impacted on the development of an epigenetic paradigm for low dose effects. We also assess the impact of technology development in supporting the paradigm shift. We then examine recent accumulated data on epigenetic modification in response to irradiation since that shift took place, and identify areas where bringing together data from developmental biology and cancer might answer some of the paradoxes and contradictions in this data. We predict that further paradigm shifts are imminent.
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Affiliation(s)
- Paul N Schofield
- a Department of Physiology, Development, and Neuroscience , University of Cambridge , Cambridge , UK
| | - Monika Kondratowicz
- a Department of Physiology, Development, and Neuroscience , University of Cambridge , Cambridge , UK
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172
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de Souza HSP, Fiocchi C, Iliopoulos D. The IBD interactome: an integrated view of aetiology, pathogenesis and therapy. Nat Rev Gastroenterol Hepatol 2017; 14:739-749. [PMID: 28831186 DOI: 10.1038/nrgastro.2017.110] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Crohn's disease and ulcerative colitis are prototypical complex diseases characterized by chronic and heterogeneous manifestations, induced by interacting environmental, genomic, microbial and immunological factors. These interactions result in an overwhelming complexity that cannot be tackled by studying the totality of each pathological component (an '-ome') in isolation without consideration of the interaction among all relevant -omes that yield an overall 'network effect'. The outcome of this effect is the 'IBD interactome', defined as a disease network in which dysregulation of individual -omes causes intestinal inflammation mediated by dysfunctional molecular modules. To define the IBD interactome, new concepts and tools are needed to implement a systems approach; an unbiased data-driven integration strategy that reveals key players of the system, pinpoints the central drivers of inflammation and enables development of targeted therapies. Powerful bioinformatics tools able to query and integrate multiple -omes are available, enabling the integration of genomic, epigenomic, transcriptomic, proteomic, metabolomic and microbiome information to build a comprehensive molecular map of IBD. This approach will enable identification of IBD molecular subtypes, correlations with clinical phenotypes and elucidation of the central hubs of the IBD interactome that will aid discovery of compounds that can specifically target the hubs that control the disease.
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Affiliation(s)
- Heitor S P de Souza
- Department of Gastroenterology & Multidisciplinary Research Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro 21941-913, Brazil
| | - Claudio Fiocchi
- Department of Pathobiology, Lerner Research Institute, Department of Gastroenterology and Hepatology, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Dimitrios Iliopoulos
- Center for Systems Biomedicine, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
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173
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Soubry A. Epigenetics as a Driver of Developmental Origins of Health and Disease: Did We Forget the Fathers? Bioessays 2017; 40. [PMID: 29168895 DOI: 10.1002/bies.201700113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/04/2017] [Indexed: 12/15/2022]
Abstract
What are the effects of our environment on human development and the next generation? Numerous studies have provided ample evidence that a healthy environment and lifestyle of the mother is important for her offspring. Biological mechanisms underlying these environmental influences have been proposed to involve alterations in the epigenome. Is there enough evidence to suggest a similar contribution from the part of the father? Animal models provide proof of a transgenerational epigenetic effect through the paternal germ line, but can this be translated to humans? To date, literature on fathers is scarce. Human studies do not always incorporate appropriate tools to evaluate paternal influences or epigenetic effects. In reviewing the literature, I stress the need to explore and recognize paternal contributions to offspring's health within the Developmental Origins of Health and Disease hypothesis, and coin this new concept the Paternal Origins of Health and Disease paradigm (POHaD). A better understanding of preconceptional origins of disease through the totality of paternal exposures, or the paternal exposome, will provide evidence-based public health recommendations for future fathers.
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Affiliation(s)
- Adelheid Soubry
- Epidemiology Research Group, Department of Public Health and Primary Care, Faculty of Medicine, KU Leuven - University of Leuven, Leuven, Belgium
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174
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Bierne H, Nielsen-LeRoux C. Is there a transgenerational inheritance of host resistance against pathogens? Lessons from the Galleria mellonella-Bacillus thuringiensis interaction model. Virulence 2017; 8:1471-1474. [PMID: 28758839 PMCID: PMC5810474 DOI: 10.1080/21505594.2017.1356538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
- Hélène Bierne
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
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175
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Houfflyn S, Matthys C, Soubry A. Male Obesity: Epigenetic Origin and Effects in Sperm and Offspring. CURRENT MOLECULAR BIOLOGY REPORTS 2017; 3:288-296. [PMID: 29387521 PMCID: PMC5768668 DOI: 10.1007/s40610-017-0083-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW The prevalence of obesity has increased substantially in the current generations of Western countries, and the burden of obesity-related complications has been growing steadily. In men, obesity is not only a major risk factor for serious chronic diseases, concern is growing that the reproductive capacity, and more particularly, their offspring's health may be affected. Obesity-related impaired spermatogenesis is associated with a decrease in microscopic and molecular sperm characteristics and pregnancy success. We hypothesize that epigenetics is an important mediator explaining interactions between an obesogenic environment and sperm/offspring outcomes. RECENT FINDINGS Recent studies have explored inter- and transgenerational epigenetic effects in sperm cells and in offspring. Father-to-child effects have been reported in relation to preconceptional nutritional and life-style related factors. SUMMARY Here, we summarize the current understanding about obesity and molecular or epigenetic underlying mechanisms in sperm. We identify the obesogenic environment of the father before conception as a potential origin of health or disease in the offspring and include it as part of a new concept, the Paternal Origins of Health and Disease (POHaD).
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Affiliation(s)
- Sam Houfflyn
- Epidemiology Research Unit, Department of Public Health and Primary Care, University of Leuven, 3000 Leuven, Belgium
| | - Christophe Matthys
- Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven University, Leuven, Belgium
| | - Adelheid Soubry
- Epidemiology Research Unit, Department of Public Health and Primary Care, University of Leuven, 3000 Leuven, Belgium
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176
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Yung PYK, Elsässer SJ. Evolution of epigenetic chromatin states. Curr Opin Chem Biol 2017; 41:36-42. [PMID: 29078152 DOI: 10.1016/j.cbpa.2017.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/06/2017] [Accepted: 10/03/2017] [Indexed: 01/08/2023]
Abstract
The central dogma of gene expression entails the flow of genetic information from DNA to RNA, then to protein. Decades of studies on epigenetics have characterized an additional layer of information, where epigenetic states help to shape differential utilization of genetic information. Orchestrating conditional gene expressions to elicit a defined phenotype and function, epigenetics states distinguish different cell types or maintain a long-lived memory of past signals. Packaging the genetic information in the nucleus of the eukaryotic cell, chromatin provides a large regulatory repertoire that capacitates the genome to give rise to many distinct epigenomes. We will discuss how reversible, heritable functional annotation mechanisms in chromatin may have evolved from basic chemical diversification of the underlying molecules.
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Affiliation(s)
- Philip Yuk Kwong Yung
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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177
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Le Q, Li Y, Hou W, Yan B, Yu X, Song H, Wang F, Ma L. Binge-Like Sucrose Self-Administration Experience Inhibits Cocaine and Sucrose Seeking Behavior in Offspring. Front Behav Neurosci 2017; 11:184. [PMID: 29021748 PMCID: PMC5623684 DOI: 10.3389/fnbeh.2017.00184] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/15/2017] [Indexed: 11/13/2022] Open
Abstract
Recent studies show that emotional and environmental stimuli promote epigenetic inheritance and influence behavioral development in the subsequent generations. Caloric mal- and under-nutrition has been shown to cause metabolic disturbances in the subsequent generation, but the incentive properties of paternal binge-like eating in offspring is still unknown. Here we show that paternal sucrose self-administration experience could induce inter-generational decrease in both sucrose and cocaine-seeking behavior, and sucrose responding in F1 rats, but not F2, correlated with the performance of F0 rats in sucrose self-administration. Higher anxiety level and decreased cocaine sensitivity were observed in Sucrose F1 compared with Control F1, possibly contributing to the desensitization phenotype in cocaine and sucrose self-administration. Our study revealed that paternal binge-like sucrose consumption causes decrease in reward seeking and induces anxiety-like behavior in the F1 offspring.
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Affiliation(s)
- Qiumin Le
- State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Yanqing Li
- State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Weiqing Hou
- State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Biao Yan
- State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Xiangchen Yu
- State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Haikun Song
- State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Feifei Wang
- State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Lan Ma
- State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
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178
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Abstract
In recent years, a Lamarckian theme has found its way back into academic discourse on evolution and inheritance. Especially the emerging field of transgenerational small RNAs has provided at least a proof of concept for the inheritance of acquired traits. Yet it remains unclear whether the Lamarckian concept of inheritance will in fact have its rennaisance or whether it will remain the rallying cry for the outlaws, heretics and enfants terribles of molecular biology. As unclear as the future of Lamarckian theory is its content and reference. Since the formulation of the Philosophie Zoologique, Lamarckian thought has been de- and reconfiguring in and out of the scientific literature and become an umbrella-term for all kinds of unconventional modes of inheritance. This essay will argue that heritable small RNAs might in fact provide a case of genuine Lamarckian inheritance. Moreover, it will be claimed that not only the very broad concept of “inheritance of acquired traits“ applies, but also that Lamarck's mechanistic insight into a use/disuse relation might help to explain a specific mode of transgenerational inheritance.
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179
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Gapp K, Bohacek J. Epigenetic germline inheritance in mammals: looking to the past to understand the future. GENES BRAIN AND BEHAVIOR 2017; 17:e12407. [PMID: 28782190 DOI: 10.1111/gbb.12407] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 07/15/2017] [Accepted: 08/03/2017] [Indexed: 12/25/2022]
Abstract
Life experiences can induce epigenetic changes in mammalian germ cells, which can influence the developmental trajectory of the offspring and impact health and disease across generations. While this concept of epigenetic germline inheritance has long been met with skepticism, evidence in support of this route of information transfer is now overwhelming, and some key mechanisms underlying germline transmission of acquired information are emerging. This review focuses specifically on sperm RNAs as causal vectors of inheritance. We examine how they might become altered in the germline, and how different classes of sperm RNAs might interact with other epimodifications in germ cells or in the zygote. We integrate the latest findings with earlier pioneering work in this field, point out major questions and challenges, and suggest how new experiments could address them.
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Affiliation(s)
- K Gapp
- Gurdon Institute, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - J Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Department of Health Sciences and Technology of ETH Zurich, Neuroscience Center Zurich, Switzerland
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180
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Acharya S, Hartmann M, Erhardt S. Chromatin-associated noncoding RNAs in development and inheritance. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28840663 DOI: 10.1002/wrna.1435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) have emerged as crucial players in chromatin regulation. Their diversity allows them to partake in the regulation of numerous cellular processes across species. During development, long and short ncRNAs act in conjunction with each other where long ncRNAs (lncRNAs) are best understood in establishing appropriate gene expression patterns, while short ncRNAs (sRNAs) are known to establish constitutive heterochromatin and suppress mobile elements. Additionally, increasing evidence demonstrates roles of sRNAs in several typically lncRNA-mediated processes such as dosage compensation, indicating a complex regulatory network of noncoding RNAs. Together, various ncRNAs establish many mitotically heritable epigenetic marks during development. Additionally, they participate in mechanisms that regulate maintenance of these epigenetic marks during the lifespan of the organism. Interestingly, some epigenetic traits are transmitted to the next generation(s) via paramutations or transgenerational inheritance mediated by sRNAs. In this review, we give an overview of the various functions and regulations of ncRNAs and the mechanisms they employ in the establishment and maintenance of epigenetic marks and multi-generational transmission of epigenetic traits. WIREs RNA 2017, 8:e1435. doi: 10.1002/wrna.1435 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Sreemukta Acharya
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, and CellNetworks, Im Neuenheimer Feld 282, Heidelberg, Germany
| | - Mark Hartmann
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sylvia Erhardt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, and CellNetworks, Im Neuenheimer Feld 282, Heidelberg, Germany
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181
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Abstract
Stochasticity is harnessed by organisms to generate functionality. Randomness does not, therefore, necessarily imply lack of function or 'blind chance' at higher levels. In this respect, biology must resemble physics in generating order from disorder. This fact is contrary to Schrödinger's idea of biology generating phenotypic order from molecular-level order, which inspired the central dogma of molecular biology. The order originates at higher levels, which constrain the components at lower levels. We now know that this includes the genome, which is controlled by patterns of transcription factors and various epigenetic and reorganization mechanisms. These processes can occur in response to environmental stress, so that the genome becomes 'a highly sensitive organ of the cell' (McClintock). Organisms have evolved to be able to cope with many variations at the molecular level. Organisms also make use of physical processes in evolution and development when it is possible to arrive at functional development without the necessity to store all information in DNA sequences. This view of development and evolution differs radically from that of neo-Darwinism with its emphasis on blind chance as the origin of variation. Blind chance is necessary, but the origin of functional variation is not at the molecular level. These observations derive from and reinforce the principle of biological relativity, which holds that there is no privileged level of causation. They also have important implications for medical science.
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Affiliation(s)
- Denis Noble
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
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182
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Abstract
The Modern Evolutionary Synthesis (MS) forged in the mid-twentieth century was built on a notion of heredity that excluded soft inheritance, the inheritance of the effects of developmental modifications. However, the discovery of molecular mechanisms that generate random and developmentally induced epigenetic variations is leading to a broadening of the notion of biological heredity that has consequences for ideas about evolution. After presenting some old challenges to the MS that were raised, among others, by Karl Popper, I discuss recent research on epigenetic inheritance, which provides experimental and theoretical support for these challenges. There is now good evidence that epigenetic inheritance is ubiquitous and is involved in adaptive evolution and macroevolution. I argue that the many evolutionary consequences of epigenetic inheritance open up new research areas and require the extension of the evolutionary synthesis beyond the current neo-Darwinian model.
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Affiliation(s)
- Eva Jablonka
- The Cohn Institute for the History and Philosophy of Science and Ideas, Tel-Aviv University, Tel-Aviv 69978, Israel
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183
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184
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Arshad SH, Karmaus W, Zhang H, Holloway JW. Multigenerational cohorts in patients with asthma and allergy. J Allergy Clin Immunol 2017; 139:415-421. [PMID: 28183434 DOI: 10.1016/j.jaci.2016.12.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 12/16/2022]
Abstract
Recent observations that disease risk can be transmitted across generations without the need for direct exposure of the child to the index environmental insult has sparked interest in transgenerational inheritance. Epigenetics describes processes that modify gene expression without a change in the nucleotide sequence. Epigenetic processes can be induced in response to environmental exposures, can influence disease risk, and might explain these multigenerational effects. In experimental models a number of epigenetic mechanisms have been identified that could mediate vertical transmission of epigenetic inheritance. However, relevance of these findings to human disease is not yet clear. An alternative model is one in which transgenerational inheritance of disease risk requires the presence of exposure-related diseases in the mother during pregnancy (termed induced epigenetic transmission model). A number of cross-sectional studies have investigated multigenerational effects in allergy and asthma. However, given the early-life origins of asthma and allergy, birth cohort studies are ideal to investigate the effect of genetic predisposition, epigenetics, and environmental exposures, avoiding pitfalls, such as recall bias and confounding by ongoing exposures, disease, and treatment. The well-characterized 3 generations of the Isle of Wight cohort include 2 consecutive birth cohorts, providing longitudinal data that can be studied for epigenetic transfer of information, such as the effect of grand parental smoking or exposure to other toxic compounds. Further large multigenerational birth cohorts are needed to establish the clinical relevance of this phenomenon and differentiate between vertical and induced transmission models, which might influence future preventive strategies.
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Affiliation(s)
- S Hasan Arshad
- David Hide Asthma and Allergy Research Centre, Isle of Wight, United Kingdom; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, Tenn
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, Tenn
| | - John W Holloway
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
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185
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Vaiserman AM, Koliada AK, Jirtle RL. Non-genomic transmission of longevity between generations: potential mechanisms and evidence across species. Epigenetics Chromatin 2017; 10:38. [PMID: 28750655 PMCID: PMC5531095 DOI: 10.1186/s13072-017-0145-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 07/21/2017] [Indexed: 02/06/2023] Open
Abstract
Accumulating animal and human data indicate that environmental exposures experienced during sensitive developmental periods may strongly influence risk of adult disease. Moreover, the effects triggered by developmental environmental cues can be transgenerationally transmitted, potentially affecting offspring health outcomes. Increasing evidence suggests a central role of epigenetic mechanisms (heritable alterations in gene expression occurring without changes in underlying DNA sequence) in mediating these effects. This review summarizes the findings from animal models, including worms, insects, and rodents, and also from human studies, indicating that lifespan and longevity-associated characteristics can be transmitted across generations via non-genetic factors.
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Affiliation(s)
- Alexander M Vaiserman
- D.F. Chebotarev Institute of Gerontology, NAMS, Vyshgorodskaya st. 67, Kiev, 04114, Ukraine.
| | - Alexander K Koliada
- D.F. Chebotarev Institute of Gerontology, NAMS, Vyshgorodskaya st. 67, Kiev, 04114, Ukraine
| | - Randy L Jirtle
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA.,Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53706, USA
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186
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Zenk F, Loeser E, Schiavo R, Kilpert F, Bogdanović O, Iovino N. Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition. Science 2017; 357:212-216. [DOI: 10.1126/science.aam5339] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/16/2017] [Indexed: 12/30/2022]
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187
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Affiliation(s)
- W P T James
- Nutrition Group, Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
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188
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Abstract
From March 27-29 2017, the RIKEN Center for Developmental Biology held a symposium entitled 'Towards Understanding Human Development, Heredity, and Evolution' in Kobe, Japan. Recent advances in technologies including stem cell culture, live imaging, single-cell approaches, next-generation sequencing and genome editing have led to an expansion in our knowledge of human development. Organized by Yoshiya Kawaguchi, Mitinori Saitou, Mototsugu Eiraku, Tomoya Kitajima, Fumio Matsuzaki, Takashi Tsuji and Edith Heard, the symposium covered a broad range of topics including human germline development, epigenetics, organogenesis and evolution. This Meeting Review provides a summary of this timely and exciting symposium, which has convinced us that we are moving into the era of science targeted on humans.
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Affiliation(s)
- Ryuichi Nishinakamura
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Minoru Takasato
- RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
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189
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Teotónio H, Estes S, Phillips PC, Baer CF. Experimental Evolution with Caenorhabditis Nematodes. Genetics 2017; 206:691-716. [PMID: 28592504 PMCID: PMC5499180 DOI: 10.1534/genetics.115.186288] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 03/07/2017] [Indexed: 12/17/2022] Open
Abstract
The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic variation; (2) role of natural selection during transitions from outcrossing to selfing, as well as the maintenance of mixed breeding modes during evolution; and (3) evolution of phenotypic plasticity and its role in adaptation to variable environments, including host-pathogen coevolution. We conclude by suggesting some future directions for which experimental evolution with Caenorhabditis would be particularly informative.
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Affiliation(s)
- Henrique Teotónio
- Institut de Biologie de l´École Normale Supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre Nationnal de la Recherche Scientifique Unité Mixte de Recherche 8197, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Suzanne Estes
- Department of Biology, Portland State University, Oregon 97201
| | - Patrick C Phillips
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, Oregon 97403, and
| | - Charles F Baer
- Department of Biology, and
- University of Florida Genetics Institute, University of Florida, Gainesville, Florida 32611
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190
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The RNAi Inheritance Machinery of Caenorhabditis elegans. Genetics 2017; 206:1403-1416. [PMID: 28533440 DOI: 10.1534/genetics.116.198812] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/17/2017] [Indexed: 12/30/2022] Open
Abstract
Gene silencing mediated by dsRNA (RNAi) can persist for multiple generations in Caenorhabditis elegans (termed RNAi inheritance). Here we describe the results of a forward genetic screen in C. elegans that has identified six factors required for RNAi inheritance: GLH-1/VASA, PUP-1/CDE-1, MORC-1, SET-32, and two novel nematode-specific factors that we term here (heritable RNAi defective) HRDE-2 and HRDE-4 The new RNAi inheritance factors exhibit mortal germline (Mrt) phenotypes, which we show is likely caused by epigenetic deregulation in germ cells. We also show that HRDE-2 contributes to RNAi inheritance by facilitating the binding of small RNAs to the inheritance Argonaute (Ago) HRDE-1 Together, our results identify additional components of the RNAi inheritance machinery whose conservation provides insights into the molecular mechanism of RNAi inheritance, further our understanding of how the RNAi inheritance machinery promotes germline immortality, and show that HRDE-2 couples the inheritance Ago HRDE-1 with the small RNAs it needs to direct RNAi inheritance and germline immortality.
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191
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Pang TYC, Short AK, Bredy TW, Hannan AJ. Transgenerational paternal transmission of acquired traits: Stress-induced modification of the sperm regulatory transcriptome and offspring phenotypes. Curr Opin Behav Sci 2017; 14:140-147. [PMID: 29270445 PMCID: PMC5734660 DOI: 10.1016/j.cobeha.2017.02.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In recent years, it has become evident that pre-conceptual exposure of males to various environmental factors induces epigenetic changes in sperm, which can mediate the transmission of acquired traits in their offspring. The most thoroughly examined paternal exposures involve stress and elevated corticosterone, which have been shown to modulate offspring phenotypes in a manner that is relevant to predisposition to brain disorders, and psychiatric illness in particular. Recent seminal studies have demonstrated that key epigenetic information transmitted via the paternal germline involves small non-coding (snc) RNA transcripts such as microRNAs. Following fertilisation, these sncRNAs appear to regulate development so as to modify the phenotype of the offspring. Understanding the mechanisms involved in such transgenerational effects may facilitate future screening of human sperm for 'epigenetic health' and the tailoring of therapeutic interventions according to genetic and epigenetic contributions to illness.
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Affiliation(s)
- Terence Y C Pang
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
| | - Annabel K Short
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Anatomy and Neurobiology, University of California, Irvine, CA 92617, USA
| | - Timothy W Bredy
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
- Center for the Neurobiology of Learning and Memory and Department of Neurobiology and Behavior, University of California, Irvine, CA 92617, USA
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC 3010, Australia
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192
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Abstract
Exposing male mice to nicotine or cocaine enables their male offspring to cope with high doses of either, which suggests that such paternal effects are generic, rather than being a response to a specific type of stress.
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Affiliation(s)
- Claude Becker
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
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193
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Sales VM, Ferguson-Smith AC, Patti ME. Epigenetic Mechanisms of Transmission of Metabolic Disease across Generations. Cell Metab 2017; 25:559-571. [PMID: 28273478 PMCID: PMC5404272 DOI: 10.1016/j.cmet.2017.02.016] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Both human and animal studies indicate that environmental exposures experienced during early life can robustly influence risk for adult disease. Moreover, environmental exposures experienced by parents during either intrauterine or postnatal life can also influence the health of their offspring, thus initiating a cycle of disease risk across generations. In this Perspective, we focus on epigenetic mechanisms in germ cells, including DNA methylation, histone modification, and non-coding RNAs, which collectively may provide a non-genetic molecular legacy of prior environmental exposures and influence transcriptional regulation, developmental trajectories, and adult disease risk in offspring.
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Affiliation(s)
- Vicencia Micheline Sales
- Integrative Physiology and Metabolism, Research Division, Joslin Diabetes Center and Harvard Medical School, One Joslin Place, Sixth Floor, Boston, MA 02215, USA
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Mary-Elizabeth Patti
- Integrative Physiology and Metabolism, Research Division, Joslin Diabetes Center and Harvard Medical School, One Joslin Place, Sixth Floor, Boston, MA 02215, USA.
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194
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Leroux S, Gourichon D, Leterrier C, Labrune Y, Coustham V, Rivière S, Zerjal T, Coville JL, Morisson M, Minvielle F, Pitel F. Embryonic environment and transgenerational effects in quail. Genet Sel Evol 2017; 49:14. [PMID: 28125975 PMCID: PMC5270212 DOI: 10.1186/s12711-017-0292-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 01/19/2017] [Indexed: 12/27/2022] Open
Abstract
Background Environmental exposures, for instance to chemicals, are known to impact plant and animal phenotypes on the long term, sometimes across several generations. Such transgenerational phenotypes were shown to be promoted by epigenetic alterations such as DNA methylation, an epigenetic mark involved in the regulation of gene expression. However, it is yet unknown whether transgenerational epigenetic inheritance of altered phenotypes exists in birds. The purpose of this study was to develop an avian model to investigate whether changes to the embryonic environment had a transgenerational effect that could alter the phenotypes of third-generation offspring. Given its impact on the mammalian epigenome and the reproductive system in birds, genistein was used as an environment stressor. Results We compared several third-generation phenotypes of two quail “epilines”, which were obtained from genistein-injected eggs (Epi+) or from untreated eggs (Epi−) from the same founders. A “mirrored” crossing strategy was used to minimize between-line genetic variability by maintaining similar ancestor contributions across generations in each line. Three generations after genistein treatment, a significant difference in the sexual maturity of the females, which, after three generations, could not be attributed to direct maternal effects, was observed between the lines, with Epi+ females starting to lay eggs later. Adult body weight was significantly affected by genistein treatment applied in a previous generation, and a significant interaction between line and sex was observed for body weight at 3 weeks. Behavioral traits, such as evaluating the birds’ reaction to social isolation, were also significantly affected by genistein treatment. Yet, global methylation analyses revealed no significant difference between the epilines. Conclusions These findings demonstrate that embryonic environment affects the phenotype of offspring three generations later in quail. While one cannot rule out the existence of some initial genetic variability between the lines, the mirrored animal design should have minimized its effects, and thus, the observed differences in animals of the third generation may be attributed, at least partly, to transgenerational epigenetic phenomena. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0292-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sophie Leroux
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326, Castanet Tolosan, France
| | | | - Christine Leterrier
- UMR INRA PRC, 37380, Nouzilly, France.,CNRS, 37380, Nouzilly, France.,UFR Tours, 37380, Nouzilly, France.,IFCE, 37380, Nouzilly, France
| | - Yann Labrune
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326, Castanet Tolosan, France
| | | | | | - Tatiana Zerjal
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jean-Luc Coville
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Mireille Morisson
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Francis Minvielle
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326, Castanet Tolosan, France.
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195
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Li Y, Hou L, Song B, Yang L, Li L. Effects of Increased Nitrogen and Phosphorus Deposition on Offspring Performance of Two Dominant Species in a Temperate Steppe Ecosystem. Sci Rep 2017; 7:40951. [PMID: 28102339 PMCID: PMC5244414 DOI: 10.1038/srep40951] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/12/2016] [Indexed: 11/09/2022] Open
Abstract
Plants adapt to environment by plastic growth which will be transferred to offspring through transgenerational effect. Performance and response of maternal and offspring plant will affect population dynamics and community composition. However, it is scarcely understood how maternal nutrient environment affect the performance and response of offspring through transgenerational effect. Here we studied the impacts of nitrogen (N) and phosphorus (P) enrichment on maternal and offspring performances and responses of Stipa krylovii and Artemisia frigida. Seeds were collected from maternal plant experiencing N or/and P addition for three years in Inner Mongolia grassland. We found that maternal nutrient addition significantly affected seed traits, offspring biomass, and offspring responses of A. frigida. Maternal N addition significantly affected maternal reproductive biomass, seed traits of S. kryloii. Maternal P addition of S. kryloii significantly affected seed qualities, seedling biomass and seeding response to N addition. Our results suggested that transgenerational effects of N and P enrichment to the two dominant plant species existed in this ecosystem. Furthermore, the two species exhibited different adaptive strategies to future nutrient addition. These findings indicate that maternal environmental effect should be considered into the model projection of vegetation dynamics in response to ongoing environmental change.
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Affiliation(s)
- Yang Li
- Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi’an 710061, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
| | - Longyu Hou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
| | - Bing Song
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
| | - Liuyi Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
| | - Linghao Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
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196
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Zhang B. Consequences of early adverse rearing experience(EARE) on development: insights from non-human primate studies. Zool Res 2017; 38:7-35. [PMID: 28271667 PMCID: PMC5368383 DOI: 10.13918/j.issn.2095-8137.2017.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/30/2016] [Indexed: 12/18/2022] Open
Abstract
Early rearing experiences are important in one's whole life, whereas early adverse rearing experience(EARE) is usually related to various physical and mental disorders in later life. Although there were many studies on human and animals, regarding the effect of EARE on brain development, neuroendocrine systems, as well as the consequential mental disorders and behavioral abnormalities, the underlying mechanisms remain unclear. Due to the close genetic relationship and similarity in social organizations with humans, non-human primate(NHP) studies were performed for over 60 years. Various EARE models were developed to disrupt the early normal interactions between infants and mothers or peers. Those studies provided important insights of EARE induced effects on the physiological and behavioral systems of NHPs across life span, such as social behaviors(including disturbance behavior, social deficiency, sexual behavior, etc), learning and memory ability, brain structural and functional developments(including influences on neurons and glia cells, neuroendocrine systems, e.g., hypothalamic-pituitary-adrenal(HPA) axis, etc). In this review, the effects of EARE and the underlying epigenetic mechanisms were comprehensively summarized and the possibility of rehabilitation was discussed.
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Affiliation(s)
- Bo Zhang
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming Yunnan 650500, China; National Institute of Health, Bethesda, Maryland, USA.
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197
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Sharma A. Transgenerational epigenetics: Integrating soma to germline communication with gametic inheritance. Mech Ageing Dev 2017; 163:15-22. [PMID: 28093237 DOI: 10.1016/j.mad.2016.12.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/07/2016] [Accepted: 12/13/2016] [Indexed: 12/28/2022]
Abstract
Evidence supporting germline mediated epigenetic inheritance of environmentally induced traits has increasingly emerged over the past several years. Although the mechanisms underlying this inheritance remain unclear, recent findings suggest that parental gamete-borne epigenetic factors, particularly RNAs, affect post-fertilization and developmental gene regulation, ultimately leading to phenotypic appearance in the offspring. Complex processes involving gene expression and epigenetic regulation are considered to perpetuate across generations. In addition to transfer of germline factors, epigenetic inheritance via gametes also requires a mechanism whereby the information pertaining to the induced traits is communicated from soma to germline. Despite violating a century-old view in biology, this communication seems to play a role in transmission of environmental effects across generations. Circulating RNAs, especially those associated with extracellular vesicles like exosomes, are emerging as promising candidates that can transmit gene regulatory information in this direction. Cumulatively, these new observations provide a basis to integrate epigenetic inheritance. With significant implications in health, disease and ageing, the latter appears poised to revolutionize biology.
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Affiliation(s)
- Abhay Sharma
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.
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198
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Shi J, Zhang X, Liu Y, Chen Q. Epigenetic information in gametes: Gaming from before fertilization: Comment on "Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition" by Qian Wang et al. Phys Life Rev 2017; 20:146-149. [PMID: 28089374 DOI: 10.1016/j.plrev.2017.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/03/2017] [Indexed: 02/07/2023]
Affiliation(s)
- Junchao Shi
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89512, USA
| | - Xudong Zhang
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89512, USA
| | - Ying Liu
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89512, USA
| | - Qi Chen
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89512, USA.
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Kieling C. Here/In This Issue and There/Abstract Thinking: From Families to Mechanisms. J Am Acad Child Adolesc Psychiatry 2017; 56:1-2. [PMID: 27993222 DOI: 10.1016/j.jaac.2016.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 11/18/2022]
Affiliation(s)
- Christian Kieling
- Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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