Adaptation and changing phenotypes through transgenerational epigenetics

Andrea Cupp made a serendipitous discovery when she was a postdoctoral fellow at Washington State University: While investigating how chemicals affect sex determination in embryonic animals, she bred the offspring of pregnant rats that had been dosed with an insecticide called methoxyclor. When the males from that litter grew into adults, they had decreased sperm counts and higher rates of infertility. Cupp had seen these same abnormalities in the animals’ fathers, which had been exposed to methoxyclor in the womb. But this latest generation hadn’t been exposed that way, which suggested that methoxyclor’s toxic effects had carried over generations. “At first I couldn’t believe it,” says Cupp’s advisor, Michael Skinner, a biochemist and Washington State professor. “But then we repeated the breeding experiments and found that the results held up.” Skinner and Cupp, who is now a professor at the University of Nebraska–Lincoln, published their findings in 2005.1 Since that paper—which showed that reproductive effects not just from methoxyclor but also from the fungicide vinclozolin persisted for at least four generations—the number of published articles reporting similar transgenerational findings has increased steadily. “In the last year and half there’s been an explosion in studies showing transgenerational effects from exposure to a wide array of environmental stressors,” says Lisa Chadwick, a program administrator at the National Institute of Environmental Health Sciences (NIEHS). “This is a field that’s really starting to take off.” According to Chadwick, the new findings compel a reevaluation of how scientists perceive environmental health threats. “We have to think more long-term about the effects of chemicals that we’re exposed to every day,” she says. “This new research suggests they could have consequences not just for our own health and for that of our children, but also for the health of generations to come.” Figure 1 Glossary The NIEHS recently issued requests for applications totaling $3 million for research on transgenerational effects in mammals.2 Chadwick says funded studies will address two fundamental data needs, one pertaining to potential transgenerational mechanisms and another to the number of chemicals thought to exert these effects. These studies will extend to what’s known as the F3 generation—the great-grandchildren of the originally exposed animal. That’s because chemicals given to pregnant females (the F0 generation) interact not only with the fetal offspring (the F1 generation) but also the germ cells developing within those offspring, which mature into the sperm and eggs that give rise to the F2 generation. Thus, the F3 animals are the first generation to be totally unexposed to the original agent. Effects that extend to the F2 generation are known as “multigenerational,” whereas those that extend to the F3 generation are known as “transgenerational.”3 Transgenerational effects have now been reported for chemicals including permethrin, DEET, bisphenol A, certain phthalates, dioxin, jet fuel mixtures, nicotine, and tributyltin, among others. Most of these findings come from rodent studies.4,5,6,7 But preliminary evidence that chemical effects can carry over generations in humans is also emerging, although no F3 data have been published yet. Given the challenges of tracking effects over multiple human lifespans, the evidence is more difficult to interpret, particularly with respect to potential mechanisms, says Tessa Roseboom, a professor of early development and health at the Academic Medical Center in Amsterdam, the Netherlands. Still, some reports have linked nutritional deficiencies from famine and exposure to diethylstilbestrol (DES)—a nonsteroidal estrogen used to protect against miscarriage from the 1940s to the 1970s—to effects that persist among the grandchildren of exposed women.8,9,10,11,12,13

Darwin meets Waddington

“Epigenetics” refers to changes in gene expression that occur through changes in DNA methylation, histone modification, small or micro‐RNAs, or most inclusively, other mechanisms that alter how DNA sequences are translated into functional gene products. With the discovery that epigenetic modifications to gene expression can be inherited across cell lineages or even across organismal generations, enormous interest has been generated in the potential evolutionary consequences of epigenetic inheritance. This collection of articles addresses how epigenetic inheritance may influence adaptive evolution, focusing on epigenetic stability and inheritance itself as a potentially evolving trait. It has frequently been argued that epigenetic modifications that are stable across multiple generations can act as an important source of heritable phenotypic variation upon which natural selection can act, and that such variation, unlike random genetic mutation, may even be nonrandom with respect to environmental context and adaptive value. This bold hypothesis raises a number of compelling questions. First, when changes in gene expression are not caused by changes in DNA sequence, what sort of epigenetic changes are stochastic versus environmentally induced, and do they differ in their stability of inheritance? Second, what is the adaptive value of such random and environmentally induced epigenetic modifications in the wild? Third, is the stability of epigenetic alterations itself heritable and is it adaptive, and if so, under what conditions? Does natural selection actually favor epigenetic stability, or not, and does selection for or against stability determine how frequently we may observe adaptation via epigenetic inheritance? These articles begin to address these questions by reviewing recent advances in studies of epigenetics in natural populations.

Introduction: Epigenetic inheritance refers to the mechanisms for transmission of gene regulatory information which is not coded in the DNA sequence (i.e. not genetic) through successive cellular divisions (mitosis and/or meiosis). It plays a crucial role for the development and importantly, through epigenetic changes, environmental influences (food, smoking, etc.) can be `remembered` and could have long lasting effects after exposure. Transgenerational epigenetic inheritance (TEI) refers to the transmittance of epigenetic information between successive generations and it is generally accepted that such a process (with a few exceptions) does not occur as there is extensive epigenetic reprogramming and every new generation starts with an epigenetically `clean slate`. Currently, there are convincing demonstrations of transgenerational inheritance of an epigenetic state at a few loci in plants and mice and the evidence in humans is mainly indirect. Nonetheless, even if the epigenetic state of a small number of genes in humans is transgenerationally inherited, it would herald a major shift in the way we think about the inheritance of phenotype. With this in mind, our aim is to review current literature to assess the evidence for existence of TEI in humans and to review its possible mechanisms. Materials and Methods: We performed a PubMed search and analysis of articles containing the term `transgenerational epigenetic inheritance` in their title. Results: At the time of writing there were 31 articles indexed in PubMed corresponding to the given search criteria, nine of which concern TEI in humans. A major drawback in the field is the lack of a clear definition of transgenerational epigenetic inheritance and clear discrimination from inherited epimutation. There are no articles presenting solid evidence for the TEI phenomenon in humans. Possible key mechanisms of transmission are DNA methylation, histone modifications, and non-coding RNAs. Conclusions: There is still lack of solid evidence for the phenomenon of transgenerational epigenetic inheritance in humans.

Chapter Two - Transgenerational Epigenetics and Brain Disorders

Chronic ethanol ingestion, achieved by feeding ethanol at a constant rate using intragastric tube feeding, alters the expression of genes in the liver. This is done by epigenetic mechanisms, which depend on the blood alcohol levels at the time of killing. However, acute bolus feeding of ethanol changes gene expression without lasting epigenetic changes. This occurs with histone 3 methylation and acetylation modifications. The gene expression response to an acute bolus of ethanol might be modified by feeding S-adenosylmethionine (SAMe), a methyl donor. In the present study, rats were given a bolus of ethanol (6 g/kg body weight (bw), SAMe (1 g/kg bw), ethanol + SAMe, or isocaloric glucose. The group of rats (n = 3) were killed at 3 and 12 h post bolus, and gene microarray analysis was performed on their liver cells. SAMe reduced the 3 h blood ethanol levels and increased the ALT levels at 3 h. Venn diagrams showed that alcohol changed the expression of 646 genes at 3 h post bolus and 586 genes at 12 h. SAMe changed the expression of 1,012 genes when fed with ethanol 3 h post ethanol bolus and 554 genes at 12 h post ethanol bolus. SAMe alone changed the expression of 1,751 genes at 3 h and 1,398 at 12 h. There were more changes in gene expression at 3 h than at 12 h post ethanol when ethanol alone was compared to the dextrose control. The same was true when SAMe was compared to SAMe + ethanol. Ethanol up regulated gene expression in most functional pathways at 3 h. However, when SAMe was fed with ethanol at 3 h, most pathways were down regulated. At 12 h, however, when ethanol was fed, the pathways were half up regulated and half down regulated. The same was true when SAMe + ethanol was fed. The expression of epigenetically important genes, such as BHMT and Foxn3, was up regulated 3 h post alcohol bolus. At 3 h, SAMe down regulated the expression of genes, such as BHMT, Mat2a, Jun, Tnfrs9, Ahcy 1, Tgfbr1 and 2, and Pcaf. At 12 h, the insulin signaling pathways were half down regulated by ethanol, which was partly prevented by SAMe. The MAPK pathway was up regulated by ethanol, but SAMe did not prevent this. In conclusion, profound changes in gene expression evolved between 3 h and 12 post ethanol bolus. SAMe down regulated these changes in gene expression at 3 h, and less so at 12 h.

Elusive inheritance: Transgenerational effects and epigenetic inheritance in human environmental disease

Do genes define your destiny? The field of epigeneticsexamines how genes and the environment interact to formthe basis of heredity and comes up with some surprisingfindings. We often think of deoxyribonucleic acid (DNA) asthe sole physical basis for heredity, the genetic code thatdetermines everything from eye and hair color to specificpersonality traits. The growing field of epigenetics suggeststhat this traditional paradigm is an oversimplification. Epi-genetics is the study of factors that are heritable, but whichoccur by mechanisms other than changes in the DNA codeitself. C.H. Waddington first used the term epigenetics in theearly 1940s to describe ‘‘the interactions of genes with theirenvironment, which bring the phenotype into being.’’ Epi-genetic marks are susceptible to environmental influences—both chemical and nonchemical—and can be inherited inways that may seem counterintuitive (see sidebar, ExpandingIdeas About Biological Inheritance). Effects of early lifeexperiences, such as parental care or nutrition, can showup later in life and even be passed on to future generations.This emerging area of research has interesting and importantimplications for the field of ecotoxicology—from basicscience to international policy.In classic genetics, genetic material is in the form of DNAand encodes all of the information necessary for life. Thisinformation is copied faithfully and passed down as cellsdivide. Every cell contains a complete copy of the DNAcode, but the pattern of gene expression—that is, whichgenes are turned ‘‘on’’ (expressed) or ‘‘off’’ (nonex-pressed)—determines the cell type and function. A skin cellon your arm contains the same DNA code as a nerve cell inyour brain, but their extreme differences in structure andfunction are due to the particular set of genes that each isexpressing. Epigenetics refers to an annotation in the form ofchemical marks on top of the DNA code; the prefix ‘‘epi’’comesfromaGreekwordmeaning‘‘over’’or‘‘above.’’Thesechemical marks, which are discussed in detail below, affectwhich genes are expressed and at what levels. Epigeneticmarks are highly influenced by the environment and can beinherited along with the genetic code as cells divide mitoti-cally, and in some cases meiotically, from one generation tothe next.Epigenetics is receiving significant attention in the field ofbiomedicine. A PubMed search for ‘‘epigenetic’’ revealedthat more than 1,300 review articles have been written on thetopic, of which more than 50% were published in the lastthree years alone. Epigenetics provides a mechanism for theBarker hypothesis, which postulates that nutrition and otherenvironmentalfactorsearlyindevelopmentcanaltersuscept-ibility to chronic diseases in adulthood. A classic exampleof this is that individuals who were conceived during theDutchWinterHunger(1944–1945)havepersistentepigeneticalterations on a characteristic gestational marker, the IGF2gene, as adults. Furthermore, individuals who experiencedthe Dutch Winter Hunger have higher rates of metabolicdisorders and cardiovascular disease, the epigenetic mecha-nisms of which are the focus of ongoing studies. Nutritionaldeprivation may also have an impact on human longevity;indeed, lifespanisnegativelycorrelated withfoodabundance

Although the evidence for transgenerational epigenetic inheritance from animal experiments is strong, there is very little evidence from human studies. The few studies in human populations that have been able to investigate several generations seem to suggest that transgenerational epigenetic inheritance occurs in humans as well and that this may occur both through the maternal and through the paternal line. We are only beginning to appreciate the generation‐spanning effects of poor environmental conditions during early life, which may be particularly relevant to populations in transition between traditional and Western lifestyles. This may shed light on the epidemic of diabetes, obesity and cardiovascular disease. Public health strategies that focus on improved nutrition during critical periods of growth and development may provide a means of promoting cardiovascular and metabolic health and ultimately benefit generations to come. However, the full impact of the strategies may not be apparent for decades. Key Concepts: A popular definition of epigenetics states that it concerns the study of mitotically and/or meiotically heritable changes in gene expression that occur without a change in DNA sequence. Under this definition, epigenetic regulation has a role at two levels. First, it is involved in development, leading to the differentiation of cells in different tissues and organs and assuring the faithful inheritance of their differentiated state over mitotic cell divisions. Second, epigenetic states can be inherited meiotically, from one generation to the next. Transgenerational effects refer to effects being transmitted from one generation to another. Although some biologists consider all effects that concern both parents and offspring to be transgenerational, the author would like to distinguish transgenerational effects from parental and grandparental effects. In addition to contributing their DNA, parents can influence their offspring in many ways, for example, by contributing bioactive molecules in the egg and sperm cytoplasm, by providing nutrients and hormonal information during embryogenesis and by provisioning and taking care of offspring after birth. Many of these parental and grandparental effects will not have an epigenetic basis. In a pregnant woman, for instance, not only are the mother and foetus exposed to the environmental stimuli but also are exposed the foetus' primordial germ cells, which will eventually produce the grandoffspring. Transgenerational epigenetics is defined here as the study of the transfer of nongenetic information between organisms, setting it apart from the transfer of epigenetic information between cells of the same organism.

Chapter 33 - Transgenerational epigenetics and psychiatric disorders

Epigenetic pathways are essential in different biological processes and in phenotype-environment interactions in response to different stressors and they can induce phenotypic plasticity. They encompass several processes that are mitotically and, in some cases, meiotically heritable, so they can be transferred to subsequent generations via the germline. Transgenerational Epigenetic Inheritance (TEI) describes the phenomenon that phenotypic traits, such as changes in fertility, metabolic function, or behavior, induced by environmental factors (e.g., parental care, pathogens, pollutants, climate change), can be transferred to offspring generations via epigenetic mechanisms. Investigations on TEI contribute to deciphering the role of epigenetic mechanisms in adaptation, adversity, and evolution. However, molecular mechanisms underlying the transmission of epigenetic changes between generations, and the downstream chain of events leading to persistent phenotypic changes, remain unclear. Therefore, inter-, (transmission of information between parental and offspring generation via direct exposure) and transgenerational (transmission of information through several generations with disappearance of the triggering factor) consequences of epigenetic modifications remain major issues in the field of modern biology.In this article, we review and describe the major gaps and issues still encountered in the TEI field: the general challenges faced in epigenetic research; deciphering the key epigenetic mechanisms in inheritance processes; identifying the relevant drivers for TEI and implement a collaborative and multi-disciplinary approach to study TEI. Finally, we provide suggestions on how to overcome these challenges and ultimately be able to identify the specific contribution of epigenetics in transgenerational inheritance and use the correct tools for environmental science investigation and biomarkers identification.

Epigenetic gene regulation refers to changes in the expression of genes that are not associated with changes in the underlying DNA sequence yet are heritable through cell division. Epigenetic gene regulation is fundamental in the development of multicellular organisms as it enables different cells to express different sets of genes despite identical DNA sequence. Recently, it has become increasingly clear that some epigenetic changes can be propagated across generations, known as transgenerational epigenetic inheritance. Despite many striking examples of transgenerational epigenetic inheritance phenomena, the mechanisms underlying them are still unclear. Even more debatable is whether transgenerational epigenetic inheritance has an adaptive role either in short-term responses to the environment or in long-term evolutionary processes. Here I will discuss how insights from model organisms, including the mouse, nematode worms, and flies, have enhanced our understanding of the mechanisms of transgenerational epigenetic inheritance. I will then explore the extent to which these experimental systems support an adaptive role for transgenerational epigenetic inheritance. Finally, I will discuss the potential significance of transgenerational epigenetic inheritance processes for understanding human disease, behaviour and evolution, and cultural memory.

Much controversy surrounds the idea of transgenerational epigenetics. Recent papers argue that epigenetic marks acquired through experience are passed to offspring, but as in much of the field of epigenetics, there is lack of precision in the definitions and perhaps too much eagerness to translate animal research to humans. Here, we review operational definitions of transgenerational inheritance and the processes of epigenetic programing during early development. Subsequently, based on this background, we critically examine some recent findings of studies investigating transgenerational inheritance. Finally, we discuss possible mechanisms that may explain transgenerational inheritance, including transmission of an epigenetic blueprint, which may predispose offspring to specific epigenetic patterning. Taken together, we conclude that presently, the evidence suggesting that acquired epigenetic marks are passed to the subsequent generation remains limited.

Transgenerational epigenetic inheritance

Chapter 28 - Transgenerational (Heritable) Epigenetics and Psychiatric Disorders