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In the last couple of decades, extreme weather events have been increasing, exceeding plants’ tolerance thresholds, and driving mass mortalities in many tree species. Furthermore, many studies suggest that due to their longevity, trees are not able to adapt rapidly enough to keep pace with global climate change. Understanding how trees respond to such weather events and other environmental conditions (such as biotic stress) has thus become crucial for conservation policies and forest management programs. To cope with unpredictable environmental conditions, plants have evolved the ability to alter their physiology, morphology, or development or, in other words, the ability to produce different phenotypes from one genotype. This ability is called phenotypic plasticity, and it plays a major role in plant adaptation. Three factors have been suggested to increase phenotypic variability and thus potentially the resilience of tree populations: intraspecific genetic variability, (micro-)environmental variation, and epigenetic variation. Indeed, a growing body of literature suggests that epigenetic variation might contribute to local adaptation of natural plant populations. Epigenetic mechanisms, such as DNA methylation, can in fact quickly alter phenotypes in response to environmental changes. Variation in DNA methylation can be under genetic control, arise stochastically, or be induced by environmental conditions. Furthermore, phenotypic changes induced by epigenetic variation can be inherited across several generations (especially across clonal generations), suggesting that variation in DNA methylation might contribute to heritable phenotypic variation and, eventually, to adaptation. Although considerable progress has been made in recent years, the link between epigenetic variation and phenotypic variation remains poorly understood.

Infertility is rarely life threatening, however, it poses a serious global health issue posing far-reaching socio-economic impacts affecting 12–15% of couples worldwide where male factor accounts for 70%. Functional spermatogenesis which is the result of several concerted coordinated events to produce sperms is at the core of male fertility, Alternative splicing and microRNA (miRNA) mediated RNA silencing (RNAi) constitute two conserved post-transcriptional gene (re)programming machinery across species. The former by diversifying transcriptome signature and the latter by repressing target mRNA activity orchestrate a spectrum of testicular events, and their dysfunctions has several implications in male infertility. This review recapitulates the knowledge of these mechanistic events in regulation of spermatogenesis and testicular homoeostasis. In addition, miRNA payload in sperm, vulnerable to paternal inputs, including unhealthy diet, infection and trauma, creates epigenetic memory to initiate intergenerational phenotype. Naive zygote injection of sperm miRNAs from stressed father recapitulates phenotypes of offspring of stressed father. The epigenetic inheritance of paternal pathologies through miRNA could be a tantalizing avenue to better appreciate ‘Paternal Origins of Health and Disease’ and the power of tiny sperm.

The success of genetically depauperate populations in the face of environmental change is contrary to the expectation that high genetic diversity is required for rapid adaptation. Alternative pathways such as environmentally induced genetic modifications and non-genetic heritable phenotypes have been proposed mechanisms for heritable adaptation within an ecologically relevant time frame. However, experimental evidence is currently lacking to establish if, and to what extent, these sources of phenotypic variation can produce a response. To test if adaptation can rapidly occur in the absence of initial standing genetic variation and recombination in small populations, we (a) exposed replicate monoclonal populations of the microzooplankton Brachionus calyciflorus to a culturing regime that selected for phenotypic variants with elevated population growth with either high or low phosphorus food for a period of 55 days and (b) examined population level response in two fully factorial common garden experiments at day 15 and 35 of the exposure experiment. Within six generations, we observed heritable local adaptation to nutrient limitation. More specifically, populations with a history of exposure to low P food exhibited higher population growth rates under low P food conditions than populations with a high P exposure history. However, the capacity for such a response was found to vary among clones. Our study finds that although standing genetic variation is considered essential for rapid heritable adaptation, the rapid emergence of de novo genetic variation or alternative sources of phenotypic variation could aid in the establishment and persistence of low-diversity populations.

Cellular fate and gene expression patterns are modulated by different epigenetic factors including non-coding RNAs (ncRNAs) and chromatin organization. Both factors are dynamic throughout male germ cell differentiation on the seminiferous tubule, despite the transcriptional inactivation in the last stages of spermatogenesis. Sperm maturation during the caput-to-cauda transit on the epididymis involves changes in chromatin organization and the soma-to-germ line transference of ncRNAs that are essential to obtain a functional sperm for fertilization and embryo development. Here, the male environment (diseases, drugs, mental stress) is crucial to modulate these epigenetic factors throughout sperm maturation, affecting the corresponding offspring. Paternal transgenerational inheritance has been directly related to sperm epigenetic changes, most of them associated with variations in the ncRNA content and chromatin marks. Our aim is to give an overview about how epigenetics, focused on ncRNAs and chromatin, is pivotal to understand spermatogenesis and sperm maturation, and how the male environment impacts the sperm epigenome modulating the offspring gene expression pattern.

The reduction of excessive weight remains a major public health challenge, with control currently limited to a calorie reduction strategy. Currently, attempts are being made at revisiting the fibre hypothesis based on the African studies of Denis Burkitt, that the lack of dietary fibre in the modern diet was responsible for the occurrence of obesity and many of the other non-communicable diseases of what he called “Western civilization”. However, the dilemma is that Burkitt himself stressed that other peoples of his day, such as the Maasai, remained healthy without consuming such high fibre diets. Equally, the present obesity epidemic is accompanied by diseases of a malfunctioning immune system and of poor mental health that do not seem to be adequately explained simply by a deficiency of dietary fibre. Though unknown in Burkitt’s day, an increasing degradation of a mutualistic intestinal microbiome would offer a better fit to the observed epidemiology, especially if the microbiome is not effectively passed on from mother to child at birth. Taking the broader view, in this article we posit a view of the microbiome as a cofactor of mammalian evolution, in which a maternal microbial inheritance complements the parental genetic inheritance of the animal, both engaging epigenetic processes. As this would require the microbiome to be fully integrated with the animal as it develops into an adult, so we have a meaningful evolutionary role for the microbiome–gut–brain axis. By a failure to correctly establish a microbiome–gut interface, the inhibition of maternal microbial inheritance sets the scene for the future development of non-communicable disease: compromised immune system function on the one hand and dysfunctional gut–brain communication on the other. The basic principle is that the fully functioning, diverse, microbiome achieves interkingdom communication by the generation of messenger chemicals, semiochemicals. It is envisaged that the in situ detection of these as yet ill-defined chemical entities by means of an ingestible sensor would indicate the severity of disease and provide a guide as to its amelioration.

This project contains the materials for a project testing the generality and robustness of adaptive "transgenerational" effects across species, environments... It re-analyzes a published dataset to show that adaptive "transgenerational" effects - more specifically, anticipatory parental effects, despite existing in some species, are not as widespread as generally believe.

Background Non-crossover (NCO) refers to a mechanism of homologous recombination in which short tracks of DNA are copied between homologue chromatids. The allelic changes are typically restricted to one or few SNPs, which potentially allow for the gradual adaptation and maturation of haplotypes. It is assumed to be a stochastic process but the analysis of archaic and modern human haplotypes revealed a striking variability in local NCO recombination rates. Methods NCO recombination rates of 1.9 million archaic SNPs shared with Denisovan hominids were defined by a linkage study and correlated with functional and genomic annotations as well as ChIP-Seq data from modern humans. Results We detected a strong correlation between NCO recombination rates and the function of the respective region: low NCO rates were evident in introns and quiescent intergenic regions but high rates in splice sites, exons, 5′- and 3′-UTRs, as well as CpG islands. Correlations with ChIP-Seq data from ENCODE and other public sources further identified epigenetic modifications that associated directly with these recombination events. A particularly strong association was observed for 5-hydroxymethylcytosine marks (5hmC), which were enriched in virtually all of the functional regions associated with elevated NCO rates, including CpG islands and ‘poised’ bivalent regions. Conclusion Our results suggest that 5hmC marks may guide the NCO machinery specifically towards functionally relevant regions and, as an intermediate of oxidative demethylation, may open a pathway for environmental influence by specifically targeting recently opened gene loci.

Epigenetic inheritance can drive adaptive evolution independently of DNA sequence variation. However, to what extent epigenetic variation represents an autonomous evolutionary force remains largely elusive. Through gene ontology and comparative analyses of genomic and epigenomic variation of wild strawberry plants raised in distinct drought settings, we characterised genome-wide covariation between single nucleotide polymorphisms (SNPs) and differentially methylated cytosines (DMCs). Covariation between SNPs and DMCs was independent of genomic proximity, but instead associated with fitness-related processes such as stress responses, genome regulation and reproduction. We expected this functional SNP-DMC covariation to be driven by adaptive evolution canalising SNP and DMC variation, but instead observed significantly lower covariation with DMCs for adaptive rather than for neutral SNPs. Drought-induced DMCs frequently co-varied with tens of SNPs, suggesting high genomic redundancy as a broad potential basis for polygenic adaptation of gene expression. Our findings suggest that stress-responsive DMCs initially co-vary with many SNPs under increased environmental stress, and that natural selection acting upon several of these SNPs subsequently reduces standing covariation with stress-responsive DMCs. Our study supports DNA methylation profiles that represent complex quantitative traits rather than autonomous evolutionary forces. We provide a conceptual framework for polygenic regulation and adaptation shaping genome-wide methylation patterns in plants.

Epigenetic mechanisms are moving to the forefront of environmental sciences, as environmentally induced epigenetic changes shape biological responses to chemical contamination. This work focused on Daphnia as a representative of potentially threatened freshwater biota, aiming to gain an insight into the involvement of epigenetic mechanisms in their response and eventual adaptation to metal contamination. Copper-induced DNA methylation changes, their potential transgenerational inheritance, and life-history traits were assessed. Or-ganisms with different histories of past exposure to copper were exposed to toxic levels of the element for one generation (F0) and then monitored for three subsequent unexposed generations (F1, F2, and F3). Overall, methylation changes targeted important genes for counteracting the effects of metals and oxidative stress, including dynein light chain, ribosomal kinase and nuclear fragile X mental retardation-interacting protein. Also, contrasting overall and gene-specific methylation responses were observed in organisms differing in their history of exposure to copper, with different transgenerational methylation responses being also identified among the two groups, without apparent life-history costs. Taken together, these results demonstrate the capacity of copper to promote epigenetic transgenerational inheritance in a manner related explicitly to history of exposure, thereby supporting the development and incorporation of epigenetic biomarkers in risk assessment frameworks.

The essay focuses on the methodological and theoretical premises of an emerging research area with both ethological and (bio)ethical implications: the ethology of the freed animal (EFA). Unlike existing ethological fields, EFA does not focus on the observation of nonhuman (NH) animals in a natural condition of freedom, nor on situations of captivity. Rather, EFA consists of a comparative study of NH animals that are removed from a condition of captivity, from the status of “living tool” of human beings and from any form of exploitation – instead relocated in an environment fairly appropriate to their speciesspecific and individual characteristics. Ideal places for this study are animal sanctuaries and parks/reserves where a previously captive NH animal can be reintroduced in their natural habitat or, when this proves impossible, in a contest appropriate to their characteristics and needs. Even though EFA exists already, as a de facto practice of the personnel running sanctuaries and parks, the field still lacks a recognizable scholarly paradigm, and is not yet acknowledged at institutional/academic level, nor were its moral implications thoroughly discussed. Consequently, one important aim for such a field is the establishment of an active interaction between the two parties involved (researchers and sanctuaries/parks operators).

Perinatal exposure to smoking has been associated with childhood asthma, one of the most common pediatric conditions affecting millions of children globally. Of great interest, this disease phenotype appears heritable as it can persist across multiple generations even in the absence of persistent exposure to smoking in subsequent generations. Although the molecular mechanisms underlying childhood asthma induced by perinatal exposure to smoking or nicotine remain elusive, an epigenetic mechanism has been proposed, which is supported by the data from our earlier analyses on germline DNA methylation (5mC) and histone marks (H3 and H4 acetylation). To further investigate the potential epigenetic inheritance of childhood asthma induced by perinatal nicotine exposure, we profiled both large and small RNAs in the sperm of F1 male rats. Our data revealed that perinatal exposure to nicotine leads to alterations in the profiles of sperm-borne RNAs, including mRNAs and small RNAs, and that rosiglitazone, a PPARγ agonist, can attenuate the effect of nicotine and reverse the sperm-borne RNA profiles of F1 male rats to close to placebo control levels.

This review addresses the concept of ontogenetic origin of health and disease (DOHaD) and the new concept of paternal origin of health and disease (POHaD). These concepts are based on scientific evidence that environmental factors impacting mother or father can play a role in reprogramming the health of their off springs throughout their life span. Moreover, the changes that have arisen can be transmitted through generations via diverse epigenetic mechanisms. Terms, such as epigenetics (a kind of “driver” for these concepts), epigenetic inheritance (including Intergenerational Inheritance – from generation to the next generation and Transgenerational Inheritance – through generations), epigenetic changes caused by the environment (Environmental Epigenetics) are discussed. Vulnerable periods towards epigenetic changes (Windows of Susceptibility) that occur in male germ cells responsible for epigenetic inheritance are considered. Epigenetic epidemiological studies in the field of reproductology are described; their advantages and disadvantages are discussed. These studies can serve as the basis for obtaining new knowledge about the causes of epigenetic variations in germ cells that occur in health and upon exposure to environmental factors as well as the inherited phenotypic outcomes.

Stres oluşturan sosyal olaylar, canlı üzerinde epigenetik değişimlere sebep olabilmektedir. Bir bireyin sosyal açıdan yaşadığı olayların genom üzerindeki epigenetik işaretlere olan etkisinin incelenmesi, sosyal epigenetik alanını oluşturmuştur. Sosyal epigenetik; yoksulluk, savaş travması, çocukluk dönemi istismarı gibi psikososyal stres faktörlerinin epigenetik mekanizmalar üzerine etkisini incelemektedir. Epigenetik mekanizmalar DNA dizilimini değiştirmeden genom yapısındaki kimyasal işaretleri değiştirmektedir. Bu mekanizmalardan özellikle DNA metilasyonu, psikososyal ortamlarda oluşabilecek stres faktörlerine yanıt vererek farklı fenotipik etkiler meydana getirebilir. Travma sonrası stres bozukluğu (TSSB), travmatik olaylar sonucu değişen epigenetik ifadelerin fenotipteki etkilerinin en büyük kanıtlarından biridir. Epigenetik kalıtım alanı, çevresel etkilerin tetiklediği epigenetik değişimlerin bazı durumlarda nesiller boyu aktarılabildiği göstermiştir. Bu alan birçok psikolojik rahatsızlığın temelinin daha iyi anlaşılabilmesine olanak sağlamaktadır. Bu derlemede sosyal epigenetik, TSSB ve epigenetik kalıtım konularına genel bir bakış sunulmuştur., Social events that cause stress can cause epigenetic changes on living things. The study of the effects of social events experienced by an individual on epigenetic marks on the genome has created the field of social epigenetics. Social epigenetics examines the effects of psychosocial stress factors such as poverty, war trauma and childhood abuse on epigenetic mechanisms. Epigenetic mechanisms alter chemical markers in the genome structure without changing the DNA sequence. Among these mechanisms, DNA methylation in particular may have different phenotypic effects in response to stressors that may occur in the psychosocial environment. Post-traumatic stress disorder is one of the most significant proofs of the effects of epigenetic expressions altered due to traumatic events on the phenotype. The field of epigenetic inheritance has shown that epigenetic changes triggered by environmental influences can, in some cases, be transmitted through generations. This field provides a better understanding of the basis of many psychological disorders. This review provides an overview of social epigenetics, PTSD, and epigenetic inheritance.

Epigenetic inheritance has emerged as a new research discipline that aims to study the mechanisms underlying the transmission of acquired traits across generations. Such transmission is well established in plants and invertebrates but remains not well characterized and understood in mammals. Important questions are how life experiences and environmental factors induce phenotypic changes that are passed to the offspring of exposed individuals, sometimes across several successive generations, what is the contribution of germ cells and what are the consequences for health and disease. These questions were recently discussed at the symposium Epigenetic Inheritance: Impact for Biology and Society organized every 2 years in Zürich, Switzerland. This review provides a summary of the research presented during the symposium and discusses current important questions, perspectives and challenges for the feld in the future., Environmental Epigenetics, 8 (1), ISSN:2058-5888

Three decades ago, interactions between evolutionary biology and physiology gave rise to evolutionary physiology. This caused comparative physiologists to improve their research methods by incorporating evolutionary thinking. Simultaneously, evolutionary biologists began focusing more on physiological mechanisms that may help to explain constraints on and trade-offs during microevolutionary processes, as well as macroevolutionary patterns in physiological diversity. Here we argue that evolutionary physiology has yet to reach its full potential, and propose new avenues that may lead to unexpected advances. Viewing physiological adaptations in wild animals as potential solutions to human diseases offers enormous possibilities for biomedicine. New evi dence of epigenetic modifications as mechanisms of phenotypic plasticity that regulate physiological traits may also arise in coming years, which may also represent an overlooked enhancer of adaptation via natural selection to explain physiological evolution. Synergistic interactions at these intersections and other areas will lead to a novel understanding of organismal biology., Figures were created with BioRender.com. T.G. was supported by U.S. National Science Foundation grant IOS-2038528.

In light of the current opioid epidemic, the past 20 years have made it clear that parental life experiences can significantly impact the behavior and neurobiology of their offspring. Preclinical studies indicate that addiction reflects the interaction of an individual’s environment, genetics, and epigenetic modifications they inherit from their parents. Epigenetic mechanisms - including DNA methylation, histone modification, and small non-coding RNAs – refer to the complex interaction between genes and the environment, which produce heritable changes in germ cells that are transmitted to offspring to ultimately influence the brain development and subsequent vulnerability to develop a substance use disorder. The overarching goal of this dissertation was to characterize the behavioral and neurobiological effects of paternal morphine exposure on addiction-related endpoints in offspring. A highly translational rodent model of paternal morphine self-administration was used to produce first-generation (F1) male and female adolescent and adult offspring. As a reference, offspring derived from morphine-exposed fathers were called morphine-sired offspring, and offspring from saline-exposed fathers were called saline-sired offspring. In chapter 2, we revealed that male morphine-sired progeny are more sensitive over time to the pain-relieving effects of morphine. In the periaqueductal grey, an important pain-related brain region, we identified gene expression changes in regulators of G-protein signaling proteins that could partly account for this phenotype. In chapter 3, we demonstrated that adult morphine-sired male offspring self-administered more morphine; were more motived to earn morphine infusions compared to controls; and had more baseline mu-opioid receptor binding in the ventral tegmental area. Next, in chapter 4, we found that a drug-abstinence period of 90 consecutive days following 60 days of morphine exposure in sires was sufficient to prevent morphine-sired males from self-administering more morphine than controls. In chapter 5, we showed that this addiction-like phenotype did not extend to adolescent male or female offspring. Lastly, in chapter 6, using the incubation of craving paradigm, we found that paternal morphine exposure significantly reduced cue-induced active lever pressing for heroin in morphine-sired males. Taken together, these results add to the growing body of literature that show paternal preconception experiences can impact behavioral and neurobiological endpoints in offspring, perhaps via a(n) epigenetically inherited mechanism(s) in the germline.

Background 5-Methylcytosine (5mC) is an important epigenetic mark in eukaryotes. Little information about its role exists for invertebrates. To investigate the contribution of 5mC to phenotypic variation in invertebrates, alteration of methylation patterns needs to be produced. Here, we apply new non-nucleoside DNA methyltransferase inhibitors (DNMTi) to introduce aleatory changes into the methylome of mollusk species. Results Flavanone inhibitor Flv1 was efficient in reducing 5mC in the freshwater snails Biomphalaria glabrata and Physa acuta, and to a lesser degree, probably due to lower stability in sea water, in the oyster Crassostrea gigas. Flv1 has no toxic effects and significantly decreased the 5mC level in the treated B. glabrata and in its offspring. Drug treatment triggers significant variation in the shell height in both generations. A reduced representation bisulfite-sequencing method called epiGBS corroborates hypomethylation effect of Flv1 in both B. glabrata generations and identifies seven Differential Methylated Regions (DMR) out of 32 found both in Flv1-exposed snails and its progeny, from which 5 were hypomethylated, demonstrating a multigenerational effect. By targeted bisulfite sequencing, we confirmed hypomethylation in a locus and show that it is associated with reduced gene expression. Conclusions Flv1 is a new and efficient DNMTi that can be used to induce transient and heritable modifications of the epigenetic landscape and phenotypic traits in mollusks, a phylum of the invertebrates in which epigenetics is understudied.

An epigenetic basis for transgenerational plasticity in animals is widely theorized, but convincing empirical support is limited by taxa-specific differences in the presence and role of epigenetic mechanisms. In teleost fishes, DNA methylation generally does not undergo extensive reprogramming and has been linked with environmentally induced intergenerational effects, but solely in the context of early life environmental differences. Using whole-genome bisulfite sequencing, we demonstrate that differential methylation of sperm occurs in response to captivity during the maturation of Atlantic Salmon (Salmo salar), a species of major economic and conservation significance. We show that adult captive exposure further induces differential methylation in an F1 generation that is associated with fitness-related phenotypic differences. Some genes targeted with differential methylation were consistent with genes differential methylated in other salmonid fishes experiencing early-life hatchery rearing, as well as genes under selection in domesticated species. Our results support a mechanism of transgenerational plasticity mediated by intergenerational inheritance of DNA methylation acquired late in life for salmon. To our knowledge, this is the first-time environmental variation experienced later in life has been directly demonstrated to influence gamete DNA methylation in fish.

Candida auris is an emerging fungal pathogen that is thermotolerant and often resistant to standard antifungal treatments. To trace its evolutionary history, the Sanyal lab conducted a comparative genomic study focusing on the positions of centromeres in C. auris and eight other species from the Clavispora/Candida clade of yeasts (A. Narayanan et al., mBio 12:e00905-12, 2021). These researchers discovered that these species possess small regional centromeres that are highly stable, having remained in the same syntenic positions for over 100 million years. This stability is remarkable, given the lack of a conserved sequence underlying the centromeres and the relative ease with which other yeasts form neocentromeres. Thus, this work provides an opportunity to investigate the molecular mechanism of centromere inheritance in a genetically tractable and medically important yeast.

Testis-specific histone variants are crucial to promote open chromatin structure to enable nucleosome disassembly in the final stages of spermiogenesis. However, even after histone replacement, mature sperm retain a proportion of these variants, the function of which is unknown. The present study aimed to understand the functional relevance of the retained H2B and H2A variants, TH2B and TH2A. While no literature is available on the phenotype of TH2A knockouts, TH2B/TH2A double knockout male mice are reported to be infertile. In this study, ChIP-seq analysis was done for TH2B and TH2A to understand the epigenomics of the retained TH2B and TH2A, using murine caudal sperm. Distribution across genomic partitions revealed ∼35% of the TH2B peaks within ±5 kb of TSS whereas TH2A peaks distribution was sparse at TSS. Gene Ontology revealed embryo development as the most significant term associated with TH2B. Also, based on genomic regions, TH2B was observed to be associated with spindle assembly and various meiosis-specific genes, which is an important finding as TH2A/TH2B DKO mice have been reported to have defective cohesin release. A comparison of mouse and human TH2B-linked chromatin revealed 26% overlap between murine and human TH2B-associated genes. This overlap included genes crucial for embryogenesis. Most importantly, heterogeneity in the epigenetic landscape of TH2A and TH2B was seen, which is intriguing as TH2B and TH2A are well reported to be present in the same nucleosomes to promote open chromatin. Additionally, unlike TH2B, TH2A was enriched on the mitochondrial chromosome. TH2A was found to be associated with Nuclear insertion of Mitochondrial DNA sequences (NUMTs) in sperm. A comprehensive analysis of these observations indicates novel functions for the sperm-retained TH2B and TH2A.

CRISPR/dCas9 is an important DNA modification tool in which a disarmed Cas9 protein with no nuclease activity is fused with a specific DNA modifying enzyme. A previous study reported that overexpression of the TET1 catalytic domain (TET1cd) reduces genome-wide methylation in Arabidopsis. A spontaneous naturally occurring methylation region (NMR19-4) was identified in the promoter region of the PPH (Pheophytin Pheophorbide Hydrolase) gene, which encodes an enzyme that can degrade chlorophyll and accelerate leaf senescence. The methylation status of NMR19-4 is associated with PPH expression and leaf senescence in Arabidopsis natural accessions. In this study, we show that the CRISPR/dCas9-TET1cd system can be used to target the methylation of hypermethylated NMR19-4 region to reduce the level of methylation, thereby increasing the expression of PPH and accelerating leaf senescence. Furthermore, hybridization between transgenic demethylated plants and hypermethylated ecotypes showed that the demethylation status of edited NMR19-4, along with the enhanced PPH expression and accelerated leaf senescence, showed Mendelian inheritance in F1 and F2 progeny, indicating that spontaneous epialleles are stably transmitted trans-generationally after demethylation editing. Our results provide a rational approach for future editing of spontaneously mutated epialleles and provide insights into the epigenetic mechanisms that control plant leaf senescence.

AimsResearch evidence indicates that epigenetic modifications of gametes in obese or diabetic parents may contribute to metabolic disorders in offspring. In the present study, we sought to address the effect of diabetic uterine environment on the offspring metabolism.MethodsType 2 diabetes mouse model was induced by high-fat diet combined with streptozotocin (STZ) administration. We maintained other effect factors constant and changed uterine environment by zygote transfers, and then determined and compared the offspring numbers, symptoms, body weight trajectories, and metabolism indices from different groups.ResultWe found that maternal type 2 diabetes mice had lower fertility and a higher dystocia rate, accompanying the increased risk of offspring malformations and death. Compared to only a pre-gestational exposure to hyperglycemia, exposure to hyperglycemia both pre- and during pregnancy resulted in offspring growth restriction and impaired metabolism in adulthood. But there was no significant difference between a pre-gestational exposure group and a no exposure group. The deleterious effects, no matter bodyweight or glucose tolerance, could be rescued by transferring the embryos from diabetic mothers into normal uterine environment.ConclusionOur data demonstrate that uterine environment of maternal diabetes makes critical impact on the offspring health.

Human phenotype, the set of characteristics manifested by a living organism, is determined by genetic information expression dependent on genome, epigenome and microbiome. There is a kind of bidirectionality between humans and their genome with significant influence by environment and human behaviour. In the timeline of evolution we see that genetic modifications take millions of years to take place and consolidate, as per Darwinian principles, but environment and our habits are able much more rapidly to influence our phenotypic response, through epigenetic and microbiotic pathways, as per Lamarckian hypothesis (Fig. 1). Our habits (physical, psychological, environment) are able to determine changes in gene expression and potentially influence our children’s one. The evidence of these new concepts should be a further stimulus to a more conscious lifestyle.

Perinatal smoke/nicotine exposure alters lung development and causes asthma in exposed offspring, transmitted transgenerationally. The mechanism underlying the transgenerational inheritance of perinatal smoke/nicotine-induced asthma remains unknown, but germline epigenetic modulations may play a role. Using a well-established rat model of perinatal nicotine-induced asthma, we determined the DNA methylation pattern of spermatozoa of F1 rats exposed perinatally to nicotine in F0 gestation. To identify differentially methylated regions (DMRs), reduced representation bisulfite sequencing was performed on spermatozoa of F1 litters. The top regulated gene body and promoter DMRs were tested for lung gene expression levels, and key proteins involved in lung development and repair were determined. The overall CpG methylation in F1 sperms across gene bodies, promoters, 5'-UTRs, exons, introns, and 3'-UTRs was not affected by nicotine exposure. However, the methylation levels were different between the different genomic regions. Eighty one CpG sites, 16 gene bodies, and 3 promoter regions were differentially methylated. Gene enrichment analysis of DMRs revealed pathways involved in oxidative stress, nicotine response, alveolar and brain development, and cellular signaling. Among the DMRs, Dio1 and Nmu were the most hypermethylated and hypomethylated genes, respectively. Gene expression analysis showed that the mRNA expression and DNA methylation were incongruous. Key proteins involved in lung development and repair were significantly different (FDR < 0.05) between the nicotine and placebo-treated groups. Our data show that DNA methylation is remodeled in offspring spermatozoa upon perinatal nicotine exposure. These epigenetic alterations may play a role in transgenerational inheritance of perinatal smoke/nicotine induced asthma.

Hormonal imprinting takes place perinatally at the first encounter between the developing hormone receptor and its target hormone. This process is needed for the normal function of the receptor- hormone pair and its effect is life-long. However, in this critical period, when the developmental window is open, related molecules (members of the same hormone family, synthetic hormones and hormone-like molecules, endocrine disruptors) also can be bound by the receptor, causing life-long faulty imprinting. In this case, the receptors’ binding capacity changes and alterations are caused at adult age in the sexual and behavioral sphere, in the brain and bones, inclination to diseases and manifestation of diseases, etc. Hereby, faulty hormonal imprinting is the basis of metabolic and immunological imprinting as well as the developmental origin of health and disease (DOHaD). Although the perinatal period is the most critical for faulty imprinting, there are other critical periods as weaning and adolescence, when the original imprinting can be modified or new imprintings develop. Hormonal imprinting is an epigenetic process, without changing the base sequence of DNA, it is inherited in the cell line of the imprinted cells and also transgenerationally (up to 1000 generations in unicellulars and up to the 3rd generation in mammals are justified). Considering the enormously growing number and amount of faulty imprinters (endocrine disruptors) and the hereditary character of faulty imprinting, this latter is threatening the whole human endocrine system.

Aquaculture production is expanding rapidly around the world. To tackle rising production and species diversity issues, innovations in the field of aquaculture feeds, breeding, disease management and other improvements must be addressed. In this framework, the study of epigenetic mechanisms behind different aquaculture rearing processes presents great opportunities. The transcriptional impact of epigenetic modifications, triggered by environmental stimuli, has been shown to influence the organism's phenotype. Therefore, understanding the environmental-induced epigenetic markers related to disease resistance or other economically important traits will allow the establishment of favourable breeding conditions with increased economical revenue. Several studies have shown epigenetic effects in various species, induced by different rearing conditions, with benefits for the organisms and evidences for heritability of the acquired adaptive phenotypic traits across generations, making these studies even more relevant in a production context. These studies have demonstrated the great potential of epigenetics to positively induce disease resistance, stress tolerance and attain better sex ratios in the aquatic organism. Also, in the field of nutritional epigenetics, the possibility of early nutritional programming to improve the performance of broodstock or even the long-term performance of their progeny has been suggested. In sum, an increased understanding of epigenetic mechanisms in economically important species, and the epigenetic markers leading to the most favourable phenotypic traits, will contribute to the expansion of economically viable commercial aquaculture industries. The major epigenetic mechanisms and respective analysis methods, as well as the state of the art and potential applications in aquaculture, are addressed in this review.

Environmental exposures have been linked to increased asthma risk, particularly during pregnancy and in early life. Here we use a mouse model of allergic lung disease to examine the effects of pre- and perinatal house dust mite (HDM) allergen exposure on offspring phenotypic and transcriptional outcomes in three generations. We show that maternal HDM exposure (F0) acts synergistically with adult HDM exposure, leading to enhanced airway hyperresponsiveness (AHR) and lung inflammation when compared to mice exposed solely in adulthood. Additionally, a subset of F1 males were not challenged in adulthood, and used to generate F2 progeny, which was then used to generate F3 progeny. Upon adult challenge to HDM, F2, and F3 males generated from the maternal HDM (F0) exposure lineage displayed increased airway reactivity and inflammation when compared to mice exposed solely in adulthood. These findings indicate that maternal allergen exposure is capable of enhancing either susceptibly to or severity of allergic airway disease. To examine the role of epigenetic inheritance of asthma susceptibility induced by maternal HDM exposure, we utilized a genome-wide MeDIP-seq and hMeDIP-seq analysis to identify genes differentially methylated (DMG) and hydroxymethylated (DHG), and their association with the enhanced AHR. In addition, we validated the relationship between DNA methylation and mRNA expression of the DMGs and DHGs in the male sub-generations (F1-F3). We found the expression of Kchn1, Nron, and Spag17 to be differentially hydroxymethylated and upregulated in the F1 exposed to HDM both in early life and in adulthood when compared to F1 mice exposed solely in adulthood. Kcnh1 remained upregulated in the F2 and F3 from the maternal HDM (F0) exposure lineage, when compared to F1 mice exposed solely in adulthood. In summary, we demonstrated that maternal HDM exposure in early life can alter the gene expression and phenotype of offspring upon adult HDM exposure, resulting in more severe disease. These effects persist at least two generations past the initial insult, transmitted along the paternal line.

Approximately 10% of the mouse genome consists of endogenous retroviruses (ERVs), a class of retrotransposon, which includes the murine-specific intracisternal A particle (IAP) elements. To prevent their mobilisation and suppress the function of the TE- encoded regulatory sequences, TEs are generally targeted by repressive histone modifications and DNA methylation. The Avy allele results from an IAP insertion into the endogenous Agouti gene locus which is variably silenced between isogenic individuals. Variable DNA methylation at the IAP inversely correlates with ectopic expression of Agouti, resulting in a spectrum of coat colours between littermates. This, and other similarly behaving loci, are termed metastable epialleles, or variably methylated IAPs (VM-IAPs), and are widely cited as the best examples of mammalian epigenetic inheritance. A recent screen in the C57BL/6J mouse strain identified over 100 candidate VM-IAPs providing novel insights into metastable epialleles. In this thesis, I revisit the phenotypic and epigenetic heritability associated with the classic metastable epiallele Avy and further characterise novel variably methylated loci in the mouse genome through transcriptional and cross-strain comparative analyses. First, breeding-intensive experiments of the Avy allele in two genetic backgrounds (C57BL/6J and C3H/HeJ) show that coat colour is weakly heritable upon maternal transmission, while DNA methylation is only weakly heritable upon paternal transmission. This implies that coat colour cannot be used as a phenotypic read-out of an epigenetic state as previously reported, since DNA methylation and coat colour appear to be uncoupled at this locus. Additionally, both coat colour and DNA methylation at Avy are subject to genetic background effects. Second, thorough experimental validations of candidate variably methylated regions result in the identification of a novel class of VM-IAP with tissue-specific variability and the potential to affect neighbouring gene expression. VM-IAPs with constitutive methylation levels across tissues (cVM-IAPs) are full-length IAP LTR1 elements or solo LTR2s and are enriched for certain sequences, although sequence alone is not predictive of variable methylation at IAP elements. The IAP elements which are variably methylated on a C57BL/6J genetic background are highly polymorphic between inbred mouse strains and are differentially epigenetically regulated between strains. Finally, I show that variable methylation exists in non-repetitive regions which can affect gene expression and is also sensitive to genetic background. Overall, this body of work indicates that: variable methylation outside of evolutionarily young ERVs is rare; variable methylation can, albeit rarely, affect neighbouring gene expression and, in all contexts studied so far, is subject to strain-specific regulation suggesting that genetic background-specific modifiers contribute to the establishment of metastable epialleles within and across generations. Furthermore, my data indicates that our previous understanding of Avy is open to alternative interpretations.

The rise of metabolic disorders in modern times is mainly attributed to the environment. However, heritable effects of environmental chemicals on mammalian offsprings' metabolic health are unclear. Inorganic arsenic (iAs) is the top chemical on the Agency for Toxic Substances and Disease Registry priority list of hazardous substances. Here, we assess cross‐generational effects of iAs in an exclusive male‐lineage transmission paradigm. The exposure of male mice to 250 ppb iAs causes glucose intolerance and hepatic insulin resistance in F1 females, but not males, without affecting body weight. Hepatic expression of glucose metabolic genes, glucose output, and insulin signaling are disrupted in F1 females. Inhibition of the glucose 6‐phosphatase complex masks the intergenerational effect of iAs, demonstrating a causative role of hepatic glucose production. F2 offspring from grandpaternal iAs exposure show temporary growth retardation at an early age, which diminishes in adults. However, reduced adiposity persists into middle age and is associated with altered gut microbiome and increased brown adipose thermogenesis. In contrast, F3 offspring of the male‐lineage iAs exposure show increased adiposity, especially on a high‐calorie diet. These findings have unveiled sex‐ and generation‐specific heritable effects of iAs on metabolic physiology, which has broad implications in understanding gene‐environment interactions., Inorganic arsenic (iAs) has sex‐ and generation‐specific heritable effects on metabolic physiology in mammals through the male germline lineage. Paternal exposure to iAs causes glucose intolerance and hepatic insulin resistance in F1 females, but not males. F2 offspring from grand paternal iAs exposure show reduced adiposity. F3 offspring of the male‐lineage iAs exposure show increased adiposity.

Evidence suggests that engineered nanomaterials (ENM) can induce epigenetic modifications. In this review, we provide an overview of the epigenetic modulation of gene expression induced by ENM used in a variety of applications: titanium dioxide (TiO2), silver (Ag), gold (Au), silica (SiO2) nanoparticles and carbon-based nanomaterials (CNM). Exposure to these ENM can trigger alterations in cell patterns of DNA methylation, post-transcriptional histone modifications and expression of non-coding RNA. Such effects are dependent on ENM dose and physicochemical properties including size, shape and surface chemistry, as well as on the cell/organism sensitivity. The genes affected are mostly involved in the regulation of the epigenetic machinery itself, as well as in apoptosis, cell cycle, DNA repair and inflammation related pathways, whose long-term alterations might lead to the onset or progression of certain pathologies. In addition, some DNA methylation patterns may be retained as a form of epigenetic memory. Prenatal exposure to ENM may impair the normal development of the offspring by transplacental effects and/or putative transmission of epimutations in imprinting genes. Thus, understanding the impact of ENM on the epigenome is of paramount importance and epigenetic evaluation must be considered when assessing the risk of ENM to human health. This work was supported by the NanoBioBarriers project (PTDC/MED‐TOX/31162/2017), co-financed by the Operational Program for Competitiveness and Internationalization (POCI) through European Regional Development Funds (FEDER/FNR) and through national funds by the Portuguese Foundation for Science and Technology (FCT). Thanks are also due to FCT/MCTES for the financial support to EPIUnit (info:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB/04750/2020/PT).

Intelligent robots have been widely studied and investigated to replace, fulfilling a complex mission in a hazardous environment. Lately, swarm robotics, a group of collaborative robots, has become popular because it offers benefits over a single intelligent system. Many strategies have been developed to achieve collective and decentralised control applying evolutionary algorithms. However, since the evolutionary algorithm relies principally on an individual fitness function to explore the solution space, achieving swarm robotics' collaborative behaviour in a dynamic environment becomes a problem. This is due to the lack of adaptation in most of the evolutionary methods. In order to thrive in such environment, external stimuli and rewards from the environment should be utilised as ``knowledge'' to achieve the intelligent behaviour currently lacking in evolutionary swarm robotics. The aims of this research are: (1) to develop novel reward-based evolutionary swarm learning using mechanisms of epigenetic inheritance; and (2) to identify an efficient learning method for the epigenetic layer achieving a decision-making strategy in a dynamic environment. This research's contributions are the development of reward-based co-learning algorithm and co-evolution using epigenetic-based knowledge backup. The reward-based co-learning algorithm enables the swarm to obtain knowledge of the dynamic environment and override the objective-based function to evaluate internal and external problems. An advantage of this is that the learning mechanism also enables the swarm to explore potentially better behaviour without the constraint of an ill-defined objective function. Simulated search-and-rescue missions using a swarm of UAVs shows that individual behaviour evolves differently although each member has the same physical characteristics and the same set of actions. As an addition to reward-based multi-agent learning mechanisms, epigenetics is introduced as a decision-making layer. The epigenetic layer has two functions: there are genetic regulators, as well as an epigenetic inheritance (the epigenetic mechanism). The first is the function of an epigenetic layer regulating how genetic information is expressed as agent’s behaviour (the ``phenotype''). Thus, utilising the regulatory function, the agent is able to switch genetic strategy or decision-making based on external stimulus from the aforementioned reward-based learning. The second function is that epigenetic inheritance enables sharing of genetic regulation and decision-making layer between agents. In summary, this research extends the current literature on evolutionary swarm robotics and decentralised multi-agent learning mechanisms. The combination of both advances the decentralised mechanism in obtaining information and improve collective behaviour.

Mechanistic research suggests that lifestyle and environmental factors impact respiratory health across generations by epigenetic changes transmitted through male germ cells. Evidence from studies on humans is very limited. We investigated multigeneration causal associations to estimate the causal effects of tobacco smoking on lung function within the paternal line. We analysed data from 383 adult offspring (age 18–47 years; 52.0% female) and their 274 fathers, who had participated in the European Community Respiratory Health Survey (ECRHS)/Respiratory Health in Northern Europe, Spain and Australia (RHINESSA) generation study and had provided valid measures of pre-bronchodilator lung function. Two counterfactual-based, multilevel mediation models were developed with: paternal grandmothers’ smoking in pregnancy and fathers’ smoking initiation in prepuberty as exposures; fathers’ forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC), or FEV1/FVC z-scores as potential mediators (proxies of unobserved biological mechanisms that are true mediators); and offspring's FEV1 and FVC, or FEV1/FVC z-scores as outcomes. All effects were summarised as differences (Δ) in expected z-scores related to fathers’ and grandmothers’ smoking history. Fathers’ smoking initiation in prepuberty had a negative direct effect on both offspring's FEV1 (Δz-score –0.36, 95% CI −0.63– −0.10) and FVC (−0.50, 95% CI −0.80– −0.20) compared with fathers’ never smoking. Paternal grandmothers’ smoking in pregnancy had a negative direct effect on fathers’ FEV1/FVC (−0.57, 95% CI −1.09– −0.05) and a negative indirect effect on offspring's FEV1/FVC (−0.12, 95% CI −0.21– −0.03) compared with grandmothers’ not smoking before fathers’ birth nor during fathers’ childhood. Fathers’ smoking in prepuberty and paternal grandmothers’ smoking in pregnancy may cause lower lung function in offspring. Our results support the concept that lifestyle-related exposures during these susceptibility periods influence the health of future generations., Fathers’ prepuberty and paternal grandmothers’ pregnancy are vulnerable periods to the adverse effects of smoking on offspring's lung function. Preventing smoking in these susceptibility time windows might improve the next generation's health. https://bit.ly/3vvgjsN

The most prevalent diseases worldwide are non-communicable such as obesity and type 2 diabetes. Noteworthy, the prevalence of obesity and type 2 diabetes is expected to steadily increase in the next decades, mostly fueled by bad feeding habits, stress, and sedentarism. The reproductive function of individuals is severely affected by abnormal metabolic environments, both at mechanical and biochemical levels. Along with mechanical dysfunctions, and decreased sperm quality (promoted both directly and indirectly by metabolic abnormalities), several studies have already reported the potentially harmful effects of metabolic disorders in the genetic and epigenetic cargo of spermatozoa, and the epigenetic inheritance of molecular signatures induced by metabolic profile (paternal diet, obesity, and diabetes). The inheritance of epigenetic factors towards the development of metabolic abnormalities means that more people in reproductive age can potentially suffer from these disorders and for longer periods. In its turn, these individuals can also transmit this (epi)genetic information to future generations, creating a vicious cycle. In this review, we collect the reported harmful effects related to acquired metabolic disorders and diet in sperm parameters and male reproductive potential. Besides, we will discuss the novel findings regarding paternal epigenetic inheritance, particularly the ones induced by paternal diet rich in fats, obesity, and type 2 diabetes. We analyze the data attained with in vitro and animal models as well as in long-term transgenerational population studies. Although the findings on this topic are very recent, epigenetic inheritance of metabolic disease has a huge societal impact, which may be crucial to tackle the ‘fat epidemic’ efficiently.

Although the invention of right heart catheterisation in the 1950s enabled accurate clinical diagnosis of pulmonary arterial hypertension (PAH), it was not until 2000 when the landmark discovery of the causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH. Since then several genes have been discovered, which now account for around 25% of cases with the clinical diagnosis of idiopathic PAH. Despite the ongoing efforts, in the majority of patients the cause of the disease remains elusive, a phenomenon often referred to as “missing heritability”. In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes, forward and reverse genetics, and finally reverse phenotyping. We then discuss potential sources of “missing heritability” and how functional genomics and multi-omics methods are employed to tackle this problem.

Although the invention of right heart catheterisation in the 1950s enabled accurate clinical diagnosis of pulmonary arterial hypertension (PAH), it was not until 2000 when the landmark discovery of the causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH. Since then several genes have been discovered, which now account for around 25% of cases with the clinical diagnosis of idiopathic PAH. Despite the ongoing efforts, in the majority of patients the cause of the disease remains elusive, a phenomenon often referred to as "missing heritability". In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes, forward and reverse genetics, and finally reverse phenotyping. We then discuss potential sources of "missing heritability" and how functional genomics and multi-omics methods are employed to tackle this problem.

Environmental factors such as nutrition, stress, and toxicants can influence epigenetic programming and phenotypes of a wide variety of species from plants to humans. The current study was designed to investigate the impacts of hatchery spawning and rearing on steelhead trout (Oncorhynchus mykiss) vs the wild fish on a molecular level. Additionally, epigenetic differences between feeding practices that allow slow growth (2 years) and fast growth (1 year) hatchery trout were investigated. The sperm and red blood cells (RBC) from adult male slow growth/maturation hatchery steelhead, fast growth/maturation hatchery steelhead, and wild (natural-origin) steelhead were collected for DNA preparation to investigate potential alterations in differential DNA methylation regions (DMRs) and genetic mutations, involving copy number variations (CNVs). The sperm and RBC DNA both had a large number of DMRs when comparing the hatchery vs wild steelhead trout populations. The DMRs were cell type specific with negligible overlap. Slow growth/maturation compared to fast growth/maturation steelhead also had a larger number of DMRs in the RBC samples. A number of the DMRs had associated genes that were correlated to various biological processes and pathologies. Observations demonstrate a major epigenetic programming difference between the hatchery and wild natural-origin fish populations, but negligible genetic differences. Therefore, hatchery conditions and growth/maturation rate can alter the epigenetic developmental programming of the steelhead trout. Interestingly, epigenetic alterations in the sperm allow for potential epigenetic transgenerational inheritance of phenotypic variation to future generations. The impacts of hatchery exposures are not only important to consider on the fish exposed, but also on future generations and evolutionary trajectory of fish in the river populations.

Background: The Drosophila melanogaster mutant white-mottled is a well-established model for position-effect variegation (PEV). Transposition of the euchromatic white gene into the vicinity of the pericentric heterochromatin caused variegated expression of white due to heterochromatin spreading. The establishment of the euchromatin-heterochromatin boundary and spreading of silencing is regulated by mutually exclusive histone modifications, i.e. the methylations of histone H3 at lysine 9 and lysine 4. Demethylation of H3K4, catalysed by lysine-specific demethylase LSD1, is required for subsequent methylation of H3K9 to establish heterochromatin. LSD1 is therefore essential for heterochromatin formation and spreading. We asked whether drug-mediated inhibition of LSD affects the expression of white and if this induced change can be transmitted to those generations that have never been exposed to the triggering signal, i.e. transgenerational epigenetic inheritance.Results: We used the lysine-specific demethylase 1 (LSD1)-inhibitor Tranylcypromine to investigate its effect on eye colour expression in consecutive generations by feeding the parental and F1 generations of the Drosophila melanogaster mutant white-mottled. Quantitative Western blotting revealed that Tranylcypromine inhibits H3K4-demethylation both in vitro in S2 cells as well as in embryos when used as feeding additive. Eye colour expression in male flies was determined by optical measurement of pigment extracts and qRT-PCR of white gene expression. Flies raised in the presence of Tranylcypromine and its solvent DMSO showed increased eye pigment expression. Beyond that, eye pigment expression was also affected in consecutive generations including F3, which is the first generation without contact with the inhibitor. Conclusions: Our results show that feeding of Tranylcypromine and DMSO caused desilencing of white in treated flies of generation F1. Consecutive generations, raised on standard food without further supplements, are also affected by the drug-induced alteration of histone modifications. Although eye pigment expression eventually returned to the basal state, the observed long-lasting effect points to a memory capacity of previous epigenomes. Furthermore, our results indicate that food compounds potentially affect chromatin modification and hence gene expression and that the alteration is putatively inherited not only parentally but transgenerationally.

Phenotypic variation determines the capacity of plants to adapt to changing environments and to colonize new habitats. Deciphering the mechanisms contributing to plant phenotypic variation and their effects on plant ecological interactions and evolutionary dynamics is thus central to all biological disciplines. In the past few decades, research on plant epigenetics is showing that (1) epigenetic variation is related to phenotypic variation and that some epigenetic marks drive major phenotypic changes in plants; (2) plant epigenomes are highly diverse, dynamic, and can respond rapidly to a variety of biotic and abiotic stimuli; (3) epigenetic variation can respond to selection and therefore play a role in adaptive evolution. Yet, current information in terms of species, geographic ranges, and ecological contexts analyzed so far is too limited to allow for generalizations about the relevance of epigenetic regulation in phenotypic innovation and plant adaptation across taxa. In this report, we contextualize the potential role of the epigenome in plant adaptation to the environment and describe the latest research in this field presented during the symposium “Plant epigenetics: phenotypic and functional diversity beyond the DNA sequence” held within the Botany 2020 conference framework in summer 2020.

In most eukaryotes, the genome is packaged with histones and other proteins to form chromatin. One of the major mechanisms for chromatin regulation is through post-translational modification of histone proteins. Recognition of these modifications by effector proteins, often dubbed histone “readers,” provides a link between the chromatin landscape and gene regulation. The diversity of histone reader proteins for each modification provides an added layer of regulatory complexity. In this review, we will focus on the roles of chromatin organization modifier (chromo) domain containing proteins in the model nematode, Caenorhabditis elegans. An amenability to genetic and cell biological approaches, well-studied development and a short life cycle make C. elegans a powerful system to investigate the diversity of chromo domain protein functions in metazoans. We will highlight recent insights into the roles of chromo domain proteins in the regulation of heterochromatin and the spatial conformation of the genome as well as their functions in cell fate, fertility, small RNA pathways and transgenerational epigenetic inheritance. The spectrum of different chromatin readers may represent a layer of regulation that integrates chromatin landscape, genome organization and gene expression.

A rapidly growing body of literature in several organisms suggests that environmentally-induced adaptive changes in phenotype can be transmitted across multiple generations. Although within-generation plasticity has been well documented, multigenerational plasticity represents a significant departure from conventional evolutionary thought. Studies ofC. eleganshave been particularly influential because this species exhibits extensive phenotypic plasticity, it is often essentially isogenic, and it has well-documented molecular and cellular mechanisms through which nongenetic inheritance occurs. However, while experimentalists are eager to claim that nongenetic modes of inheritance characterized in this and other model systems enhance fitness, many biologists remain skeptical given the extraordinary nature of this claim. We establish three criteria to evaluate how compelling the evidence for adaptive multigenerational plasticity is, and we use these criteria to critically examine putative cases of it inC. elegans.We conclude by suggesting potentially fruitful avenues for future research.

The notion that epigenetic information can be transmitted across generations is supported by mounting waves of data, but the underlying mechanisms remain elusive. Here, a model is proposed which combines different lines of experimental evidence. First, it has been shown that somatic tissues exposed to stressing stimuli release circulating RNA-containing extracellular vesicles; second, epididymal spermatozoa can take up, internalize and deliver the RNA-containing extracellular vesicles to oocytes at fertilization; third, early embryos can process RNA-based information. These elements constitute the building blocks upon which the model is built. The model proposes that a continuous stream of epigenetic information flows from parental somatic tissues to the developing embryos. The flow can cross the Weismann barrier, is mediated by circulating vesicles and epididymal spermatozoa, and has the potential to generate epigenetic traits that are then stably acquired in the offspring. In a broader perspective, it emerges that a natural ‘assembly line’ operates continuously, aiming at passing the parental epigenetic blueprint in growing embryos.

A rapidly growing body of literature in several organisms suggests that environmentally-induced adaptive changes in phenotype can be transmitted across multiple generations. Although within-generation plasticity has been well documented, multigenerational plasticity represents a significant departure from conventional evolutionary thought. Studies of C. elegans have been particularly influential because this species exhibits extensive phenotypic plasticity, it is often essentially isogenic, and it has well-documented molecular and cellular mechanisms through which nongenetic inheritance occurs. However, while experimentalists are eager to claim that nongenetic modes of inheritance characterized in this and other model systems enhance fitness, many biologists remain skeptical given the extraordinary nature of this claim. We establish three criteria to evaluate how compelling the evidence for adaptive multigenerational plasticity is, and we use these criteria to critically examine putative cases of it in C. elegans. We conclude by suggesting potentially fruitful avenues for future research.

Half of the mammalian genome is made up of transposable elements (TEs), the vast majority of which are modified by DNA methylation and repressive histone marks. Intracisternal A-particles (IAPs) are evolutionarily young murine-specific endogenous retroviruses (ERVs). Some are capable of retrotransposition and many harbour regulatory sequences with the potential to influence host gene expression. Previous work has shown that, at the Agouti Viable Yellow (Avy) locus, an IAP insertion provides an alternative promoter for the Agouti coat colour gene. Variable methylation of this IAP is correlated with coat colour expressivity. In addition, the Avy allele exhibits transgenerational epigenetic inheritance, susceptibility to environmental exposures, and strain-specific modulation. A recent screen conducted in the C57BL/6J mouse strain identified a subset of IAPs that show variable methylation levels across genetically identical individuals. This thesis characterises this novel repertoire of variably methylated IAPs (VM-IAPs) and in doing so assesses the extent to which endogenous retroviruses in the mammalian genome display Avy-like properties. Findings indicate that VM-IAPs become hypermethylated in the male germline by the DNA methyltransferase DNMT3C and are reconstructed as variable loci in the next generation. An exploration of inter-individual VM-IAP methylation levels in the C57BL/6J population demonstrates that their frequency distributions form skewed bell curves that are locus-specific. Only one out of six VM-IAPs analysed via linear mixed effects models shows memory of maternal methylation level, and the effect size is small. This challenges the generalisability of epigenetic inheritance at these regions. In studying environmental influences on VM-IAPs, results suggest that these epigenetically dynamic loci are selectively susceptible to altered environmental conditions: abnormal folate metabolism appears to shift VM-IAP methylation levels and influence VM-IAP-associated gene expression, while no significant effects are observed following exposure to the endocrine-disruptor Bisphenol-A (BPA) or to an obesogenic diet. A longitudinal ageing analysis indicates that VM-IAPs are stable across the murine lifespan, with only modest increases in methylation detected for a subset of loci. Reciprocal hybrid breeding experiments reveal that VM-IAP methylation levels are subject to maternal and genetic background effects that can be harnessed to map strain-specific VM IAP modifiers. Finally, a naturally occurring genetically-conferred epiallele that influences neighbouring gene expression is identified and characterised. This body of work highlights the value of using VM-IAPs as a model to study TE regulation and mammalian epigenetic stochasticity, and serves as a foundation to elucidate the consequences of partially methylated repeat elements on genome structure and function., Cambridge International Scholarship (Cambridge Trust) and Downing Scholarship.

Spermatogenesis requires radical restructuring of germline chromatin at multiple stages, involving co-ordinated waves of DNA methylation and demethylation, histone modification, replacement and removal occurring before, during and after meiosis. This Special Issue has drawn together papers addressing many aspects of chromatin organization and dynamics in the male germ line, in humans and in model organisms. Two major themes emerge from these studies: the first is the functional significance of nuclear organisation in the developing germline; the second is the interplay between sperm chromatin structure and susceptibility to DNA damage and mutation. The consequences of these aspects for fertility, both in humans and other animals, is a major health and social welfare issue and this is reflected in these nine exciting manuscripts.

1st EPIgenetics in MARine biology congress (EPIMAR) and French Groupement de Recherche Épigenétique en Ecologie et Evolution (GDR 3E) 1st WebConference Epigenetics in Ecology and Evolution, 6-9 October 2020, The European sea bass still presents important challenges to production under captivity, such as sexual growth dimorphism. In general, males grow slower than females and reach weights about 30% less at the harvest size. Farmed fish show male bias with percentages of up to 90%. The study of sex development contributes to the improvement of farming methodologies. The European sea bass has a polygenic sex determining system with temperature effects during the larval stage, which causes masculinization in a proportion of the stock. In a previous study, we created four families and exposed their larvae to low (LT) and high temperatures (HT). The DNA methylation profile of seven genes related to sexual development was examined in juvenile gonads (F1, one year). The genes most affected by both genetics and environment were cyp19a1a and dmrt1, with opposite responses to sex and temperature. Based on methylation levels of most informative CpGs and a machine-learning procedure, it was possible to develop a system for sex prediction. In the following study, we created eight families by crossing an external female with eight males among the F1: two LT, three HT and three HT neomales (NM), which were identified by genotype analysis. Based on phenotypic and genotypic data of the F2 offspring we selected individuals representative of each group according to their sex, temperature during development and sire type. Next, we are going to analyze the DNA methylation profiles of grandparents¿ gametes (F0, n=2), sires and dam gametes (F1, n=9) and offspring juvenile gonad (F2, n=119) by Reduced Representation Bisulfite sequencing. With this approach, we will obtain information on the epigenetic patterns at the genome-wide level, which will enable us to investigate grandparent, parent-to-offspring relationships, the conserved epigenetic effect of temperature regardless of the family, and the potential additive effect of temperature among the individuals exposed in multiple generations