Immunological detection of changes in genomic DNA methylation during early zebrafish development

DNA methylation of pck1 might contribute to the programming effects of early high-carbohydrate diets feeding to the glucose metabolism across two generations in zebrafish (Danio rerio)

The purpose of this study is to assess the effects of early high-carbohydrate stimulus on glucose metabolism in zebrafish (Danio rerio) over two generations and explore the mechanisms that explain those nutritional programming effects via epigenetic modifications. The larvae were delivered a high-carbohydrate diet (53.66%) that was used as an early nutritional stimulus from the first feeding to the end of the yolk sac (FF) and 5 days after yolk-sac exhaustion (YE). The larvae (F0) and their offspring (F1) were then both fed the control diet (22.69%) until adulthood (15 weeks), and they were challenged with a high-carbohydrate diet (35.36%) at the 16th week. The results indicated that early stimulus immediately raised the mRNA levels of genes involved in glycolysis and gluconeogenesis. At the end of F0 challenge, both treatment groups decreased the plasma glucose levels, increased the expression levels of glucokinase (gck), and inhibited the mRNA during gluconeogenesis. When challenged in F1, the glucose levels were lower in FF (F1), and the mRNA levels of phosphoenolpyruvate carboxykinase 1 (pck1) were decreased in FF (F1) and YE (F1). Besides, in both experimental groups (F0 and F1), the CpG island of pck1 maintained lower levels of hypermethylated expression from F0 adult, 24 h post-fertilization embryo, to F1 adult. In conclusion, these results indicated that an early high-carbohydrate stimulus could significantly reprogram glucose metabolism in adult zebrafish, that those modifications could be partially transmitted to the next generation, and that the DNA methylation of pck1 might work as a stable epigenetic marker to contribute to those processes.

DNA Methylation Profiles Suggest Intergenerational Transfer of Maternal Effects

The view of maternal effects (nongenetic maternal environmental influence on offspring phenotype) has changed from one of distracting complications in evolutionary genetics to an important evolutionary mechanism for improving offspring fitness. Recent studies have shown that maternal effects act as an adaptive mechanism to prepare offspring for stressful environments. Although research into the magnitude of maternal effects is abundant, the molecular mechanisms of maternal influences on offspring phenotypic variation are not fully understood. Despite recent work identifying DNA methylation as a potential mechanism of nongenetic inheritance, currently proposed links between DNA methylation and parental effects are indirect and primarily involve genomic imprinting. We combined a factorial breeding design and gene-targeted sequencing methods to assess inheritance of methylation during early life stages at 14 genes involved in growth, development, metabolism, stress response, and immune function of Chinook salmon (Oncorhynchus tshawytscha). We found little evidence for additive or nonadditive genetic effects acting on methylation levels during early development; however, we detected significant maternal effects. Consistent with conventional maternal effect data, maternal effects on methylation declined through development and were replaced with nonadditive effects when offspring began exogenous feeding. We mapped methylation at individual CpG sites across the selected candidate genes to test for variation in site-specific methylation profiles and found significant maternal effects at selected CpG sites that also declined with development stage. While intergenerational inheritance of methylated DNA is controversial, we show that CpG-specific methylation may function as an underlying molecular mechanism for maternal effects, with important implications for offspring fitness.

Developing an epigenetics model species - From blastula to mature adult, life cycle methylation profile of Enchytraeus crypticus (Oligochaete)

DNA methylation is an epigenetic mechanism of particular importance in developmental biology, but methylation also varies along organisms' life cycle. Recent studies have deliberated copper (Cu) exposure induced epigenetic changes in Enchytraeus crypticus, a standard species belonging to one of the most common and important genera of soil invertebrates in many ecosystems. There is however no information on how DNA methylation levels change within the life cycle of this species. We here investigate the global DNA methylation profile along the life cycle of E. crypticus and compare this to the expression of target genes involved in methylation. Results showed that after the lowest DNA methylation level at day 3 (early embryonic stage, blastula) there was an increase by day 7 (organogenesis) after which levels were maintained at days 11, 18 and 25. DNA methyltransferase associated protein 1 (DMPA1) and Methyl Binding Domain 2 (MBD2) gene expression was highest during embryo stages (3 to 7 days), then decreasing (11, 18 days) and finally unregulated in adults (25 days). Hence, we here show that DNA methylation in E. crypticus changes among the different life stages, from cocoons to adults. Such information is a key knowledge to use this endpoint and tool in an ecotoxicology context. This means that it is almost implicit that gene expression levels are age specific for a given stressor. It seems logic to recommend to always compare individuals with the same age between treatments, and to be careful when extrapolating results among life stages. Once, we understand more of these effects we may even be able to predict which life stage is more sensitive to specific stressors. An experimental design that aims to cover epigenetics of stressors in a multigenerational exposure, including transgenerational effects, should ensure the synchronous age of organisms for sampling analysis purposes.

The cellular responses of autophagy, apoptosis, and 5-methylcytosine level in zebrafish cells upon nutrient deprivation stress

Here we reported the stress responses of nutrient deprivation and extended observation of autophagy, apoptosis, and DNA methylation in zebrafish embryonic fibroblast (ZF4) cells. Our results showed that serum deprivation resulted in the changes of cell shape and adherent ability, the suppressed cell growth and viability, and the inhibited proliferation and cell cycle. Besides, the appearance of lysosome and autophagosome/autolysosome with significantly increased expression of mRNAs (ulk1a, becn1, atg12, sqstm1, maplc3, and lamp1) and proteins (Atg12, Becn1, Sqstm1, and Lamp1) indicate the autophagic activity was boosted at initial stage but relatively weakened at 48 h of serum starvation. When autophagy no longer mitigate for the stress, cell apoptosis detected by the mRNA expression of caspases, Bcl-2/Bax expression, and Annexin V/PI was gradually enhanced to execute the death plan upon prolonged starvation process. Furthermore, the methyl group metabolism was increased in accordance with autophagic activity and was suppressed by enhanced apoptotic activity. These data suggested that the recycle activity induced by autophagy could compensate the substrates and reactions of DNA transmethylation, which obviously increased 5-methylcytosine (5 mC) level in ZF4 cells. In summary, our results discovered the cellular responses under prolonged serum starvation stress and elaborated the switch from autophagy to apoptosis and corresponding correlation with 5 mC level changes in teleost fish in vitro.

Environmental epigenetics in zebrafish

It is widely accepted that the epigenome can act as the link between environmental cues, both external and internal, to the organism and phenotype by converting the environmental stimuli to phenotypic responses through changes in gene transcription outcomes. Environmental stress endured by individual organisms can also enforce epigenetic variations in offspring that had never experienced it directly, which is termed transgenerational inheritance. To date, research in the environmental epigenetics discipline has used a wide range of both model and non-model organisms to elucidate the various epigenetic mechanisms underlying the adaptive response to environmental stimuli. In this review, we discuss the advantages of the zebrafish model for studying how environmental toxicant exposures affect the regulation of epigenetic processes, especially DNA methylation, which is the best-studied epigenetic mechanism. We include several very recent studies describing the state-of-the-art knowledge on this topic in zebrafish, together with key concepts in the function of DNA methylation during vertebrate embryogenesis.

Testicular Dnmt3 expression and global DNA methylation are down-regulated by gonadotropin releasing hormones in the ricefield eel Monopterus albus

In vertebrates, DNA methyltransferase 3 (Dnmt3) homologues are responsible for de novo DNA methylation and play important roles in germ cell development. In the present study, four dnmt3 genes, dnmt3aa, dnmt3ab, dnmt3ba and dnmt3bb.1, were identified in ricefield eels. Real-time quantitative PCR analysis showed that all four dnmt3 mRNAs were detected broadly in tissues examined, with testicular expression at relatively high levels. In the testis, immunostaining for all four Dnmt3 forms was mainly localized to spermatocytes, which also contained highly methylated DNA. All three forms of Gonadotropin-releasing hormone (Gnrh) in the ricefield eel were shown to decrease the expression of dnmt3 genes in the in vitro incubated testicular fragments through cAMP and IP₃/Ca²⁺ pathways. Moreover, in vivo treatment of male fish with three forms of Gnrh decreased significantly the testicular Dnmt3 expression at both mRNA and protein levels, and the global DNA methylation levels. These results suggest that the expression of Dnmt3 and global DNA methylation in the testis of ricefield eels are potentially down-regulated by Gnrh, and reveal a novel regulatory mechanism of testicular Dnmt3 expression in vertebrates.

Zebrafish as an In Vivo Model to Assess Epigenetic Effects of Ionizing Radiation

Exposure to ionizing radiations (IRs) is ubiquitous in our environment and can be categorized into “targeted” effects and “non-targeted” effects. In addition to inducing deoxyribonucleic acid (DNA) damage, IR exposure leads to epigenetic alterations that do not alter DNA sequence. Using an appropriate model to study the biological effects of radiation is crucial to better understand IR responses as well as to develop new strategies to alleviate exposure to IR. Zebrafish, Danio rerio, is a scientific model organism that has yielded scientific advances in several fields and recent studies show the usefulness of this vertebrate model in radiation biology. This review briefly describes both “targeted” and “non-targeted” effects, describes the findings in radiation biology using zebrafish as a model and highlights the potential of zebrafish to assess the epigenetic effects of IR, including DNA methylation, histone modifications and miRNA expression. Other in vivo models are included to compare observations made with zebrafish, or to illustrate the feasibility of in vivo models when the use of zebrafish was unavailable. Finally, tools to study epigenetic modifications in zebrafish, including changes in genome-wide DNA methylation, histone modifications and miRNA expression, are also described in this review.

Developmental profiles and expression of the DNA methyltransferase genes in the fathead minnow (Pimephales promelas) following exposure to di-2-ethylhexyl phthalate

DNA methylation is an epigenetic regulator of gene expression, and this process has been shown to be disrupted by environmental contaminants. Di-2-(ethylhexyl) phthalate (DEHP) and related phthalate esters have been shown to affect development in early life stages of fish and can alter genomic methylation patterns in vertebrates. The objectives of this study were the following: (1) Describe the expression patterns of the DNA methyltransferase (dnmt) genes during early fathead minnow (FHM) development. These genes are critical for methylation and imprinting during development. (2) Determine the effects of DEHP on the development of FHM larvae [1 and 14 days post-hatch (dph)]. (3) Determine the effect of DEHP on dnmt expression and global methylation status in larval FHM. FHMs were first collected over a developmental time course [1, 3, 5, 6, and 14 days post-fertilization (dpf)] to investigate the expression patterns of five dnmt isoforms. The expression of dnmt1 and dnmt7 was relatively high in embryos at 1 dpf but was variable in expression, and these transcripts were later expressed at a lower level (>3 dpf); dnmt3 was significantly higher in embryos at 1 dpf compared to those at 3 dpf. Dnmt6 showed more of a constitutive pattern of expression during the first 2 weeks of development, and the mRNA levels of dnmt8 were higher in embryos at 5 and 6 dpf compared to those at 1 and 3 dpf, corresponding to the hatching period of the embryos. A waterborne exposure to three concentrations of DEHP (1, 10 and 100 µg/L) was conducted on 1-day FHM embryos for 24 h and on larval fish for 2 weeks, ending at 14 dpf. DEHP did not negatively affect survival, hatch rate, or the expression of dnmt isoforms in FHMs. There were no differences in global cytosine methylation following DEHP treatments in 14 dpf larvae, suggesting that environmentally relevant levels of DEHP may not affect global methylation at this stage of FHM development. However, additional targeted methylome studies are required to determine whether specific gene promoters are differently methylated following exposure to DEHP. This study offers new insight into the roles of the dnmt enzymes during FHM development.

Modulation of DNA methylation machineries in Japanese rice fish (Oryzias latipes) embryogenesis by ethanol and 5-azacytidine

As a sequel of our investigations on the impact of epigenome in inducing fetal alcohol spectrum disorder (FASD) phenotypes in Japanese rice fish, we have investigated on several DNA methylation machinery genes including DNA methyl transferase 3ba (dnmt3ba) and methyl binding proteins (MBPs), namely, mbd1b, mbd3a, mbd3b, and mecp2 at the transcription level. Studies were made during normal development, from 0day post fertilization (dpf) to hatching, and also exposing the fertilized eggs to ethanol or a DNMT inhibitor, 5-azacytidine (5-azaC). We observed that during development, all these genes followed distinct expression patterns, generally high mRNA copies in early phases (0-1dpf) and significantly low mRNA copies prior to or after hatching. Ethanol (100-500mM, 0-2dpf) was unable to alter any of these mRNAs in 2dpf; additional four day (2-6dpf) maintenance of these embryos in ethanol-free environment, on 6dpf, was also unable to establish any significant difference in these mRNA levels in comparison with the corresponding controls. However, continuous exposure of fertilized eggs in 300mM ethanol, 0-6dpf, showed significantly high mRNA copies only in MBPs (mbd1b, mbd3a, mbd3b, mecp2). 5-azaC (2mM) on 2dpf was able to enhance only mbd3b mRNA. Removal of 5-azaC and maintenance of these embryos in clean medium, 2-6dpf, showed significantly enhanced mbd3b and mecp2 mRNAs compared to corresponding controls on 6dpf. Our studies showed that in Japanese rice fish embryogenesis both ethanol and 5-azaC have the potential to specifically modulate the developmental rhythm of DNA methylation machineries.

Zebrafish as a model to study the role of DNA methylation in environmental toxicology

Environmental epigenetics is a rapidly growing field which studies the effects of environmental factors such as nutrition, stress, and exposure to compounds on epigenetic gene regulation. Recent studies have shown that exposure to toxicants in vertebrates is associated with changes in DNA methylation, a major epigenetic mechanism affecting gene transcription. Zebra fish, a well-known model in toxicology and developmental biology, are emerging as a model species in environmental epigenetics despite their evolutionary distance to rodents and humans. In this review, recent insights in DNA methylation during zebra fish development are discussed and compared to mammalian models in order to evaluate zebra fish as a model to study the role of DNA methylation in environmental toxicology. Differences exist in DNA methylation reprogramming during early development, whereas in later developmental stages, tissue distribution of both 5-methylcytosine and 5-hydroxymethylcytosine seems more conserved between species, as well as basic DNA (de)methylation mechanisms. All DNA methyl transferases identified so far in mammals are present in zebra fish, as well as a number of major demethylation pathways. However, zebra fish appear to lack some methylation pathways present in mammals, such as parental imprinting. Several studies report effects on DNA methylation in zebra fish following exposure to environmental contaminants, such as arsenic, benzo[a]pyrene, and tris(1,3-dichloro-2-propyl)phosphate. Though more research is needed to examine heritable effects of contaminant exposure on DNA methylation, recent data suggests the usefulness of the zebra fish as a model in environmental epigenetics.

Combined analysis of DNA methylation and cell cycle in cancer cells

DNA methylation is a chemical modification of DNA involved in the regulation of gene expression by controlling the access to the DNA sequence. It is the most stable epigenetic mark and is widely studied for its role in major biological processes. Aberrant DNA methylation is observed in various pathologies, such as cancer. Therefore, there is a great interest in analyzing subtle changes in DNA methylation induced by biological processes or upon drug treatments. Here, we developed an improved methodology based on flow cytometry to measure variations of DNA methylation level in melanoma and leukemia cells. The accuracy of DNA methylation quantification was validated with LC-ESI mass spectrometry analysis. The new protocol was used to detect small variations of cytosine methylation occurring in individual cells during their cell cycle and those induced by the demethylating agent 5-aza-2'-deoxycytidine (5AzadC). Kinetic experiments confirmed that inheritance of DNA methylation occurs efficiently in S phase and revealed a short delay between DNA replication and completion of cytosine methylation. In addition, this study suggests that the uncoupling of 5AzadC effects on DNA demethylation and cell proliferation might be related to the duration of the DNA replication phase.

Abnormal ovarian DNA methylation programming during gonad maturation in wild contaminated fish

There is increasing evidence that pollutants may cause diseases via epigenetic modifications. Epigenetic mechanisms such as DNA methylation participate in the regulation of gene transcription. Surprisingly, epigenetics research is still limited in ecotoxicology. In this study, we investigated whether chronic exposure to contaminants experienced by wild female fish (Anguilla anguilla) throughout their juvenile phase can affect the DNA methylation status of their oocytes during gonad maturation. Thus, fish were sampled in two locations presenting a low or a high contamination level. Then, fish were transferred to the laboratory and artificially matured. Before hormonal treatment, the DNA methylation levels of the genes encoding for the aromatase and the receptor of the follicle stimulating hormone were higher in contaminated fish than in fish from the clean site. For the hormone receptor, this hypermethylation was positively correlated with the contamination level of fish and was associated with a decrease in its transcription level. In addition, whereas gonad growth was associated with an increase in DNA methylation in fish from the clean site, no changes were observed in contaminated fish in response to hormonal treatment. Finally, a higher gonad growth was observed in fish from the reference site in comparison to contaminated fish.

DNA methylation in the 5' flanking region of cytochrome P450 17 in adult rare minnow Gobiocypris rarus - tissue difference and effects of 17α-ethinylestradiol and 17α-methyltestoterone exposures

Cytochrome P450 17 (CYP17) plays a vital role in hormone production in the body. In our previous study, mRNA expression of cyp17a1 was regulated by endocrine disrupting chemicals in rare minnow Gobiocypris rarus. However, the mechanism underlying the regulation is unclear. In the present study, we aim to explore whether the differential expression of cyp17a1 in distinct tissues and the modulation of its expression upon 17α-ethinylestradiol (EE2) and 17α-methyltestoterone (MT) are related to the DNA methylation status in G. rarus. The 732-bp fragment of 5' flanking region of cyp17a1 gene was isolated in G. rarus. The bisulfite sequencing PCR result showed that DNA methylation levels in 5' flanking of cyp17a1 in the gonads were significantly lower than those in the brains, which is negatively related to its mRNA expression in the 2 tissues in the previous study. The 7-day EE2 exposure of 25 ng/L caused a significant increase of methylation levels of cyp17a1 gene and a significant decrease of its transcript in testis. While 100 ng/L MT exposure for 7 days caused a significant decrease of methylation levels of cyp17a1 gene and a significant increase of its transcript in the ovary. The present findings indicate that the methylation status of cyp17a1 gene is negatively correlated with its mRNA expression in response to EE2 and MT in G. rarus. We hypothesize that the regulation of cyp17a1 expression by EE2 and MT might attribute to the change of its DNA methylation status in G. rarus.

Patterns of DNA methylation in animals: an ecotoxicological perspective

DNA methylation refers to the addition of a methyl group to nucleotides within DNA. As with other epigenetic endpoints, patterns of DNA methylation are susceptible to alterations due to exposure to environmental stressors, including contaminants. These alterations can persist in the absence of the initial stressor as cells divide, and can even be inherited between generations if they occur in the germ line. Although our knowledge concerning patterns of DNA methylation in animals is increasing, there remains a gap in the literature when it comes to species outside of those typically used for biomedical research. Here, I review the literature relating to DNA methylation in an array of taxa (mammals, fish, birds, amphibians, reptiles, and invertebrates) and discuss these data from an ecotoxicological perspective. The pattern and extent of DNA methylation is well conserved across species of vertebrates; methylation appears mainly on cytosine residues within a CpG context, and much of the genome is methylated, with the notable exception of cytosines within CpG islands in the promoters of genes. Highly methylated genes in vertebrates tend to be transcriptionally repressed. However, large differences occur between classes of vertebrates in terms of the timing and nature of reprogramming and genomic imprinting: epigenetic processes that establish patterns of DNA methylation in the early embryo and which are sensitive to environmental stress. In invertebrates, patterns of DNA methylation are extremely variable and differ significantly from the condition observed in vertebrates. Some invertebrate genomes exhibit no DNA methylation while others are methylated to a level that is comparable to vertebrates. Additionally, DNA methylation may have different functions in invertebrates, e.g., alternative splicing. This variability in basic patterns of DNA methylation among species during sensitive periods of development suggests that responses to epigenetically active environmental contaminants may be similarly variable. For example, the timing of exposure to a contaminant may be a critical factor when considered in the light of variable reprogramming schedules among species. With this in mind, I review data relating to the effects of contaminants on DNA methylation in animals, focusing on non-model organisms and on exposures in natural environments, when possible. An ecotoxicological perspective on patterns of DNA methylation in animals may improve our understanding of the range and diversity of epigenetic phenomena in the natural world.

Uracil-DNA glycosylase is involved in DNA demethylation and required for embryonic development in the zebrafish embryo

Uracil-DNA glycosylase (Ung) is a component of the base excision repair process and has the ability to remove uracil from U:G mispairs in DNA. However, its implications in development of vertebrate embryos are poorly understood. In this study, we found that zebrafish uracil-DNA glycosylase a (Unga) is maternally expressed at high levels and accumulated in nuclei during cleavage and blastulation periods. Knockdown of unga in zebrafish embryos causes an increase of the global DNA methylation level concomitantly with a reduction of overall transcriptional activity in the nucleus, ultimately resulting in embryonic lethality during segmentation period. Conversely, unga overexpression is sufficient to reduce the global DNA methylation level, to increase H3K4me3 and H3K27me3 marks, and to activate genome transcription. Furthermore, overexpression of unga(D132A) mRNA, encoding a mutant Unga without DNA glycosylase activity, does not affect global DNA methylation level, indicating that its involvement in DNA demethylation is dependent on its glycosylase activity. These results together suggest that Unga is implicated in postfertilization genomic DNA demethylation, zygotic gene transcription, and normal embryonic development in zebrafish.

Message control in developmental transitions; deciphering chromatin's role using zebrafish genomics

Now that the sequencing of genomes has become routine, understanding how a given genome is used in different ways to obtain cell type diversity in an organism is the next frontier. How specific transcription programs are established during vertebrate embryogenesis, however, remains poorly understood. Transcription is influenced by chromatin structure, which determines the accessibility of DNA-binding proteins to the genome. Although large-scale genomics approaches have uncovered specific features of chromatin structure that are diagnostic for different cell types and developmental stages, our functional understanding of chromatin in transcriptional regulation during development is very limited. In recent years, zebrafish embryogenesis has emerged as an excellent vertebrate model system to investigate the functional relationship between chromatin organization, gene regulation and development in a dynamic environment. Here, we review how studies in zebrafish have started to improve our understanding of the role of chromatin structure in genome activation and pluripotency and in the potential inheritance of transcriptional states from parent to progeny.

Global and gene specific DNA methylation changes during zebrafish development

DNA methylation is dynamic through the life of an organism. Previous studies have primarily focused on DNA methylation changes during very early embryogenesis. In this study, global and gene specific DNA methylation in zebrafish (Danio rerio) embryos, larvae and adult livers were compared. The percent methylation of cytosines was low in 2 to 4.3h post fertilization (hpf) zebrafish embryos and was consistently higher in zebrafish older than 6 hpf. Furthermore, quantitative real-time PCR (qPCR) results showed relatively high DNA methyltransferase 1 (dnmt1) and low glycine N-methyltransferase (gnmt) mRNA expression in early embryogenesis. By studying methylation patterns and gene expression of five developmentally important genes, namely vasa, Ras-association domain family member 1 (rassf1), telomerase reverse transcriptase (tert), c-jun and c-myca, we found that the timing of changes in DNA methylation patterns was gene specific, and changes in gene expression were not necessarily correlated with the DNA methylation patterns.

Transient reduction of 5-methylcytosine and 5-hydroxymethylcytosine is associated with active DNA demethylation during regeneration of zebrafish fin

Although dedifferentiation, transformation of differentiated cells into progenitor cells, is a critical step in the regeneration of amphibians and fish, the molecular mechanisms underlying this process, including epigenetic changes, remain unclear. Dot blot assays and immunohistochemical analyses revealed that, during regeneration of zebrafish fin, the levels of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are transiently reduced in blastema cells and cells adjacent to the amputation plane at 30 h post-amputation (hpa), and the level of 5mC, but not 5hmC, is almost restored by 72 hpa. We observed that the dedifferentiated cells showed reduced levels of 5mC and 5hmC independent of cell proliferation by 24 hpa. Furthermore, expressions of the proposed demethylation- and DNA repair-related genes were detected during fin regeneration. Taken together, our findings illustrate that the transient reduction of 5mC and 5hmC in dedifferentiated cells is associated with active demethylation during regeneration of zebrafish fin.

Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos

5-methylcytosine is a major epigenetic modification that is sometimes called "the fifth nucleotide." However, our knowledge of how offspring inherit the DNA methylome from parents is limited. We generated nine single-base resolution DNA methylomes, including zebrafish gametes and early embryos. The oocyte methylome is significantly hypomethylated compared to sperm. Strikingly, the paternal DNA methylation pattern is maintained throughout early embryogenesis. The maternal DNA methylation pattern is maintained until the 16-cell stage. Then, the oocyte methylome is gradually discarded through cell division and is progressively reprogrammed to a pattern similar to that of the sperm methylome. The passive demethylation rate and the de novo methylation rate are similar in the maternal DNA. By the midblastula stage, the embryo's methylome is virtually identical to the sperm methylome. Moreover, inheritance of the sperm methylome facilitates the epigenetic regulation of embryogenesis. Therefore, besides DNA sequences, sperm DNA methylome is also inherited in zebrafish early embryos.

The extended evolutionary synthesis and the role of soft inheritance in evolution

In recent years, a number of researchers have advocated extending the modern synthesis in evolutionary biology. One of the core arguments made in favour of an extension comes from work on soft inheritance systems, including transgenerational epigenetic effects, cultural transmission and niche construction. In this study, we outline this claim and then take issue with it. We argue that the focus on soft inheritance has led to a conflation of proximate and ultimate causation, which has in turn obscured key questions about biological organization and calibration across the life span to maximize average lifetime inclusive fitness. We illustrate this by presenting hypotheses that we believe incorporate the core phenomena of soft inheritance and will aid in understanding them.

Molecular evolution of zebrafish dnmt3 genes and thermal plasticity of their expression during embryonic development

DNA reprogramming by DNA (cytosine-5)-methyltransferases (dnmts) after fertilisation is a dynamic mechanism that is essential for early development. Amongst the three types of dnmt genes in vertebrates, dnmt3 is the one involved in de novo methylation and comprises three related genes, termed dnmt3a, dnmt3b and dnmt3L in mammals. Zebrafish (Danio rerio) has six dnmt3 paralogues, which have hitherto been termed dnmt3 to dnmt8. Bayesian inference of phylogeny and synteny analysis revealed that dnmt6 and dnmt8 are in fact duplicated dnmt3a genes, whereas the other paralogues are closely related to dnmt3b. Hence, we propose a revised nomenclature that more accurately reflects the relationship amongst zebrafish dnmt3 genes. Both dnmt3a genes were ubiquitously expressed in adult tissues, whilst the various dnmt3b paralogues were differentially expressed, with notably high expression levels in the gonads. The influence of embryonic temperature on dnmt3 expression was investigated, since it is known to have a significant impact in early development and a long-term effect on growth in some teleost species. Embryos were incubated at 23, 27 or 31°C and samples collected at six developmental stages from blastula until protruding mouth. Dnmt3 expression during early development was remarkably dynamic. In particular, mRNA levels of the two dnmt3a genes showed a marked increase throughout development and several significant differences in dnmt3a and dnmt3b transcript levels were found between temperatures at the same developmental point. Taken together, our data indicate that dnmt3 paralogues are diverging and that dnmt3a and dnmt3b may play different roles in thermal epigenetic regulation of gene expression during early development.

The key role of epigenetics in the persistence of asexual lineages

Asexual organisms, often perceived as evolutionary dead ends, can be long-lived and geographically widespread. We propose that epigenetic mechanisms could play a crucial role in the evolutionary persistence of these lineages. Genetically identical organisms could rely on phenotypic plasticity to face environmental variation. Epigenetic modifications could be the molecular mechanism enabling such phenotypic plasticity; they can be influenced by the environment and act at shorter timescales than mutation. Recent work on the asexual vertebrate Chrosomus eos-neogaeus (Pisces: Cyprinidae) provides broad insights into the contribution of epigenetics in genetically identical individuals. We discuss the extension of these results to other asexual organisms, in particular those resulting from interspecific hybridizations. We finally develop on the evolutionary relevance of epigenetic variation in the context of heritability.

DNA methylation in zebrafish

DNA methylation is crucial for normal development and cellular differentiation in many large-genome eukaryotes. The small tropical freshwater fish Danio rerio (zebrafish) has recently emerged as a powerful system for the study of DNA methylation, especially in the context of development. This review summarizes our current knowledge of DNA methylation in zebrafish and provides evidence for the general conservation of this system with mammals. In addition, emerging strategies are highlighted that use the fish model to address some of the key unanswered questions in DNA methylation research.

Epigenetics and its implications for ecotoxicology

Epigenetics is the study of mitotically or meiotically heritable changes in gene function that occur without a change in the DNA sequence. Interestingly, epigenetic changes can be triggered by environmental factors. Environmental exposure to e.g. metals, persistent organic pollutants or endocrine disrupting chemicals has been shown to modulate epigenetic marks, not only in mammalian cells or rodents, but also in environmentally relevant species such as fish or water fleas. The associated changes in gene expression often lead to modifications in the affected organism's phenotype. Epigenetic changes can in some cases be transferred to subsequent generations, even when these generations are no longer exposed to the external factor which induced the epigenetic change, as observed in a study with fungicide exposed rats. The possibility of this phenomenon in other species was demonstrated in water fleas exposed to the epigenetic drug 5-azacytidine. This way, populations can experience the effects of their ancestors' exposure to chemicals, which has implications for environmental risk assessment. More basic research is needed to assess the potential phenotypic and population-level effects of epigenetic modifications in different species and to evaluate the persistence of chemical exposure-induced epigenetic effects in multiple subsequent generations.

Expression of the dnmt3 genes in zebrafish development: similarity to Dnmt3a and Dnmt3b

The zebrafish differs from mammals in that they have six dnmt3 genes as opposed to the two that can produce a catalytically active protein in mammals. Zebrafish also do not show evidence of genomic imprinting and lack the Dnmt3l gene necessary to that process in mammals. As such, they offer a unique opportunity to compare the two genetic situations in order to define the roles of the multiple genes in developmental gene methylation. To this end, we have analyzed the developmental expression of the six dnmt3 genes in zebrafish and find that they fall into two distinct patterns. The expression patterns of the dnmt6 and dnmt8 genes, which more closely resemble the mammalian Dnmt3a gene in sequence, also show an expression pattern that is more similar to the expression of Dnmt3a rather than Dnmt3b. Conversely, the other four dnmt3 genes in zebrafish (dnmt3, dnmt4, dnmt5, and dnmt7) show an expression pattern that is more similar to Dnmt3b. The dnmt6 and dnmt8 genes are also expressed in the adult zebrafish and in the brain in particular. In situ expression analyses show that the dnmt6 and/or dnmt8 genes also show tissue-specific differences in expression with those two genes being more ubiquitously expressed in the developing zebrafish than the other dnmt3 genes. Although differences in dnmt3 function may exist between mammals and fish, our results showing similar expression patterns between the genes in fish and mammals suggest that the six dnmt3 genes in the zebrafish may be analogous to the two Dnmt3 genes in mammals.

Chromatin modification in zebrafish development

The generation of complex organisms requires that an initial population of cells with identical gene expression profiles can adopt different cell fates during development by progressively diverging transcriptional programs. These programs depend on the binding of transcritional regulators to specific genomic sites, which in turn is controlled by modifications of the chromatin. Chromatin modifications may occur directly upon DNA by methylation of specific nucleotides, or may involve post-translational modification of histones. Local regulation of histone post-translational modifications regionalizes the genome into euchromatic regions, which are more accessible to DNA-binding factors, and condensed heterochromatic regions, inhibiting the binding of such factors. In addition, these modifications may be required in a genome-wide fashion for processes such as DNA replication or chromosome condensation. From an embryologist's point of view chromatin modifications are intensively studied in the context of imprinting and have more recently received increasing attention in understanding the basis of pluripotency and cellular differentiation. Here, we describe recently uncovered roles of chromatin modifications in zebrafish development and regeneration, as well as available resources and commonly used techniques. We provide a general introduction into chromatin modifications and their respective functions with a focus on gene transcription, as well as key aspects of their roles in the early zebrafish embryo, neural development, formation of the digestive system and tissue regeneration.

Uhrf1 and Dnmt1 are required for development and maintenance of the zebrafish lens

DNA methylation is one of the key mechanisms underlying the epigenetic regulation of gene expression. During DNA replication, the methylation pattern of the parent strand is maintained on the replicated strand through the action of Dnmt1 (DNA Methyltransferase 1). In mammals, Dnmt1 is recruited to hemimethylated replication foci by Uhrf1 (Ubiquitin-like, Containing PHD and RING Finger Domains 1). Here we show that Uhrf1 is required for DNA methylation in vivo during zebrafish embryogenesis. Due in part to the early embryonic lethality of Dnmt1 and Uhrf1 knockout mice, roles for these proteins during lens development have yet to be reported. We show that zebrafish mutants in uhrf1 and dnmt1 have defects in lens development and maintenance. uhrf1 and dnmt1 are expressed in the lens epithelium, and in the absence of Uhrf1 or of catalytically active Dnmt1, lens epithelial cells have altered gene expression and reduced proliferation in both mutant backgrounds. This is correlated with a wave of apoptosis in the epithelial layer, which is followed by apoptosis and unraveling of secondary lens fibers. Despite these disruptions in the lens fiber region, lens fibers express appropriate differentiation markers. The results of lens transplant experiments demonstrate that Uhrf1 and Dnmt1 functions are required lens-autonomously, but perhaps not cell-autonomously, during lens development in zebrafish. These data provide the first evidence that Uhrf1 and Dnmt1 function is required for vertebrate lens development and maintenance.

DNA methylation levels in the 5' flanking region of the vitellogenin I gene in liver and brain of adult zebrafish (Danio rerio)--sex and tissue differences and effects of 17alpha-ethinylestradiol exposure

Vitellogenin is produced in the liver of sexually mature female fish in response to endogenous estrogens. Exogenous estrogens also induce synthesis of vitellogenin in the liver of male and juvenile fish and vitellogenin is a frequently used biomarker for estrogen exposure. The epigenetic state, e.g. histone acetylation and DNA methylation, in the region of a gene or in its 5' flanking region influences the gene expression. DNA methylation positions in multicellular eukaryotes are mostly found on cytosine bases located 5' to guanine, i.e. in CpG sites. Here, we have for the first time analyzed the DNA methylation levels of three CpG sites located in the 5' flanking region of the vitellogenin I gene in liver and brain from adult zebrafish (Danio rerio) utilizing Pyrosequencing technology. This sequencing technique allows determination of methylation levels of multiple individual CpG sites. Our purpose was to assess any differences in methylation levels related to sex, tissue and exposure to estrogen. Out of the seven vitellogenin genes identified in the zebrafish, vitellogenin I is the most highly expressed during vitellogenesis. We found that the methylation levels of all three CpG sites were higher in male liver than in female liver. In brain, which does not express vitellogenin, females and males showed similar, high methylation levels in the analyzed CpG positions. Exposure of adult zebrafish to 17alpha-ethinylestradiol (100 ng/L) for 14 days decreased the methylation levels in the 5' flanking region of vitellogenin I in the liver in both females and males. These results suggest that induced expression of vitellogenin in fish following exposure to estrogens might involve alterations in DNA methylation.

Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after

Organisms often respond to environmental changes by producing alternative phenotypes. Epigenetic processes such as DNA methylation may contribute to environmentally induced phenotypic variation by modifying gene expression. Changes in DNA methylation, unlike DNA mutations, can be influenced by the environment; they are stable at the time scale of an individual and present different levels of heritability. These characteristics make DNA methylation a potentially important molecular process to respond to environmental change. The aim of this review is to present the implications of DNA methylation on phenotypic variations driven by environmental changes. More specifically, we explore epigenetic concepts concerning phenotypic change in response to the environment and heritability of DNA methylation, namely the Baldwin effect and genetic accommodation. Before addressing this point, we report major differences in DNA methylation across taxa and the role of this modification in producing and maintaining environmentally induced phenotypic variation. We also present the different methods allowing the detection of methylation polymorphism. We believe this review will be helpful to molecular ecologists, in that it highlights the importance of epigenetic processes in ecological and evolutionary studies.

DNA methylation and methyl-CpG binding proteins: developmental requirements and function

DNA methylation is a major epigenetic modification in the genomes of higher eukaryotes. In vertebrates, DNA methylation occurs predominantly on the CpG dinucleotide, and approximately 60% to 90% of these dinucleotides are modified. Distinct DNA methylation patterns, which can vary between different tissues and developmental stages, exist on specific loci. Sites of DNA methylation are occupied by various proteins, including methyl-CpG binding domain (MBD) proteins which recruit the enzymatic machinery to establish silent chromatin. Mutations in the MBD family member MeCP2 are the cause of Rett syndrome, a severe neurodevelopmental disorder, whereas other MBDs are known to bind sites of hypermethylation in human cancer cell lines. Here, we review the advances in our understanding of the function of DNA methylation, DNA methyltransferases, and methyl-CpG binding proteins in vertebrate embryonic development. MBDs function in transcriptional repression and long-range interactions in chromatin and also appear to play a role in genomic stability, neural signaling, and transcriptional activation. DNA methylation makes an essential and versatile epigenetic contribution to genome integrity and function.

High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research

BACKGROUND

The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and express aging related biomarkers. Treatment with resveratrol and low temperature significantly extends the maximum life span. These features make N. furzeri a promising new vertebrate model for age research.

RESULTS

To contribute to establishing N. furzeri as a new model organism, we provide a first insight into its genome and a comparison to medaka, stickleback, tetraodon and zebrafish. The N. furzeri genome contains 19 chromosomes (2n = 38). Its genome of between 1.6 and 1.9 Gb is the largest among the analyzed fish species and has, at 45%, the highest repeat content. Remarkably, tandem repeats comprise 21%, which is 4-12 times more than in the other four fish species. In addition, G+C-rich tandem repeats preferentially localize to centromeric regions. Phylogenetic analysis based on coding sequences identifies medaka as the closest relative. Genotyping of an initial set of 27 markers and multi-locus fingerprinting of one microsatellite provides the first molecular evidence that the GRZ strain is highly inbred.

CONCLUSIONS

Our work presents a first basis for systematic genomic and genetic analyses aimed at understanding the mechanisms of life span determination in N. furzeri.