ALBERT

Description: Ocean environments are changing rapidly and marine organisms need to cope with these changes in order to survive, develop, and reproduce. To do so, organisms can either migrate, adapt in situ or acclimate via phenotypic plasticity. In this context, the emerging field of environmental epigenetics investigates the contribution of genetic and epigenetic information to adaptive potential of wild populations. Epigenetic modifications are based on the highly dynamic combination of DNA methylation, histone modifications, and non-coding RNAs, which may facilitate phenotypic plasticity through genotype-epigenotype-environment interactions, and can drive rapid evolution in wild populations. However, while knowledge of epigenetic contributions to phenotypes across different developmental and generational timescales is increasing for medical research model species, the mechanistic and synergistic action of these modifications remain comparatively understudied in ecological models such as teleost fishes. Here, we characterized the evolution of the gene toolkit involved in key molecular epigenetic pathways including DNA methylation, histone modifications, macroH2A histone, and miRNA biogenesis/turnover in threespine stickleback, a model species in evolution and ecology. We then investigated these genes within a phylogenetic context by comparing them in stickleback to human, mouse, chicken, tropical clawed frog, zebrafish, medaka, green spotted puffer, channel catfish, and mangrove rivulus. We found that, in general, conserved domains, in conjunction with their phylogenetic positions, suggest evolutionary conservation of putative enzyme activity in stickleback. However, molecular epigenetic pathways also revealed that teleost gene evolution is diversified and complex. Specifically, the number of genes, gene loss/duplication events, identified conserved domains, and putative protein lengths vary greatly from one species to another, particularly within fishes, which exhibit a potentially new class of histone deacetylases. This suggests different biological functions specific to fish species, and that the action of genes regulating epigenetic modifications in model species are not necessarily applicable to other related species. We integrate our results into recent advances concerning epigenetic mechanisms in teleosts, and conclude by discussing the necessity to delve deeper into the fundamental mechanics of epigenetic modifications in a wide array of taxa, particularly those relevant for assisted evolution, conservation, aquaculture, fisheries, and climate change-adaptation studies.

Description: Our climate is changing rapidly and organisms must either move, adapt or acclimate in order to persist. Epigenetic modifications such as DNA methylation may be an important mechanism underlying fast, adaptive responses, as they can contribute to heritable changes within populations and drive rapid evolution. Crucial during gametogenesis and development (embryogenesis), epigenetic modifications can be inherited both mitotically within a generation, and/or meiotically across generations (transgenerational epigenetic inheritance). However, heritable epigenetic modifications must overcome two reprogramming phases, once in the germline and once in the early embryo. Despite being well documented in plant and mammalian systems, epigenetic reprogramming studies during fish gametogenesis and embryogenesis have focused only on a few model species. Here, we investigated DNA methylation patterns, together with the molecular characterization and mRNA expression profiles of DNA-methyltransferase enzymes (DNMT) during gametogenesis and embryogenesis of marine threespine stickleback. Additionally, the impact of multiple simulated ocean warming scenarios (ambient °C, +1.5°C and +4°C) were evaluated at both the epigenetic and phenotypic level to establish a functional link between methylomes, epigenetic reprogramming and transgenerational plasticity, and their role in adaptive potential to climate change.

Description: Histone methylation patterns are important epigenetic regulators of mammalian development, notably through stem cell identity maintenance by chromatin remodeling and transcriptional control of pluripotency genes. But, the implications of histone marks are poorly understood in distant groups outside vertebrates and ecdysozoan models. However, the development of the Pacific oyster Crassostrea gigas is under the strong epigenetic influence of DNA methylation, and Jumonji histone-demethylase orthologues are highly expressed during C. gigas early life. This suggests a physiological relevance of histone methylation regulation in oyster development, raising the question of functional conservation of this epigenetic pathway in lophotrochozoan. Quantification of histone methylation using fluorescent ELISAs during oyster early life indicated significant variations in monomethyl histone H3 lysine 4 (H3K4me), an overall decrease in H3K9 mono- and tri-methylations, and in H3K36 methylations, respectively, whereas no significant modification could be detected in H3K27 methylation. Early in vivo treatment with the JmjC-specific inhibitor Methylstat induced hypermethylation of all the examined histone H3 lysines and developmental alterations as revealed by scanning electronic microscopy. Using microarrays, we identified 376 genes that were differentially expressed under methylstat treatment, which expression patterns could discriminate between samples as indicated by principal component analysis. Furthermore, Gene Ontology revealed that these genes were related to processes potentially important for embryonic stages such as binding, cell differentiation and development. These results suggest an important physiological significance of histone methylation in the oyster embryonic and larval life, providing, to our knowledge, the first insights into epigenetic regulation by histone methylation in lophotrochozoan development.

Description: Histone modifications such as methylation of key lysine residues play an important role in embryonic development in a variety of organisms such as of Pacific oysters, zebrafish and mice. The action of demethylase ("erasers") and methyltransferase ("writers") enzymes regulates precisely the methylation status of each lysine residue. However, despite fishes being very useful model organisms in medicine, evolution and ecotoxicology, most studies have focused on mammalian and plant model organisms, and mechanisms underlying regulation of histones are unknown in fish development outside of zebrafish. Here, putative histone lysine demethylases (Kdm) and methyltransferases (Kmt) were identified in an isogenic lineage of the self-fertilizing hermaphroditic vertebrate, the mangrove rivulus fish, Kryptolebias marmoratus. Evolutionary relationships with other animal demethylases and methyltransferases were examined, and expression patterns during embryonic development and in adult tissues were characterized. Twenty-five Kdm orthologues (Jarid2, Jmjd1c, Jmjd4, Jmjd6, Jmjd7, Jmjd8, Kdm1a, Kdm1b, Kdm2a, Kdm2b, Kdm3b, Kdm4a, Kdm4b, Kdm4c, Kdm5a, Kdm5b, Kdm5c, Kdm6a, Kdm6b, Kdm7a, Kdm8, Kdm9, UTY, Phf2 and Phf8) and forty-eight Kmt orthologues (Ezh1, Ezh2, Setd2, Nsd1, Nsd2, Nsd3, Ash1l, Kmt2e, Setd5, Prdm1, Prdm2, Prdm4, Prdm5, Prdm6, Prdm8, Prdm9, Prdm10, Prdm11, Prdm12, Prdm13, Prdm14, Prdm15, Prdm16, Setd3, Setd4, Setd6, Setd1a, Setd1b, Kmt2a, Kmt2b, Kmt2c, Kmt2d, Kmt5a, Kmt5b, Ehmt1, Ehmt2, Suv39h1, Setmar, Setdb1, Setdb2, Smyd1, Smyd2, Smyd3, Smyd4, Smyd5, Setd7, Setd9, Dot1l) were discovered. Expression patterns of both Kdm and Kmt were variable during embryonic development with a peak in gastrula stage and a reduction in later embryogenesis. Expression of both Kdm and Kmt was higher in male brains compared to hermaphrodite brains whereas specific expression patterns of Kdm and Kmt were observed in the hermaphrodite ovotestes and male testes, respectively. Putative histone demethylases (Kdm) and methyltransferases (Kmt) were for the first time characterized in a teleost besides zebrafish, the mangrove rivulus. Their domain conservation and expression profiles suggest that they might play important roles during development, gametogenesis and neurogenesis, which raises questions about epigenetic regulation of these processes by histone lysine methylation in K. marmoratus. Due to its peculiar mode of reproduction and the natural occurrence of isogenic lineages, this new model species is of great interest for understanding epigenetic contributions to the regulation of development and reproduction.

Description: During gametogenesis and embryonic development, precise regulation of gene expression, across cell/tissue types and over time, is crucial. In vertebrates, transcription is partly regulated by histone lysine acetylation/ deacetylation, an epigenetic mechanism mediated by lysine acetyltransferases (KAT) and histone deacetylases (HDAC). Well characterized in mammals, these enzymes are unknown in fish embryology outside of zebrafish development. Here, we characterized putative KAT and HDAC enzymes in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, a species that naturally self-fertilizes and can produce isogenic lineages. This unique feature provides an opportunity to elucidate the role of epigenetic mechanisms as a source of phenotypic plasticity. In this study, twenty-seven KAT and seventeen HDAC genes have been identified. Their conserved domains and their phylogenetic analysis suggest conservation of the enzymes' activity in our species, relative to other vertebrates in which the enzymes have been characterized. Furthermore, the dynamics of KAT and HDAC mRNA expression during embryogenesis, in adult gonads and brains, argues for a putative biological function in early and late development as well as in male/hermaphrodite gametogenesis and adult neurogenesis. Our study aimed to provide a basis about the epigenetic actors putatively regulating histone acetylation in a self-fertilizing fish, the mangrove rivulus. Unique among vertebrates, the great number of isogenic lineages occurring naturally in this species allows exploring the contribution of the enzymes regulating histone acetylation only to reproduction and development in teleost fishes, which are very powerful models in fundamental and applied researches that include aquaculture, ecotoxicology, behaviour, evolution, sexual determinism and human diseases.

Description: Our climate is changing rapidly and organisms must either move, adapt or acclimate in order to persist. Epigenetic modifications such as DNA methylation may be an important mechanism underlying fast, adaptive responses, as they can contribute to heritable changes within populations and drive rapid evolution. Crucial during gametogenesis and development (embryogenesis), epigenetic modifications can be inherited both mitotically within a generation, and/or meiotically across generations (transgenerational epigenetic inheritance). However, heritable epigenetic modifications must overcome two reprogramming phases, once in the germline and once in the early embryo. Despite being well documented in plant and mammalian systems, epigenetic reprogramming studies during fish gametogenesis and embryogenesis have focused only on a few model species. Here, we investigated DNA methylation patterns, together with the molecular characterization and mRNA expression profiles of DNA-methyltransferase enzymes (DNMT) during gametogenesis and embryogenesis of marine threespine stickleback. Additionally, the impact of multiple simulated ocean warming scenarios (ambient °C, +1.5°C and +4°C) was evaluated at the epigenetic and phenotypic level to establish a link between environment, epigenetic reprogramming and transgenerational plasticity. So far, we found that DNA methylation seems to be stable during gametogenesis, with male gonads being hypermethylated compared to female gonads. Nevertheless, environmental temperature significantly influenced mature male gonad DNA methylation, whereas for females, only egg size/number was affected, in line with previous work showing that cytoplasmic factors (e.g. mitochondria) are likely involved in transgenerational inheritance down the maternal line. Overall, our preliminary results suggest that gametogenesis in stickleback is differentially regulated compared to mammals and is sensitive to environmental perturbations, with possible implications for adaptive windows under climate change.