Windows of opportunity: Ocean warming shapes temperature-sensitive epigenetic reprogramming and gene expression across gametogenesis and embryogenesis in marine stickleback

Methylome profile of medaka eggs and sperm

Eggs and sperm are responsible for the continuation of generations. Following the epigenetic reprogramming of the embryo, core epigenetic information present in the sperm and eggs is transmitted to offspring somatic cells prior to the blastula stage, which specifically influences gene expression in the cells. Differences in the patterns of DNA methylation between the paternal and maternal genomes are critical to regulating allele-specific gene expression in the developing embryo, constituting the basis of genomic imprinting in mammals. While the information on allele-specific epigenetic information has been limited to mammals, it is not clearly understood whether non-mammalian vertebrate gametes possess any sex-specific allelic epigenetic information and whether somatic cells maintain the allele-specific epigenetic information, particularly DNA methylation. To determine the landscape of DNA methylation in paternal and maternal alleles in a non-mammalian vertebrate, we profiled the methylome of egg in medaka fish and compared it with our previously published medaka sperm methylome. We identified a set of gamete-specific differentially methylated regions (DMRs) in the genome- medaka eggs maintained a significantly lower global methylation profile than the sperm. Based on our sequencing depth and data, 10 DMRs were hypermethylated, and 237 DMRs were hypomethylated in the eggs compared to the sperm methylome. Somatic cells in blastula maintained some of those parental gamete-specific DNA methylation profiles. Those DMRs are associated with 70 genes, suggesting that they may have imprinted-like functions and warrant further investigation.

Genomic and Epigenomic Influences on Resilience across Scales: Lessons from the Responses of Fish to Environmental Stressors

Understanding the factors that influence the resilience of biological systems to environmental change is a pressing concern in the face of increasing human impacts on ecosystems and the organisms that inhabit them. However, most considerations of biological resilience have focused at the community and ecosystem levels, whereas here we discuss how including consideration of processes occurring at lower levels of biological organization may provide insights into factors that influence resilience at higher levels. Specifically, we explore how processes at the genomic and epigenomic levels may cascade up to influence resilience at higher levels. We ask how the concepts of "resistance," or the capacity of a system to minimize change in response to a disturbance, and "recovery," or the ability of a system to return to its original state following a disturbance and avoid tipping points and resulting regime shifts, map to these lower levels of biological organization. Overall, we suggest that substantial changes at these lower levels may be required to support resilience at higher levels, using selected examples of genomic and epigenomic responses of fish to climate-change-related stressors such as high temperature and hypoxia at the levels of the genome, epigenome, and organism.

The role of epigenetics in women's reproductive health: the impact of environmental factors

This paper explores the significant role of epigenetics in women's reproductive health, focusing on the impact of environmental factors. It highlights the crucial link between epigenetic modifications-such as DNA methylation and histones post-translational modifications-and reproductive health issues, including infertility and pregnancy complications. The paper reviews the influence of pollutants like PM2.5, heavy metals, and endocrine disruptors on gene expression through epigenetic mechanisms, emphasizing the need for understanding how dietary, lifestyle choices, and exposure to chemicals affect gene expression and reproductive health. Future research directions include deeper investigation into epigenetics in female reproductive health and leveraging gene editing to mitigate epigenetic changes for improving IVF success rates and managing reproductive disorders.

DNA methylation reprogramming in teleosts

Early embryonic development is crucially important but also remarkably diverse among animal taxa. Axis formation and cell lineage specification occur due to both spatial and temporal control of gene expression. This complex system involves various signaling pathways and developmental genes such as transcription factors as well as other molecular interactants that maintain cellular states, including several types of epigenetic marks. 5mC DNA methylation, the chemical modification of cytosines in eukaryotes, represents one such mark. By influencing the compaction of chromatin (a high-order DNA structure), DNA methylation can either repress or induce transcriptional activity. Mammals exhibit a reprogramming of DNA methylation from the parental genomes in the zygote following fertilization, and later in primordial germ cells (PGCs). Whether these periods of methylation reprogramming are evolutionarily conserved, or an innovation in mammals, is an emerging question. Looking into these processes in other vertebrate lineages is thus important, and teleost fish, with their extensive species richness, phenotypic diversity, and multiple rounds of whole genome duplication, provide the perfect research playground for answering such a question. This review aims to present a concise state of the art of DNA methylation reprogramming in early development in fish by summarizing findings from different research groups investigating methylation reprogramming patterns in teleosts, while keeping in mind the ramifications of the methodology used, then comparing those patterns to reprogramming patterns in mammals.

Intergenerational effects of ocean temperature variation: Early life benefits are short-lived in threespine stickleback

Current climate change models predict an increase in temperature variability and extreme events such as heatwaves, and organisms need to cope with consequent changes to environmental variation. Non-genetic inheritance mechanisms can enable parental generations to prime their offspring's abilities to acclimate to environmental change-but they may also be deleterious. When parents are exposed to predictable environments, intergenerational plasticity can lead to better offspring trait performance in matching environments. Alternatively, parents exposed to variable or unpredictable environments may use plastic bet-hedging strategies to adjust the phenotypic variance among offspring. Here, we used a model species, the threespine stickleback (Gasterosteus aculeatus), to test whether putatively adaptive intergenerational effects can occur in response to shifts in environmental variation as well as to shifts in environmental mean, and whether parents employ plastic bet-hedging strategies in response to increasing environmental variation. We used a full-factorial, split-clutch experiment with parents and offspring exposed to three temperature regimes: constant, natural variation, and increased variation. We show that within-generation exposure to increased temperature variation reduces growth of offspring, but having parents that were exposed to natural temperature variation during gametogenesis may offset some early-life negative growth effects. However, these mitigating intergenerational effects do not appear to persist later in life. We found no indication that stickleback mothers plastically altered offspring phenotypic variance (egg size or clutch size) in response to temperature variation. However, lower inter-individual variance of juvenile fish morphology in offspring of increased variation parents may imply the presence of conservative bet-hedging strategies in natural populations. Overall, in our experiment, parental exposure to temperature variation had limited effects on offspring fitness-related traits. Natural levels of environmental variation promoted a potentially adaptive intergenerational response in early life development, but under more challenging conditions associated with increased environmental variation, the effect was lost.

To live or let die? Epigenetic adaptations to climate change-a review

Anthropogenic activities are responsible for a wide array of environmental disturbances that threaten biodiversity. Climate change, encompassing temperature increases, ocean acidification, increased salinity, droughts, and floods caused by frequent extreme weather events, represents one of the most significant environmental alterations. These drastic challenges pose ecological constraints, with over a million species expected to disappear in the coming years. Therefore, organisms must adapt or face potential extinctions. Adaptations can occur not only through genetic changes but also through non-genetic mechanisms, which often confer faster acclimatization and wider variability ranges than their genetic counterparts. Among these non-genetic mechanisms are epigenetics defined as the study of molecules and mechanisms that can perpetuate alternative gene activity states in the context of the same DNA sequence. Epigenetics has received increased attention in the past decades, as epigenetic mechanisms are sensitive to a wide array of environmental cues, and epimutations spread faster through populations than genetic mutations. Epimutations can be neutral, deleterious, or adaptative and can be transmitted to subsequent generations, making them crucial factors in both long- and short-term responses to environmental fluctuations, such as climate change. In this review, we compile existing evidence of epigenetic involvement in acclimatization and adaptation to climate change and discuss derived perspectives and remaining challenges in the field of environmental epigenetics. Graphical Abstract.

The evolutionary consequences of interactions between the epigenome, the genome and the environment

The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.

Epigenetic diversity of genes with copy number variations among natural populations of the three-spined stickleback

Duplicated genes provide the opportunity for evolutionary novelty and adaptive divergence. In many cases, having more gene copies increases gene expression, which might facilitate adaptation to stressful or novel environments. Conversely, overexpression or misexpression of duplicated genes can be detrimental and subject to negative selection. In this scenario, newly duplicate genes may evade purifying selection if they are epigenetically silenced, at least temporarily, leading them to persist in populations as copy number variations (CNVs). In animals and plants, younger gene duplicates tend to have higher levels of DNA methylation and lower levels of gene expression, suggesting epigenetic regulation could promote the retention of gene duplications via expression repression or silencing. Here, we test the hypothesis that DNA methylation variation coincides with young duplicate genes that are segregating as CNVs in six populations of the three-spined stickleback that span a salinity gradient from 4 to 30 PSU. Using reduced-representation bisulfite sequencing, we found DNA methylation and CNV differentiation outliers rarely overlapped. Whereas lineage-specific genes and young duplicates were found to be highly methylated, just two gene CNVs showed a significant association between promoter methylation level and copy number, suggesting that DNA methylation might not interact with CNVs in our dataset. If most new duplications are regulated for dosage by epigenetic mechanisms, our results do not support a strong contribution from DNA methylation soon after duplication. Instead, our results are consistent with a preference to duplicate genes that are already highly methylated.

Genome-wide 5'-C-phosphate-G-3' methylation patterns reveal the effect of heat stress on the altered semen quality in Bubalus bubalis

Semen production and quality are closely correlated with different environmental factors in bovines, particularly for the buffalo (Bubalus bubalis) bulls reared under tropical and sub-tropical conditions. Factors including DNA methylation patterns, an intricate process in sperm cells, have an impact on the production of quality semen in buffalo bulls under abiotic stress conditions. The present study was conducted to identify DNA methylome signatures for semen quality in Murrah buffalo bulls, acclaimed as a major dairy breed globally, under summer heat stress. Based on semen quality parameters that significantly varied between the two groups over the seasons, the breeding bulls were classified into seasonally affected (SA = 6) and seasonally non-affected (SNA = 6) categories. DNA was isolated from purified sperm cells and sequenced using the RRBS (Reduced Representation Bisulfite Sequencing) technique for genome-wide methylome data generation. During the hot summer months, the physiological parameters such as scrotal surface temperature, rectal temperature, and respiration rate for both the SA and SNA bulls were significantly higher in the afternoon than in the morning. Whereas, the global CpG% of SA bulls was positively correlated with the afternoon's scrotal surface and rectal temperature. The RRBS results conveyed differentially methylated cytosines in the promoter region of the genes encoding the channels responsible for Ca2+ exchange, NPTN, Ca2+ activated chloride channels, ANO1, and a few structure-related units such as septins (SEPT4 and SEPT6), SPATA, etc. Additionally, the hypermethylated set of genes in SA was significantly enriched for pathways such as the FOXO signaling pathway and oocyte meiosis. The methylation patterns suggest promoter methylation in the genes regulating the sperm structure as well as surface transporters, which could contribute to the reduced semen quality in the Murrah buffalo bulls during the season-related heat stress.

Life-stage specificity and temporal variations in transcriptomes and DNA methylomes of the reef coral Pocillopora damicornis in response to thermal acclimation

Understanding the acclimation capacity of reef corals across generations to thermal stress and its underlying molecular underpinnings could provide insights into their resilience and adaptive responses to future climate change. Here, we acclimated adult brooding coral Pocillopora damicornis to high temperature (32 °C vs. 29 °C) for three weeks and analyzed the changes in phenotypes, transcriptomes and DNA methylomes of adult corals and their brooded larvae. Results showed that although adult corals did not show noticeable bleaching after thermal exposure, they released fewer but larger larvae. Interestingly, larval cohorts from two consecutive lunar days exhibited contrasting physiological resistance to thermal stress, as evidenced by the divergent responses of area-normalized symbiont densities and photochemical efficiency to thermal stress. RNA-seq and whole-genome bisulfite sequencing revealed that adult and larval corals mounted distinct transcriptional and DNA methylation changes in response to thermal stress. Remarkably, larval transcriptomes and DNA methylomes also varied greatly among lunar days and thermal treatments, aligning well with their physiological metrics. Overall, our study shows that changes in transcriptomes and DNA methylomes in response to thermal acclimation can be highly life stage-specific. More importantly, thermally-acclimated adult corals could produce larval offspring with temporally contrasting photochemical performance and thermal resilience, and such variations in larval phenotypes are associated with differential transcriptomes and DNA methylomes, and are likely to increase the likelihood of reproductive success and plasticity of larval propagules under thermal stress.

Matching maternal and paternal experiences underpin molecular thermal acclimation

The environment experienced by one generation has the potential to affect the subsequent one through non-genetic inheritance of parental effects. Since both mothers and fathers can influence their offspring, questions arise regarding how the maternal, paternal and offspring experiences integrate into the resulting phenotype. We aimed to disentangle the maternal and paternal contributions to transgenerational thermal acclimation in a reef fish, Acanthochromis polyacanthus, by exposing two generations to elevated temperature (+1.5°C) in a fully factorial design and analysing the F2 hepatic gene expression. Paternal and maternal effects showed not only common but also parent-specific components, with the father having the largest influence in shaping the offspring's transcriptomic profile. Fathers contributed to transcriptional transgenerational response to warming through transfer of epigenetically controlled stress-response mechanisms while mothers influenced increased gene expression associated with lipid metabolism regulation. However, the key to acclimation potential was matching thermal experiences of the parents. When both parents were exposed to the same condition, offspring showed increased expression of genes related to structural RNA production and transcriptional regulation, whereas environmental mismatch in parents resulted in maladaptive parental condition transfer, revealed by translation suppression and endoplasmic reticulum stress. Interestingly, the offspring's own environmental experience had the smallest influence on their hepatic transcription profiles. Taken together, our results show the complex nature of the interplay among paternal, maternal and offspring cue integration, and reveal that acclimation potential to ocean warming might depend not only on maternal and paternal contributions but importantly on congruent parental thermal experiences.

Thermoregulatory response in juvenile Hippocampus erectus: Effect of magnitude and rate of thermal increase on metabolism and antioxidative defence

Behavioural, physiological and biochemical mechanisms constitute the adaptive capacities that allow marine ectotherms to explore the environment beyond their thermal optimal. Limitations to the efficiency of these mechanisms define the transition from moderate to severe thermal stress, and serve to characterise the thermoregulatory response in the zone of thermal tolerance. We selected a tropical population of Hippocampus erectus to describe the timing of the physiological and biochemical mechanisms in response to the following increments in water temperature: (i) 4°C abrupt (26-30°C in <5 min); (ii) 7°C abrupt (26-33°C); (iii) 4°C gradual (1°C every 3 h) and (iv) 7°C gradual (1.5°C every 3 h). The routine metabolic rate (Rrout) of juvenile H. erectus was measured immediately before and after 0.5, 12 and 28 h of being exposed to each thermal treatment. Samples of muscle and abdominal organs were taken to quantify indicators of aerobic and anaerobic metabolism and antioxidant enzymes and oxidative stress at each moment throughout exposure. Results showed a full thermoregulatory response within 0.5 h: Rrout increased in direct correspondence with both the magnitude and rate of thermal increase; peroxidised lipids rapidly accumulated before the antioxidant defence was activated and early lactate concentrations suggested an immediate, yet temporary, reduction in aerobic scope. After 12 h, Rrout had decreased in sea horses exposed to 30°C, but not to 33°C, where Rrout continued high until the end of trials. Within 28 h of thermal exposure, all metabolite and antioxidant defence indicators had been restored to control levels (26°C). These findings testify to the outstanding thermal plasticity of H. erectus and explain their adjustment to rapid fluctuations in ambient temperature. Such features, however, do not protect this tropical population from the deleterious effects of chronic exposure to temperatures that have been predicted for the future.

Intergenerational effects of early life-stage temperature modulation on gene expression and DNA methylation in Atlantic cod (Gadus morhua)

After suffering several collapses, the cod farming industry is now in the process of trying to re-establish itself. We have used material from Norway's National Cod Breeding Program to study how different early life-stage temperature regimes affect DNA methylation and gene expression. Long-term effects were detected by sampling fish several weeks after the end of differential treatments, and offspring from the different exposure groups was also sampled. Many overlapping genes were found between the different exposure groups and generations, coupled with genes associated with differential CpG methylation levels. Genes involved in muscle fibre development, general metabolic processes and formation of deformities were significantly affected, and genes relevant for intergenerational transfer of epigenetic marks were also detected. We believe the use of environmental cues can be a useful strategy for improving the production of Atlantic cod.

Sex-specific transgenerational plasticity: developmental temperatures of mothers and fathers have different effects on sons and daughters

Each parent can influence offspring phenotype via provisioning of the zygote or sex-specific DNA methylation. Transgenerational plasticity may therefore depend on the environmental conditions experienced by each parent. We tested this hypothesis by conducting a fully factorial experiment across three generations of guppies (Poecilia reticulata), determining the effects of warm (28°C) and cold (21°C) thermal backgrounds of mothers and fathers on mass and length, and thermal performance (sustained and sprint swimming speeds, citrate synthase and lactate dehydrogenase activities; 18, 24, 28, 32 and 36°C test temperatures) of sons and daughters. Offspring sex was significant for all traits except for sprint speed. Warmer mothers produced sons and daughters with reduced mass and length, and warmer fathers produced shorter sons. Sustained swimming speed (Ucrit) of male offspring was greatest when both parents were raised at 28°C, and warmer fathers produced daughters with greater Ucrit. Similarly, warmer fathers produced sons and daughters with greater metabolic capacity. We show that the thermal variation experienced by parents can modify offspring phenotype, and that predicting the impacts of environmental change on populations would require knowledge of the thermal background of each mother and father, particularly where sexes are spatially segregated.

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.