Development of DNA methylation-based epigenetic age predictors in loblolly pine (Pinus taeda).

Biological ageing is connected to life history variation across ecological scales and informs a basic understanding of age-related declines in organismal function. Altered DNA methylation dynamics are a conserved aspect of biological ageing and have recently been modelled to predict chronological age among vertebrate species. In addition to their utility in estimating individual age, differences between chronological and predicted ages arise due to acceleration or deceleration of epigenetic ageing, and these discrepancies are linked to disease risk and multiple life history traits. Although evidence suggests that patterns of DNA methylation can describe ageing in plants, predictions with epigenetic clocks have yet to be performed. Here, we resolve the DNA methylome across CpG, CHG, and CHH-methylation contexts in the loblolly pine tree (Pinus taeda) and construct epigenetic clocks capable of predicting ages in this species within 6% of its maximum lifespan. Although patterns of CHH-methylation showed little association with age, both CpG and CHG-methylation contexts were strongly associated with ageing, largely becoming hypomethylated with age. Among age-associated loci were those in close proximity to malate dehydrogenase, NADH dehydrogenase, and 18S and 26S ribosomal RNA genes. This study reports one of the first epigenetic clocks in plants and demonstrates the universality of age-associated DNA methylation dynamics which can inform conservation and management practices, as well as our ecological and evolutionary understanding of biological ageing in plants.

Intrinsic and extrinsic factors interact during development to influence telomere length in a long-lived reptile.

The mechanisms connecting environmental conditions to plasticity in biological aging trajectories are fundamental to understanding individual variation in functional traits and life history. Recent findings suggest that telomere biology is especially dynamic during early life stages and has long-term consequences for subsequent reproduction and survival. However, our current understanding is mostly derived from studies investigating ecological and anthropogenic factors separately, leaving the effects of complex environmental interactions unresolved. American alligators (Alligator mississippiensis) are long-lived apex predators that rely on incubation temperature during a discrete period during development and endocrine cues to determine sex, making them especially vulnerable to current climatic variability and exposure to anthropogenic contaminants interfering with hormone function. Here, we combine field studies with a factorial design to understand how the developmental environment, along with intrinsic biological variation contribute to persistent telomere variation. We found that exposure to a common endocrine disrupting contaminant, DDE, affects telomere length, but that the directionality is highly dependent upon incubation temperature. Variation in hatchling growth, underlies a strong clutch effect. We also assess concentrations of a panel of glucocorticoid hormones and find that contaminant exposure elicits an increase in circulating glucocorticoids. Consistent with emerging evidence linking stress and aging trajectories, GC levels also appear to trend with shorter telomere length. Thus, we add support for a mechanistic link between contaminants and glucocorticoid signalling, which interacts with ecological aspects of the developmental environment to alter telomere dynamics.

Transient Copper Exposure During Embryogenesis and Temperature Affect Developmental Rate, Survival, and Fin Regeneration in Japanese Medaka (Oryzias latipes).

Combined environmental stressors that an organism experiences can have both immediate and lasting consequences. In the present study, we exposed Japanese medaka (Oryzias latipes) embryos to sublethal copper sulfate (CuSO4 ; 0, 10, and 100 ppb) in combination with different rearing temperatures (27, 30, and 33 °C) to assess acute and latent effects on development, growth, and regenerative capacity. Embryos exposed to CuSO4 and/or higher temperatures hatched significantly earlier. At 4 months post-exposure, fish exposed to low levels of CuSO4 during development had higher survival, whereas fish exposed to both 100 ppb CuSO4 and 33 °C temperatures had significantly lower survival. In addition, a sex-specific effect of embryonic CuSO4 exposure was observed as female mass decreased with increasing Cu dose. We also assessed caudal fin regenerative capabilities in both embryo-exposed fish at 4 months of age and adult medaka that were exposed to 0, 10, and 100 ppb CuSO4 at room temperature during a 14-day trial. Whereas fin regeneration was unaffected by adult exposure to Cu, fish transiently exposed during embryogenesis displayed an initial increase in fin growth rate and an increased incidence of abnormal fin morphology following regrowth. Collectively, these data suggest that developmental Cu exposure has the potential to exert long-lasting impacts to organismal growth, survival, and function. Environ Toxicol Chem 2022;41:748-757. © 2021 SETAC.

Exposure to ionizing radiation disrupts normal epigenetic aging in Japanese medaka.

Alterations to the epigenome are a hallmark of biological aging and age-dependent patterning of the DNA methylome ("epigenetic aging") can be modeled to produce epigenetic age predictors. Rates of epigenetic aging vary amongst individuals and correlate to the onset of age-related disease and all-cause mortality. Yet, the origins of epigenetic-to-chronological age discordance are not empirically resolved. Here, we investigate the relationship between aging, DNA methylation, and environmental exposures in Japanese medaka (Oryzias latipes). We find age-associated DNA methylation patterning enriched in genomic regions of low CpG density and that, similar to mammals, most age-related changes occur during early life. We construct an epigenetic clock capable of predicting chronological age with a mean error of 61.1 days (~8.4% of average lifespan). To test the role of environmental factors in driving epigenetic age variation, we exposed medaka to chronic, environmentally relevant doses of ionizing radiation. Because most organisms share an evolutionary history with ionizing radiation, we hypothesized that exposure would reveal fundamental insights into environment-by-epigenetic aging interactions. Radiation exposure disrupted epigenetic aging by accelerating and decelerating normal age-associated patterning and was most pronounced in cytosines that were moderately associated with age. These findings empirically demonstrate the role of DNA methylation in integrating environmental factors into aging trajectories.

Is CpG Density the Link between Epigenetic Aging and Lifespan?

The genetic mechanisms contributing to lifespan variation remain unresolved. Based on recent conceptual advances in our understanding of epigenetic potential and the relocalization of chromatin modifiers (RCM), we hypothesize that increased CpG density is protective against age-related erosion of the epigenetic landscape and may explain interspecific variation in lifespan.

Chronic low dose irradiation alters hepatic transcriptional profiles, but not global DNA methylation in medaka (Oryzias latipes).

Ionizing radiation (IR) resulting from both natural and anthropogenic sources is ubiquitous throughout the environment. Historically, studies on the biological impacts of radiation primarily focused on responses to acute doses of radiation, with little advancement in our understanding of environmentally relevant exposures. Epigenetic mechanisms are capable of mediating organismal responses to environmental stressors and DNA methylation plays important roles in gene regulation and promoting chromosomal stability. Here, we assess broad-scale transcriptional and epigenetic variation resulting from chronic exposure to low doses of ionizing radiation (LDIR; 5.78, 53.76, or 520.23 mGy/day) using Japanese medaka fish (Oryzias latipes) in a replicated mesocosm design. We observed significant changes to the hepatic transcriptome induced by a 3-month chronic exposure to IR, whereas global DNA methylation appeared largely unaffected. Our findings reveal a set of genes, including those involved in immune function, responding to environmentally relevant IR exposures, which do not appear to be mediated by a systemic global shift in DNA methylation.

Epigenetic Aging Clocks in Ecology and Evolution.

The development of 'epigenetic clocks' is changing how biomedical scientists approach age-associated disease and leads to new insights and questions of wider significance. We highlight recent findings concerning epigenetic aging and discuss their relevance to life history evolution and their potential for advancing the field of ecological and evolutionary aging.

Onset of Daily Activity in a Female Songbird Is Related to Peak-Induced Estradiol Levels.

Research in captive birds and mammals has demonstrated that circadian (i.e., daily) behavioral rhythms are altered in response to increases in sex-steroid hormones. Recently, we and others have demonstrated a high degree of individual repeatability in peak (gonadotropin-releasing hormone [GnRH]-induced sex) steroid levels, and we have found that these GnRH-induced levels are highly correlated with their daily (night-time) endogenous peak. Whether or not individual variation in organization and activity of the reproductive endocrine axis is related to daily timing in wild animals is not well known. To begin to explore these possible links, we tested the hypothesis that maximal levels of the sex steroid hormone estradiol (E2) and onset of daily activity are related in a female songbird, the dark-eyed junco (Junco hyemalis). We found that females with higher levels of GnRH-induced E2 departed from their nest in the morning significantly earlier than females with lower stimulated levels. We did not observe a relationship between testosterone and this measure of onset of activity. Our findings suggest an interaction between an individual's reproductive endocrine axis and the circadian system and variation observed in an individuals' daily activity onset. We suggest future studies examine the relationship between maximal sex-steroid hormones and timing of daily activity onset.

The impact of maternally derived dioxins on embryonic development and hepatic AHR signaling in a long-lived apex predator.

Dioxins and related contaminants are highly pervasive in aquatic systems and elicit deleterious effects in exposed organisms. Because dioxins exhibit a proclivity to bioaccumulate, long-lived predatory species are particularly vulnerable to their persistence in the environment. We have previously reported elevated expression of CYP1A2, a biomarker of dioxin exposure, in American alligator embryos collected from the Tom Yawkey Wildlife Center (YWC). This coastal population inhabits a system with historical dioxin contamination associated with industrial activities. Herein, we utilize ecological attributes of the alligator to address the persistence of dioxins and furans in yolk and their potential to drive changes in hepatic function. Specifically, we assess variation in expression of AHR signaling components in embryos and its connection to contaminant levels in matched yolk samples. Compared to a reference population, TEQ levels and total penta-, hexa-, octa-substituted CDDs were elevated at YWC. Contrary to predictions, TEQ levels were not significantly related to hepatic AHR1B or CYP1A2 expression. However, a significant association was detected between expression of both factors and embryo:yolk mass ratios, wherein decreasing embryo mass was negatively associated with CYP1A2 but positively associated with AHR1B. These findings suggest that variation in embryonic metabolism and developmental progression likely influence AHR signaling and dioxin toxicity in alligators and potentially other oviparous species. While dioxin concentrations observed in alligators in this study are lower than historical values reported for other wildlife species inhabiting this system, they indicate the continued presence and possible long-term influence of these contaminants in a high trophic status species.