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Effects of stresses associated with extremely preterm birth may be biologically “recorded” in the genomes of individuals born preterm via changes in DNA methylation (DNAm) patterns. Genome-wide DNAm profiles were examined in buccal epithelial cells from 45 adults born at extremely low birth weight (ELBW; ≤1000 g) in the oldest known cohort of prospectively followed ELBW survivors (Mage = 32.35 years, 17 male), and 47 normal birth weight (NBW; ≥2500 g) control adults (Mage = 32.43 years, 20 male). Sex differences in DNAm profiles were found in both birth weight groups, but they were greatly enhanced in the ELBW group (77,895 loci) versus the NBW group (3,424 loci), suggesting synergistic effects of extreme prenatal adversity and sex on adult DNAm profiles. In men, DNAm profiles differed by birth weight group at 1,354 loci on 694 unique genes. Only two loci on two genes distinguished between ELBW and NBW women. Gene ontology (GO) and network analyses indicated that loci differentiating between ELBW and NBW men were abundant in genes within biological pathways related to neuronal development, synaptic transportation, metabolic regulation, and cellular regulation. Findings suggest increased sensitivity of males to long-term epigenetic effects of extremely preterm birth. Group differences are discussed in relation to particular gene functions.
Epigenetic age acceleration (AA) has been associated with adverse environmental exposures and many chronic conditions. We estimated, in the NINFEA birth cohort, infant saliva epigenetic age, and investigated whether parental socio-economic position (SEP) and pregnancy outcomes are associated with infant epigenetic AA. A total of 139 saliva samples collected at on average 10.8 (range 7–17) months were used to estimate Horvath’s DNA methylation age. Epigenetic AA was defined as the residual from a linear regression of epigenetic age on chronological age. Linear regression models were used to test the associations of parental SEP and pregnancy outcomes with saliva epigenetic AA. A moderate positive association was found between DNA methylation age and chronological age, with the median absolute difference of 6.8 months (standard deviation [SD] 3.9). The evidence of the association between the indicators of low SEP and epigenetic AA was weak; infants born to unemployed mothers or with low education had on average 1 month higher epigenetic age than infants of mothers with high education and employment (coefficient 0.78 months, 95% confidence intervals [CIs]: −0.79 to 2.34 for low/medium education; 0.96, 95% CI: −1.81 to 3.73 for unemployment). There was no evidence for association of gestational age, birthweight or caesarean section with infant epigenetic AA. Using the Horvath’s method, DNA methylation age can be fairly accurately predicted from saliva samples already in the first months of life. This study did not reveal clear associations between either pregnancy outcomes or parental socio-economic characteristics and infant saliva epigenetic AA.
As an epigenetic modification, DNA methylation may reflect the interaction between genetic and environmental factors in the development of schizophrenia (SCZ). Catechol-O-methyltransferase (COMT) gene is a promising candidate gene of SCZ. In the present study, we investigate the association of COMT methylation with the risk of SCZ using bisulfite pyrosequencing technology. Significant association between DNA methylation of COMT and the risk of SCZ is identified (P = 1.618e−007). A breakdown analysis by gender shows that the significance is driven by males (P = 3.310e−009), but not by females. DNA methylation of COMT is not significantly associated with SCZ clinical phenotypes, including p300 and cysteine level. No interaction is found between COMT genotypes and the percent methylation of this gene. Receiver operating characteristic (ROC) curve shows that DNA methylation of COMT is able to predict the SCZ risk in males (area under curve [AUC] = 0.802, P = 1.91e−007). The current study indicates the clinical value of COMT methylation as a potential male-specific biomarker in SCZ diagnosis.
Disruption of physiological aging of the placenta can lead to pregnancy complications and increased risk for cardiometabolic diseases during childhood and adulthood. Maternal metabolic and genetic factors need to operate in concert with placental development for optimal pregnancy outcome. However, it is unknown whether maternal cardiometabolic status and genetic ancestry contribute to differences in placental epigenetic age acceleration (PAA). We investigated whether maternal prepregnancy obesity, gestational weight gain (GWG), blood pressure, and genetic ancestry influence PAA. Among 301 pregnant women from 4 race/ethnic groups who provided placenta samples at delivery as part of the National Institute of Child Health and Human Development Fetal Growth Studies, placental DNA methylation age was estimated using 62 CpGs known to predict placental aging. PAA was defined to be the difference between placental DNA methylation age and gestational age at birth. Percentage of genetic ancestries was estimated using genotype data. We found that a 1 kg/week increase in GWG was associated with up to 1.71 (95% CI: −3.11, −0.32) week lower PAA. Offspring Native American ancestry and African ancestry were associated, respectively, with higher and lower PAA among Hispanics, and maternal East Asian ancestry was associated with lower PAA among Asians (p < 0.05). Among mothers with a male offspring, blood pressure was associated with lower PAA across all three trimesters (p < 0.05), prepregnancy obesity compared to normal weight was associated with 1.24 (95% CI: −2.24, −0.25) week lower PAA. In summary, we observed that maternal cardiometabolic factors and genetic ancestry influence placental epigenetic aging and some of these influences may be male offspring-specific.
Increased fat and carbohydrate intakes based on the Western diet are important lifestyle modifications that lead to hypercaloric inputs, obesity, and male fertility negative effects. Epigenetic transmission may also predispose descended generations to chronic diseases, such as obesity, type 2 diabetes, behavioral, and reproductive disorders. The present study sought to evaluate the influence of a high-fat-high-sugar (HFHS) diet supplied to Wistar rats from 25 to 90 days of life on reproductive and metabolic parameters in male generations F0, F1, and F2. The standard group received the normocaloric – Nuvilab Quimtia® –3.86 kcal/kg. The hypercaloric diet (HD) group received the HFHS diet – PragSoluções® –4.77 kcal/kg. Body weight, adiposity, F1 and F2 prepubertal age evaluations, oral glucose tolerance test, insulin tolerance test, organ weights, sperm count and morphology assessments, and histometric testicular analyses were performed. The HFHS diet promoted dyslipidemia, higher adiposity, lower relative organ weights, and higher mean kidney weight, decreased mean testicle and parenchyma weights and lower height of seminiferous epithelium (HE) for the F0 generation. F1 and F2 offspring of HD group displayed early preprepubertal development, although did not alter the metabolic parameters. Decreased HE and tubular testicular compartment volumetric density and increased intertubular testicular compartment volumetric density and volume in the F1 generation of HD group were observed. Alterations in histometry of intertubular testicular compartment were also noted. It is concluded that the HFHS experimental model altered only paternal metabolic parameters. However, reproductive parameters of the three generations were affected.
Twin studies are one of the main tools for studying the interaction between genes and the environment in the development of complex diseases such as cancers, cardiovascular diseases and diabetes. The Isfahan Twin Registry (ITR) was launched in Isfahan in 2017 as a pilot study to establish a nationwide twin registry in Iran and aims to obtain comprehensive information about complex diseases and their risk factors from twins and multiples living in Isfahan. ITR will continue to recruit twins and multiples until all twins residing in Isfahan are registered in the registry. Twins are identified from welfare agencies, public health homes, maternity hospitals, Persian Twins Association and the local media. Demographic information, twin similarities, lifestyle, family history of diseases and past medical history are collected using validated questionnaires. Anthropometric measurements and blood pressure are measured by health professionals. Hematology panel, fasting blood sugar, total cholesterol, low-density lipoprotein, high-density lipoprotein, aspartate aminotransferase, alanine aminotransferase and quantitative C-reactive protein are measured by an automated analyzer. Extra samples are obtained for future studies. For twins aged under 6 years, parents complete the questionnaires for their children and a brief questionnaire for themselves. Currently, 998 persons (395 pairs and 67 multiples) are registered in the ITR and have provided their data. Results of preliminary data analysis are discussed in this article. We plan to carry out longitudinal assessments. ITR can play an important role in future epigenetic, biomarkers and omics studies using the biobank materials.
Minor and major zygotic genome activation (ZGA) are crucial for preimplantation development. During this process, histone variants and methylation influence chromatin accessibility and consequently regulated the expression of zygotic genes. However, the detailed exchanges of these modifications during ZGA remain to be determined. In the present study, the epigenetic modifications of histone 3 on lysine 9 (H3K9), 27 (H3K27) and 36 (H3K36), as well as four histone variants were determined during minor and major ZGA and in post-ZGA stages of mouse embryos. Firstly, microH2A1, H3K27me3 and H3K36me3 were asymmetrically stained in the female pronucleus during minor ZGA but lost staining in major ZGA. Secondly, H3K9me2 and H3K9me3 were strongly stained in the female pronucleus, but weakly stained in the male pronucleus and disappeared after ZGA. Thirdly, H2A.Z and H3.3 were symmetrically stained in male and female pronuclei during minor ZGA. Moreover, H3K27me2 was not statistically changed during mouse early development, while H3K36me2 was only detected in 2- and 4-cell embryos. In conclusion, our data revealed dynamics of histone methylation and variants during mice ZGA and provided details of their exchange in mice embryogenesis. Moreover, we further inferred that macroH2A1, H2A.Z, H3K9me2/3 and H3K27me2/3 may play crucial roles during mouse ZGA.
Male germ cell development is a critical period during which epigenetic patterns are established and maintained. The progression from diploid spermatogonia to haploid spermatozoa involves the incorporation of testis-specific histone variants, mitotic and meiotic divisions, haploid gene expression, histone–protamine transitions and massive epigenetic reprogramming. Understanding the protein players and the epigenetic mark network involved in the setting of the epigenetic programme in spermatogenesis is an exciting new clue in the field of reproductive biology with translational outcomes. As information in the existing literature regarding cross-talk between DNA methylation and histone hyperacetylation in the advanced stages of murine spermatogenesis is still scarce and controversial we have investigated the effect of a DNA-methyltransferase inhibitor, 5-aza-2′-deoxycytidine, at the cytological and molecular level (by transmission electron microscopy, immunocytochemistry and immunoprecipitation methods). Our results revealed an important role for regulation of DNA methylation in controlling histone hyperacetylation and chromatin remodelling during spermatogenesis.
It is well documented that the mother plant has much more influence than the father on seed dormancy/germination, especially of the F1 offspring, primarily by providing all material (maternally derived tissue) to the diaspore coat(s); by maternal environmental effects and provisioning of nutrient resources, mRNA transcripts, protein, the hormone abscisic acid and nitrate to the seed during its development; and by determining progeny environment via dispersal and phenology. There is some evidence that the paternal influence on seed dormancy/germination of the offspring (seeds) can be mediated through multiple paternity (including mate number and diversity), non-nuclear (cytoplasmic) and nuclear (genotypic) inheritance and paternal environmental effects. Our primary aim was to determine via a literature review the influence (or not) of the paternal parent on seed germination. Altogether, 37 of 59 studies (62.7%) indicated a positive influence of the father on seed germination, although not all of them were statistically significant. In general, however, results of studies reported in the literature do not offer strong support for the paternal parent having a major role in seed germination (or seed size) of his F1 offspring.
Posttraumatic stress disorder (PTSD) and stress/trauma exposure are cross-sectionally associated with advanced DNA methylation age relative to chronological age. However, longitudinal inquiry and examination of associations between advanced DNA methylation age and a broader range of psychiatric disorders is lacking. The aim of this study was to examine if PTSD, depression, generalized anxiety, and alcohol-use disorders predicted acceleration of DNA methylation age over time (i.e. an increasing pace, or rate of advancement, of the epigenetic clock).
Genome-wide DNA methylation and a comprehensive set of psychiatric symptoms and diagnoses were assessed in 179 Iraq/Afghanistan war veterans who completed two assessments over the course of approximately 2 years. Two DNA methylation age indices (Horvath and Hannum), each a weighted index of an array of genome-wide DNA methylation probes, were quantified. The pace of the epigenetic clock was operationalized as change in DNA methylation age as a function of time between assessments.
Analyses revealed that alcohol-use disorders (p = 0.001) and PTSD avoidance and numbing symptoms (p = 0.02) at Time 1 were associated with an increasing pace of the epigenetic clock over time, per the Horvath (but not the Hannum) index of cellular aging.
This is the first study to suggest that posttraumatic psychopathology is longitudinally associated with a quickened pace of the epigenetic clock. Results raise the possibility that accelerated cellular aging is a common biological consequence of stress-related psychopathology, which carries implications for identifying mechanisms of stress-related cellular aging and developing interventions to slow its pace.
The use of assisted reproductive technologies (ART) has increased significantly, allowing many coping with infertility to conceive. However, an emerging body of evidence suggests that ART could carry epigenetic risks for those conceived through the use of these technologies. In accordance with the Developmental Origins of Health and Disease hypothesis, ART could increase the risk of developing late-onset diseases through epigenetic mechanisms, as superovulation, fertilization methods and embryo culture could impair the embryo’s epigenetic reprogramming. Such epigenetic risks raise ethical issues for all stakeholders: prospective parents and children, health professionals and society. This paper focuses on ethical issues raised by the consideration of these risks when using ART. We apply two key ethical principles of North American bioethics (respect for autonomy and non-maleficence) and suggest that an ethical tension may emerge from conflicting duties to promote the reproductive autonomy of prospective parents on one hand, and to minimize risks to prospective children on the other. We argue that this tension is inherent to the entire enterprise of ART and thus cannot be addressed by individual clinicians in individual cases. We also consider the implications of the ‘non-identity problem’ in this context. We call for additional research that would allow a more robust evidence base for policy. We also call upon professional societies to provide clinicians with guidelines and educational resources to facilitate the communication of epigenetic risks associated with ART to patients, taking into consideration the challenges of communicating risk information whose validity is still uncertain.
Medically assisted reproductive technologies, such as in vitro embryo production, are increasingly being used to palliate infertility. Eggs are produced following a hormonal regimen that stimulates the ovaries to produce a large number of oocytes. Collected oocytes are then fertilized in vitro and allowed to develop in vitro until they are either frozen or transferred to mothers. There are controversial reports on the adverse impacts of these technologies on early embryos and their potential long-term effects. Using newly developed technological platforms that enable global gene expression and global DNA methylation profiling, we evaluated gene perturbations caused by such artificial procedures. We know that cells in the early embryo produce all cells in the body and are able to respond to their in vitro environment. However, it is not known whether gene perturbations are part of a normal response to the environment or are due to distress and will have long-term impacts. While the mouse is an established genetic model used for quality control of culture media in clinics, the bovine is a large mono-ovulating mammal with similar embryonic kinetics as humans during the studied developmental window. These model systems are critical to understand the effects of assisted reproduction without the confounding impact of infertility and without the limitations imposed by the scarcity of donated human samples and ethical issues. The data presented in this review come mostly from our own experimentation, publications, and collaborations. Together they demonstrate that the in vitro environment has a significant impact on embryos at the transcriptomic level and at the DNA methylation level.
Organic pollutants are present in drinking waters due to inefficient detection and removal treatments. For this reason, zebrafish is proposed as a complementary indicator in conventional potabilization treatments. Based on the most sensitive parameters detected in our previous work, in this study we attempted to examine the possible cumulative effect between generations of environmental pollutants likely present in drinking waters, when specimens were cultured in the same water and/or the possible reversibility of these effects when cultured in control water. To this end, embryos with the chorion intact were cultured in three drinking waters from different sources and in one control water for up to 5 months in 20 l glass tanks. Four replicates were performed in all water groups. Results in water group C (tap water from a city also located in a region with intensive agricultural activity, but from the hydrological basin of the river Xúquer) revealed a non-reversible effect on fertility rate. Also in water C there was an alteration of sex ratio towards females, although in this case the alteration was reversible. A transgenerational alteration in the germ-line via an epigenetic mechanism from the previous generation is proposed as the most plausible explanation of this effect.
Stress based on high temperature and humidity reduces the production performance of fast-growing broilers and causes high mortality. Temperatures higher than optimum have been applied to broilers in the embryonic period in order to overcome thermal stress. This study was conducted to investigate the effects of exposure to two long-term high-thermal environments on the developmental stability of embryonic growth, hatchability and chick quality. For this purpose, 600 broiler eggs were incubated. Treatments consisted of eggs incubated at 37.8°C at 55% relative humidity throughout (control), heated to 39.6°C at 60% relative humidity for 6 h daily from 0 to 8th day, and heated to 39.6°C at 60% relative humidity for 6 h daily from the 10 to 18th day. Embryo weights and lengths of face, wing, femur, tibia and metatarsus were measured daily between the 10th and 21st day of the experiment. Daily relative asymmetry values of bilateral traits were estimated. The hatchability, the weight of the 1-day-old chicks and chick quality were determined. In conclusion, no negative effects of the treatments of the long-term high-thermal environment in the early and late stages of incubation for epigenetic adaptation were determined on the embryo morphology, development stability and weight of the chick. Moreover, regressed hatchability of embryos that were exposed to a long-term high-thermal environment was detected. Especially between the 10 and 18th day, the thermal manipulation considerably reduced the quality of the chicks. Acclimation treatments of high temperature on the eggs from cross-breeding flocks should not be made long term; instead, short-term treatments should be made by determining the stage that generates epigenetic adaptation.
The loss of estrogen during menopause causes changes in the female body, with wide-ranging effects on health. Estrogen-containing hormone replacement therapy (HRT) leads to a relief of typical menopausal symptoms, benefits bone and muscle health, and is associated with tissue-specific gene expression profiles. As gene expression is controlled by epigenetic factors (including DNA methylation), many of which are environmentally sensitive, it is plausible that at least part of the HRT-associated gene expression is due to changes in DNA methylation profile. We investigated genome-wide DNA methylation and gene expression patterns of white blood cells (WBCs) and their associations with body composition, including muscle and bone measures of monozygotic (MZ) female twin pairs discordant for HRT. We identified 7,855 nominally significant differentially methylated regions (DMRs) associated with 4,044 genes. Of the genes with DMRs, five (ACBA1, CCL5, FASLG, PPP2R2B, and UHRF1) were also differentially expressed. All have been previously associated with HRT or estrogenic regulation, but not with HRT-associated DNA methylation. All five genes were associated with bone mineral content (BMC), and ABCA1, FASLG, and UHRF1 were also associated with body adiposity. Our study is the first to show that HRT associates with genome-wide DNA methylation alterations in WBCs. Moreover, we show that five differentially expressed genes with DMRs associate with clinical measures, including body fat percentage, lean body mass, bone mass, and blood lipids. Our results indicate that at least part of the known beneficial HRT effects on body composition and bone mass may be regulated by DNA methylation associated alterations in gene expression in circulating WBCs.
This study was conducted to investigate the effect of in ovo feeding (IOF) of folic acid on the folate metabolism, immune function and the involved epigenetic modification of broilers. A total of 400 (Cobb) hatching eggs were randomly divided into four groups (0, 50, 100 and 150 µg injection of folic acid at embryonic age 11 d), and chicks hatched from each treatment were randomly divided into six replicates with 12 broilers/replicate after incubation. The results indicated that, in ovo, 100- and 150-µg folic acid injections improved the hatchability. The average daily gain and feed conversion ratio increased in the 150-µg group during the late growth stage. Simultaneously, in the 100- and 150-µg groups, an increase was observed in hepatic folate content and the expression of methylenetetrahydrofolate reductase (d1 and 42) and methionine synthase reductase (d21). IgG and IgM concentrations, as well as plasma lysozyme activity of broilers, showed a marked increase along with increasing folic acid levels. The splenic expression levels of IL-2 and IL-4 were up-regulated, whereas that of IL-6 was down-regulated, in the 100- and 150-µg folic acid treatment groups. In addition, histone methylation in IL-2 and IL-4 promoters exhibited an enrichment of H3K4m2 but a loss of H3K9me2 with the increased amount of folic acid additive. In contrast, a decrease in H3K4m2 and an increase in H3K9me2 were observed in the IL-6 promoter in folic acid treatments. Furthermore, in ovo, the 150-µg folic acid injection improved the chromatin tightness of the IL-2 and IL-4 promoter regions. Our findings suggest that IOF of 150 µg of folic acid can improve the growth performance and folate metabolism of broilers, and enhance the relationship between immune function and epigenetic regulation of immune genes, which are involved with the alterations in chromatin conformation and histone methylation in their promoters.
Asthma is a common childhood disease and several risk factors have been identified; however, the impact of genes and environment is not fully understood. The aim of the Swedish Twin study On Prediction and Prevention of Asthma (STOPPA) is to identify environmental (birth characteristics and early life) and genetic (including epigenetic) factors as determinants for asthmatic disease. Based on the Child and Adolescent Twin Study in Sweden (CATSS) (parental interview at 9 or 12 years, N ~23,900) and an asthma and/or wheezing algorithm, we identified a sample of monozygotic (MZ) and dizygotic (DZ) same-sexed twin pairs. The twin pairs were classified as asthma concordant (ACC), asthma discordant (ADC) and healthy concordant (HCC). A sample of 9- to 14-year-old twins and their parents were invited to participate in a clinical examination. Background characteristics were collected in questionnaires and obtained from the National Health Registers. A clinical examination was performed to test lung function and capacity (spirometry with reversibility test and exhaled nitric oxide) and collect blood (serology and DNA), urine (metabolites), feces (microbiota), and saliva (cortisol). In total, 376 twin pairs (752 individual twins) completed the study, response rate 52%. All participating twins answered the questionnaire and >90% participated in lung function testing, blood-, and saliva sampling. This article describes the design, recruitment, data collection, measures, and background characteristics, as well as ongoing and planned analyses in STOPPA. Potential gains of the study include the identification of biomarkers, the emergence of candidates for drug development, and new leads for prevention of asthma and allergic disease.
An epigenetic mechanism has been suggested to explain the effects of the maternal diet on the development of disease in offspring. The present study aimed to observe the effects of a maternal high-lipid, high-energy (HLE) diet on the DNA methylation pattern of male offspring in mice. Female C57BL/6J mice were fed an HLE diet during gestation and lactation. The genomic DNA methylations at promoter sites of genes in the liver, mRNA and protein levels of selected genes related to lipid and glucose metabolism were measured by microarray, real-time PCR and Western blot. The results indicated that the percentage of methylated DNA in offspring from dams that were fed an HLE diet was significantly higher than that from dams that were fed a chow diet, and most of these genes were hypermethylated in promoter regions. The nuclear protein content and mRNA levels of hypermethylated genes, such as PPARγ and liver X receptor α (LXRα), were decreased significantly in offspring in the HLE group. The results suggested that the DNA methylation profile in adult offspring livers was changed by the maternal HLE diet during gestation and lactation.
Telomeres are specialised nucleoprotein end structures of eukaryotic chromosomes and protect and maintain genome integrity from recombination, exonuclease degradation and end-to-end fusion. Because of the end replication problem, telomere length in somatic cells tends to decrease with organismal age. Telomere shortening is known to occur in chicken somatic tissues and correlates with advanced developmental age. However, age is not the only determinant of telomere length in an individual. Several factors at the genetic and epigenetic levels are known to affect telomere length in different ways. Herein, we review several factors that affect telomere length in the chicken. Genetic factors include breed and sex, while the epigenetic factors include environmental and stochastic influences. Age, stocking density and living or housing systems were reviewed as environmental factors pertaining to the habitat of the organism. Factors such as oxidative stress, antioxidants in feed and restriction feeding were the stochastic factors that we reviewed.
Adult canine fibroblasts stably transfected with either cytomegalovirus (CMV) or POU5F1 promoter-driven enhanced green fluorescent protein (EGFP) were used to investigate if pre-treatment of these donor cells with two epigenetic drugs [trichostatin A (TSA), or S-adenosylhomocysteine (SAH)] can improve the efficiency of interspecies somatic cell nuclear transfer (iSCNT). Fluorescence-activated cell sorting (FACS), analyses revealed that TSA, but not SAH, treatment of both transgenic and non-transgenic fibroblasts significantly increased acetylation levels compared with untreated relatives. The expression levels of Bcl2 and P53 were significantly affected in TSA-treated cells compared with untreated cells, whereas SAH treatment had no significant effect on cell apoptosis. Irrespective of epigenetic modification, dog/bovine iSCNT embryos had overall similar rates of cleavage and development to 8–16-cell and morula stages in non-transgenic groups. For transgenic reconstructed embryos, however, TSA and SAH could significantly improve development to 8–16-cell and morula stages compared with control. Even though, irrespective of cell transgenesis and epigenetic modification, none of the iSCNT embryos developed to the blastocyst stage. The iSCNT embryos carrying CMV–EGFP expressed EGFP at all developmental stages (2-cell, 4-cell, 8–16-cell, and morula) without mosaicism, while no POU5F1–EGFP signal was observed in any stage of developing iSCNT embryos irrespective of TSA/SAH epigenetic modifications. These results indicated that bovine oocytes partially remodel canine fibroblasts and that TSA and SAH have marginal beneficial effects on this process.