Dynamic Changes In DNA Methylation Research Articles

Genome-wide high-resolution mapping of DNA methylation reveals epigenetic variation in the offspring of sexual and asexual propagation in Robinia pseudoacacia.

We detected the genome-wide pattern of DNA methylation and its association with gene expression in sexual and asexual progenies of mature Robinia pseudoacacia trees. DNA methylation plays an important role in plant reproduction and development. Although some studies on sexual reproduction have been carried out in model plants, little is known about the dynamic changes in DNA methylation and their effect on gene expression in sexual and asexual progeny of woody plants. Here, through whole-genome bisulfite sequencing, we revealed DNA methylation patterns in the sexual and asexual progenies of mature Robinia pseudoacacia to understand the regulation of gene expression by DNA methylation in juvenile seedlings. An average of 53% CG, 34% CHG and 5% CHH contexts was methylated in the leaves of mature and juvenile individuals. The CHH methylation level of asexually propagated seedlings was significantly lower than that of seed-derived seedlings and mature trees. The intergenic regions had the highest methylation level. Analysis of differentially methylated regions (DMRs) showed that most of them were hypermethylated and located in the gene upstream and introns. A total of 24, 108 and 162 differentially expressed genes containing DMRs were identified in root sprouts (RSs), root cuttings (RCs) and seed-derived seedlings (SSs), respectively, and a large proportion of them showed hypermethylation. In addition, DMRs were enriched within GO subcategories including catalytic activity, metabolic process and cellular process. The results reveal widespread DNA methylation changes between mature plants and their progenies through sexual/asexual reproduction, which provides novel insights into DNA methylation reprogramming and the regulation of gene expression in woody plants.

DNA methylation dynamics of long noncoding RNA during human fetal development.

Aim: To determine whether the promoters of long noncoding RNAs (lncRNAs) undergo dynamic changes in DNA methylation during fetal development. Methods: ANOVA and the tissue specificity index were used to identify and validate tissue-specific methylation sites. Age-associated DNA methylation signatures were identified by applying the elastic net method. Results: The lncRNA methylome landscape was characterized in four types of fetal tissue and at three gestational time points, and specific characteristics relative to the tissue of origin and developmental age were identified. Higher levels of lncRNA methylation might be involved in tissue differentiation. LncRNAs harboring age-associated methylation signatures mayparticipate in the fetal developmental process. Conclusion: This study provides novel insights into the role of lncRNA methylomes in fetal tissue specification and development.

The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles.

In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.

Characterization of DNA Methylomic Signatures in Induced Pluripotent Stem Cells During Neuronal Differentiation.

In development, differentiation from a pluripotent state results in global epigenetic changes, although the extent to which this occurs in induced pluripotent stem cell-based neuronal models has not been extensively characterized. In the present study, induced pluripotent stem cell colonies (33Qn1 line) were differentiated and collected at four time-points, with DNA methylation assessed using the Illumina Infinium Human Methylation EPIC BeadChip array. Dynamic changes in DNA methylation occurring during differentiation were investigated using a data-driven trajectory inference method. We identified a large number of Bonferroni-significant loci that showed progressive alterations in DNA methylation during neuronal differentiation. A gene–gene interaction network analysis identified 60 densely connected genes that were influential in the differentiation of neurons, with STAT3 being the gene with the highest connectivity.

Dynamic changes in transposable element and gene methylation in mulberry (Morus notabilis) in response to Botrytis cinerea

DNA methylation has been proposed to regulate plant stress resistance. However, the dynamic changes in DNA methylation in woody plants and their correlations with pathogenic responses are not fully understood. Here, we present single-base maps of the DNA methylomes of mulberry (Morus notabilis) leaves that were subjected to a mock treatment or inoculation with Botrytis cinerea. Compared with the former, the latter showed decreased mCG and mCHG levels and increased mCHH levels. DNA methylation inhibitors reduced resistance gene methylation levels and enhanced mulberry resistance, suggesting that the hypomethylation of resistance genes affects mulberry resistance to B. cinerea. Virus-induced gene silencing of MnMET1 enhanced the expression of mulberry-resistance genes, thereby increasing the plant’s resistance to B. cinerea. We also found that MITEs play a dominant role in controlling DNA methylation levels. MITEs appear to be the main sources of 24-nt siRNAs that regulate gene expression through the RNA-directed DNA methylation pathway.

ZFP36L1, a Novel Potential Tumor Supressor Gene in Myelofibrosis, Epigenetically Deregulated By Methylation of the Enhancer Region

IntroductionMyelofibrosis (MF) is known for frequent alterations in genes involved in epigenetic machinery, particularly in the regulation of DNA methylation. Enhancer regions experience changes in DNA methylation throughout myelopoiesis and may also experience aberrant DNA methylation in hematologic neoplasms, leading to altered expression of relevant genes. We aim to describe the DNA methylome of MF focusing on dynamic changes of DNA methylation in enhancer-regions, in order to identify new potential gene candidates with epigenetic deregulation who might have a role in the pathogenesis of MF and become therapeutic targets for this disease.MethodsDNA methylation profiles of 39 MF samples compared to 8 healthy controls were analysed using the Infinum Human-methylation 450K BeadChip platform. Differentially methylated CpG dinucleotides (DMCs) were validated with bisulfite sequencing. Enhancer regions were defined using publicly available data from the ChromHMM algorithm (H3K27Ac and H3K4Me3; Wijetunga, Nat Comm, 2014;5:5195). DNA methylation of DMCs mapped to enhancer regions was correlated to public gene expression datasets (GSE26049). The subgroup of genes with hypermethylated enhancers and downregulated expression was further studied, selecting candidate genes for epigenetic regulation through enhancer DNA methylation. Luciferase reporter assay using a CpG-free vector (pCPGL) was performed to confirm the functional effect of hypermethylated enhancers. SET2 cell line (JAK2V617F mutated) was used as in vitro model for pharmacologic treatment and lentiviral induction of selected gene candidates.ResultsWe found a total of 35216 differentially methylated CpGs (DMCs) between MF and controls (FDR <0.05). DMCs were significantly enriched to enhancer regions accounting for 8764 probes (24.8%; p<0.001 vs global DMC). 4182 enhancer-specific DMCs were hypermethylated (27.6%), comprising 2131 genes, whereas the remaining 10936 enhancer DMC were hypomethylated. Among genes showing reduced expression and enhancer hypermethylation in MF samples, we identified the ZFP36L1 gene as potential candidate. Moreover, gene targets of ZFP36L1 showed a significant enrichment among the genes overexpressed in MF indicating that ZFP36L1 downregulation could play an important role in MF. A novel algorithm to search for genes with putative 5´UTR AU rich elements was used (DREME motif discovery algorithm; E-value=4.5*10-15).We detectedabsence of DNA methylation in the promoter region of ZFP36L1 in SET2 cell line, MF samples and healthy controls, whereas the enhancer region showed intermediate DNA methylation in healthy controls and hypermethylation in SET2 and MF samples. DNA hypermethylation of the enhancer correlated with reduced ZFP36L1 gene expression (p<0.05). 5-azacytidine partially rescued ZFP36L1 expression in SET2 cell line, which was associated with a reduction of enhancer DNA methylation. Luciferase reporter assays with the pCPGL-vector showed that DNA methylation of the ZFP36L1 enhancer region abrogated the luciferase activity, demonstrating for the first time that this enhancer region regulates the expression of ZFP36L1 in MF.Finally, we demonstrated that lentiviral induction of ZFP36L1 in SET2 cell line, significantly reduced cell proliferation and increased apoptosis (Annexin V). We observed similar results by treatment of SET2 cells with PMA, a known inductor of ZFP36L1 . Additionally, we found that rescue of ZFP36L1 expression was associated with a decrease in CDK6, suggesting a potential role of ZFP36L1-CDK6 axis in the pathogenesis of MF.ConclusionWe detected a significant inappropriate DNA methylation of enhancer regions in MF, showing a novel pathogenetic mechanism for this disease that might be extrapolated to other haematologic malignancies. Aberrant DNA methylation of enhancer regions affects genes with potential functional implications. ZFP36L1 is an example of this phenomenon, harbouring DNA hypermethylation of the enhancer region and constituting a potential tumour suppressor gene with inappropriate epigenetic silencing. ZFP36L1 might be relevant for the control of cell cycle progression in MF through modulation of the expression of CDK6 . DisclosuresNo relevant conflicts of interest to declare.

Dynamic changes in DNA methylation occur in TE regions and affect cell proliferation during leaf-to-callus transition in Arabidopsis

ABSTRACT Plant somatic cells can be reprogrammed into pluripotent cell mass, called callus, through a two-step in vitro tissue culture method. Incubation on callus-inducing medium triggers active cell proliferation to form a pluripotent callus. Notably, DNA methylation is implicated during callus formation, but a detailed molecular process regulated by DNA methylation remains to be fully elucidated. Here, we compared genome-wide DNA methylation profiles between leaf and callus tissues in Arabidopsis using whole-genome bisulphite-sequencing. Global distribution of DNA methylation showed that CHG methylation was increased, whereas CHH methylation was reduced especially around transposable element (TE) regions during the leaf-to-callus transition. We further analysed differentially expressed genes around differentially methylated TEs (DMTEs) during the leaf-to-callus transition and found that genes involved in cell cycle regulation were enriched and also constituted a coexpression gene network along with pluripotency regulators. In addition, a conserved DNA sequence analysis for upstream cis-elements led us to find a putative transcription factor associated with cell fate transition. CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) was newly identified as a regulator of plant regeneration, and consistently, the cca1lhy mutant displayed altered phenotypes in callus proliferation. Overall, these results suggest that DNA methylation coordinates cell cycle regulation during callus formation, and CCA1 may act as a key upstream coordinator at least in part in the processes.

Polyglutamine-expanded ataxin3 alter specific gene expressions through changing DNA methylation status in SCA3/MJD.

DNA methylation has recently been linked to transcriptional dysregulation and neuronal dysfunction in polyglutamine (polyQ) disease. This study aims to determine whether (CAG)n expansion in ATXN3 perturbs DNA methylation status and affects gene expression. We analyzed DNA methylation throughout the genome using reduced representation bisulfite sequencing (RRBS) and confirmed the results using MethylTarget sequencing. Dynamic changes in DNA methylation, transcriptional and translational levels of specific genes were detected using BSP, qRT-PCR and western blot. In total, 135 differentially methylated regions (DMRs) were identified between SCA3/MJD and WT mouse cerebellum. KEGG analysis revealed differentially methylated genes involved in amino acid metabolism, Hedgehog signaling pathway, thyroid cancer, tumorigenesis and other pathways. We focused on DMRs that were directly associated with gene expression. On this basis, we further assessed 7 genes, including 13 DMRs, for DNA methylation validation and gene expression. We found that the methylation status of the DMRs of En1 and Nkx2-1 was negatively associated with their transcriptional and translational levels and that alteration of the DNA methylation status of DMRs and the corresponding transcription occurred before dyskinesia in SCA3/MJD mice. These results revealed novel DNA methylation-regulated genes, En1 and Nkx2-1, which may be useful for understanding the pathogenesis of SCA3/MJD.

Dynamic DNA methylation changes in early versus late adulthood suggest nondeterministic effects of childhood adversity: a meta-analysis.

Adverse childhood experiences (ACEs) are associated with a high risk of developing chronic diseases and decreased life expectancy, but no ACE epigenetic biomarkers have been identified until now. The latter may result from the interaction of multiple factors such as age, sex, degree of adversity, and lack of transcriptional effects of DNA methylation changes. We hypothesize that DNA methylation changes are related to childhood adversity levels and current age, and these markers evolve as aging proceeds. Two Gene Expression Omnibus datasets, regarding ACE, were selected (GSE72680 and GSE70603), considering raw- and meta-data availability, including validated ACE index (Childhood Trauma Questionnaire (CTQ) score). For DNA methylation, analyzed probes were restricted to those laying within promoters and first exons, and samples were grouped by CTQ scores terciles, to compare highly (ACE) with non-abused (control) cases. Comparison of control and ACE methylome profile did not retrieve differentially methylated CpG sites (DMCs) after correcting by false discovery rate < 0.05, and this was also observed when samples were separated by sex. In contrast, grouping by decade age ranges (i.e., the 20s, 30s, 40s, and 50s) showed a progressive increase in the number of DMCs and the intensity of changes, mainly related with hypomethylation. Comparison with transcriptome data for ACE subjects in the 40s, and 50s showed a similar age-dependent effect. This study provides evidence that epigenetic markers of ACE are age-dependent, but not defined in the long term. These differences among early, middle, and late adulthood epigenomic profiles suggest a window for interventions aimed to prevent the detrimental effects of ACE.

Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation

Congenital heart disease (CHD), the leading birth defect worldwide, has a largely unknown etiology, likely to result from complex interactions between genetic and environmental factors during heart development, at a time when the heart adapts to diverse physiological and pathophysiological conditions. Crucial among these is the regulation of cardiomyocyte development and postnatal maturation, governed by dynamic changes in DNA methylation. Previous work from our laboratory has shown that exposure to the environmental toxicant tetrachlorodibenzo-p-dioxin (TCDD) disrupts several molecular networks responsible for heart development and function. To test the hypothesis that the disruption caused by TCDD in the heart results from changes in DNA methylation and gene expression patterns of cardiomyocytes, we established a stable mouse embryonic stem cell line expressing a puromycin resistance selectable marker under control of the cardiomyocyte-specific Nkx2-5 promoter. Differentiation of these cells in the presence of puromycin induces the expression of a large suite of cardiomyocyte-specific markers. To assess the consequences of TCDD treatment on gene expression and DNA methylation in these cardiomyocytes, we subjected them to transcriptome and methylome analyses in the presence of TCDD. Unlike control cardiomyocytes maintained in vehicle, the TCDD-treated cardiomyocytes showed extensive gene expression changes, with a significant correlation between differential RNA expression and DNA methylation in 111 genes, many of which are key elements of pathways that regulate cardiovascular development and function. Our findings provide an important clue toward the elucidation of the complex interactions between genetic and epigenetic mechanisms after developmental TCDD exposure that may contribute to CHD.

Is Any Cardiovascular Disease-Specific DNA Methylation Biomarker Within Reach?

A detailed understanding of the epigenome of cardiovascular disease (CVD) should broaden current insights into mechanisms of atherogenesis and help identify suitable biomarkers for disease risk and progression. This review addresses the question whether a consensus has been reached on identifying the main aberrant DNA methylation profile in CVD. Additionally, it presents advances and setbacks in the search for specific CVD biomarkers. Although the literature points to DNA hypermethylation as an epigenetic landmark of CVD, inconsistencies are significant. In particular, the DNA methylomes of peripheral blood cells and the vascular wall do not show a consistent direction of change in all studies. An additional significant hurdle is the relatively low study-to-study reproducibility and the difficulty to assess specificity for CVD. Nonetheless, a number of biologically plausible markers have been proposed that warrant further studies. An integrated model for dynamic changes of DNA methylation during the natural history of atherosclerosis predisposition and progression is presented, that might reconcile conflicting findings. Cohort design and technical criteria for DNA methylation analysis need to be further homogenized to allow for meaningful validation. As stable DNA methylation profiles are likely determined by genetic variants, many of which might control a range of diseases, it is anticipated that CVD biomarker discovery will be a delicate balancing act between reproducibility and specificity.

Abstract 140: Deregulated genes by abnormal promoter methylation in early and late stages in a linear model of melanoma progression

Abstract Metastatic melanomas are extremely aggressive tumors, accounting for 70% of skin cancer deaths, which incidence is increasing globally. Despite the advances in their treatment, metastatic melanomas are still associated with a poor prognosis, with a median survival of 6 to 12 months. The study of the molecular alterations affecting key pathways during melanoma progression may contribute to a better understanding of the biology underlying the aggressiveness of the disease and lead to the identification of biomarkers for prognosis and novel targets for therapy. In addition to mutations, epigenetic alterations are important contributors to malignant transformation and tumor progression. Aberrant DNA methylation is an epigenetic hallmark of cancer, known to play important roles in melanoma development. Although different genes were described as presenting methylation alterations in their promoters in melanomas, the dynamics of these alterations along melanocyte malignant transformation and melanoma progression is still unclear. Our laboratory developed a linear model of melanoma progression in which different pre-malignant and melanoma cell lines were established after subjecting murine melanocytes to a sustained stressful condition (adhesion impediment). In this study, we used the spontaneously immortalized melanocyte lineage (melan-a); pre-malignant melanocytes (4C), obtained after subjecting melan-a cells to 4 cycles of adhesion impediment; a non-metastatic tumorigenic cell line (4C11-), obtained after a limiting dilution of spheroids formed by 4C adhesion impediment; and a metastatic cell line (4C11+), resulting from the spontaneously loss of p53 by 4C11- cells. The aim of this work was to identify genes that have their expression altered by promoter and gene body methylation that are related to the malignant transformation of melanocytes and metastasis. Through the integrative analysis of methylome (ERRBS) with transcriptome (RNAseq) data, it was possible to identify the dynamic changes in DNA methylation in promoters and gene bodies, and their relation with gene expression in both early and late stages of melanoma progression. Among those genes are Foxd1, Lrrk2, Adcy1 and Adcy3, which had their expression validated by qPCR, and their epigenetic regulation validated by the treatment of the cells with epigenetic drugs (5-aza-2'-deoxycytidine and Trichostatin A). The gene expression and promoter methylation profiles found in the murine model of melanoma progression were correlated with clinical data from melanoma patients available in cancers cohorts, revealing potential novel prognostic markers. Supported by FAPESP, CNPQ and CAPES Citation Format: Débora Papaiz, Flávia E. Rius, Diogo Pessoa, Eduardo M. Reis, Christopher E. Mason, Gangning Liang, Miriam G. Jasiulionis. Deregulated genes by abnormal promoter methylation in early and late stages in a linear model of melanoma progression [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 140.

Methylation-sensitive amplification polymorphism analysis reveals the DNA methylation dynamics during capitulum development in Chrysanthemum lavandulifolium

Chrysanthemum lavandulifolium (Fischer ex Trautv.) Makino is a diploid plant belonging to the Asteraceae family, with typical capitula composed of female ray florets and bisexual disc florets. The differentiation and development of these two types of florets have long been important research focuses; however, the potential epigenetic mechanisms governing these processes have not been elucidated. In the present study, methylation-sensitive amplification polymorphism method was used to trace the dynamic changes of DNA methylation during capitulum development in C. lavandulifolium. DNA methylation patterns and levels were detected in the whole capitula during seven developmental stages, and the obtained results revealed that DNA demethylation was dominant during this process. In addition, DNA methylation patterns and levels showed significant differences between ray and disc florets. Moreover, the expression patterns of candidate genes potentially involved in the development processes of two types of florets were analyzed by real-time quantitative reverse transcription polymerase chain reaction, and correlation analysis indicated that the expression levels of ClPI, ClAG2, ClSEP1, ClCYC2c, ClCYC2d, and ClCYC2e were highly correlated with DNA methylation levels. These results indicate that DNA methylation may be involved in the differentiation and development of ray and disc florets. This study provides epigenetic insights into the capitulum development in C. lavandulifolium.

Nutritional Epigenomics and Age-Related Disease.

Recent advances in epigenetic research have enabled the development of epigenetic clocks, which have greatly enhanced our ability to investigate molecular processes that contribute to aging and age-related disease. These biomarkers offer the potential to measure the effect of environmental exposures linked to dynamic changes in DNA methylation, including nutrients, as factors in age-related disease. They also offer a compelling insight into how imbalances in the supply of nutrients, particularly B-vitamins, or polymorphisms in regulatory enzymes involved in 1-carbon metabolism, the key pathway that supplies methyl groups for epigenetic reactions, may influence epigenetic age and interindividual disease susceptibility. Evidence from recent studies is critically reviewed, focusing on the significant contribution of the epigenetic clock to nutritional epigenomics and its impact on health outcomes and age-related disease. Further longitudinal studies and randomized nutritional interventions are required to advance the field.

Dynamic changes in DNA methylation during postnatal development in zebra finches Taeniopygia guttata exposed to different temperatures

Epigenetic changes associated with early life conditions are known to play a significant role in shaping the adult phenotype. Studies of DNA methylation in wild animals are lacking, yet are important for understanding the fitness consequences of environmentally induced epigenetic change. In our study, we quantified variation in DNA methylation in wild, post‐hatch zebra finches Taeniopygia guttata developing at seasonally variable temperatures in the Australian desert. We also compared variation in DNA methylation among captive zebra finch siblings raised in temperature controlled ‘hot’ or ‘cool’ rooms. We detected an increase in genome‐wide levels of DNA methylation between day 3 and day 11 of post hatch development in wild zebra finches. In the wild, ambient temperatures were also found to affect genome‐wide levels of DNA methylation and plasticity in the methylation state of individual loci. Family effects had a significant influence on DNA methylation throughout our study, and while we did not detect an effect of temperature on DNA methylation levels in non‐related captive birds, our sibling pair analyses revealed that within families, elevated temperatures were associated with higher levels of DNA methylation. Our findings suggest a wide window in early development during which climatically induced variation in DNA methylation could occur. Further work is necessary to understand the potential for such variation to promote ecologically relevant variation in wild birds.

Oxidative DNA Damage Modulates DNA Methylation Pattern in Human Breast Cancer 1 (BRCA1) Gene via the Crosstalk between DNA Polymerase β and a de novo DNA Methyltransferase.

DNA damage and base excision repair (BER) are actively involved in the modulation of DNA methylation and demethylation. However, the underlying molecular mechanisms remain unclear. In this study, we seek to understand the mechanisms by exploring the effects of oxidative DNA damage on the DNA methylation pattern of the tumor suppressor breast cancer 1 (BRCA1) gene in the human embryonic kidney (HEK) HEK293H cells. We found that oxidative DNA damage simultaneously induced DNA demethylation and generation of new methylation sites at the CpGs located at the promoter and transcribed regions of the gene ranging from −189 to +27 in human cells. We demonstrated that DNA damage-induced demethylation was mediated by nucleotide misincorporation by DNA polymerase β (pol β). Surprisingly, we found that the generation of new DNA methylation sites was mediated by coordination between pol β and the de novo DNA methyltransferase, DNA methyltransferase 3b (DNMT3b), through the interaction between the two enzymes in the promoter and encoding regions of the BRCA1 gene. Our study provides the first evidence that oxidative DNA damage can cause dynamic changes in DNA methylation in the BRCA1 gene through the crosstalk between BER and de novo DNA methylation.

Dynamic Changes of DNA Methylation and Transcriptome Expression in Porcine Ovaries during Aging.

The biological function of human ovaries declines along with aging. To identify the underlying molecular changes during ovarian aging, pigs were used as model animals. Genome-wide DNA methylation and transcriptome-wide RNA expression analyses were performed via high-throughput sequencing of ovaries from young pigs (180 days, puberty stage of first ovulation) and old pigs (eight years, reproductive exhaustion stage). The results identified 422 different methylation regions between old and young pigs; furthermore, a total of 2,243 mRNAs, 95 microRNAs, 248 long noncoding RNAs (lncRNAs), and 116 circular RNAs (circRNAs) were differentially expressed during both developmental stages. Gene ontology analysis showed that these genes related to different methylation and expression are involved in the ovarian aging cycle. Specifically, these are involved in cell apoptosis, death effector domain binding, embryonic development, reproduction and fertilization process, ovarian cumulus expansion, and the ovulation cycle. Multigroup cooperative control relationships were also assessed, and competing endogenous RNA (ceRNA) networks were constructed in the ovarian aging cycle. These data will help to clarify ovary age-associated potential molecular changes in DNA methylation and transcriptional patterns over time.

Body Mass Index Drives Changes in DNA Methylation: A Longitudinal Study.

Previous EWASs (Epigenome-Wide Association Studies) suggest that obesity may be the cause, not a consequence, of changes in DNA methylation (DNAm). However, longitudinal observations are lacking. To identify 5'-cytosine-phosphate-guanine-3' in DNA (CpG) sites associated with body mass index (BMI) and examine the temporal relationship between dynamic changes in DNAm and BMI in a longitudinal cohort. Race-specific EWASs were performed in 995 whites and 490 blacks from the Bogalusa Heart Study. Suggestive CpG sites were further replicated in 252 whites and 228 blacks from the Georgia Stress and Heart Study. Cross-lagged panel analysis was used to examine the temporal relationship between DNAm and BMI in 439 whites and 201 blacks who were examined twice 6.2 years apart. In discovery and replication samples, 349 CpG sites (266 novel) in whites and 36 (21 novel) in blacks were identified to be robustly associated with BMI, with 8 (1 novel) CpG sites overlapping between the 2 races. Cross-lagged panel analyses showed significant unidirectional paths (PFDR <0.05) from baseline BMI to follow-up DNAm at 18 CpG sites in whites and 7 in blacks; no CpG sites showed significant paths from DNAm at baseline to BMI at follow-up. Baseline BMI was associated with a DNAm score (calculated from DNAm levels at the associated CpG sites) at follow-up (P<0.001 both in blacks and in whites). The findings provide strong evidence that obesity is the cause, not a consequence, of changes in DNAm over time.

Dynamic changes in DNA methylation during embryonic and postnatal development of an altricial wild bird.

DNA methylation could shape phenotypic responses to environmental cues and underlie developmental plasticity. Environmentally induced changes in DNA methylation during development can give rise to stable phenotypic traits and thus affect fitness. In the laboratory, it has been shown that the vertebrate methylome undergoes dynamic reprogramming during development, creating a critical window for environmentally induced epigenetic modifications. Studies of DNA methylation in the wild are lacking, yet are essential for understanding how genes and the environment interact to affect phenotypic development and ultimately fitness. Furthermore, our knowledge of the establishment of methylation patterns during development in birds is limited. We quantified genome‐wide DNA methylation at various stages of embryonic and postnatal development in an altricial passerine bird, the great tit Parus major. While, there was no change in global DNA methylation in embryonic tissue during the second half of embryonic development, a twofold increase in DNA methylation in blood occurred between 6 and 15 days posthatch. Though not directly comparable, DNA methylation levels were higher in the blood of nestlings compared with embryonic tissue at any stage of prenatal development. This provides the first evidence that DNA methylation undergoes global change during development in a wild bird, supporting the hypothesis that methylation mediates phenotypic development. Furthermore, the plasticity of DNA methylation demonstrated during late postnatal development, in the present study, suggests a wide window during which DNA methylation could be sensitive to environmental influences. This is particularly important for our understanding of the mechanisms by which early‐life conditions influence later‐life performance. While, we found no evidence for differences in genome‐wide methylation in relation to habitat of origin, environmental variation is likely to be an important driver of variation in methylation at specific loci.

Dynamic DNA methylation changes in the maternal oxytocin gene locus (OXT) during pregnancy predict postpartum maternal intrusiveness

Maternal behavior (MB) is observable across mammals and represents an important feature of environmental variation during early postnatal development. Oxytocin (OT) plays a crucial role in MB. Even prior to childbirth, pregnancy induces epigenetic and other downstream changes in the maternal OT-system, likely mediated by the actions of steroid hormones. However, little is known about the nature and consequences of epigenetic modifications in the maternal OT-encoding gene (OXT) during pregnancy. Our study aims to investigate temporal dynamics of OXT promoter DNA methylation (DNAm) throughout pregnancy in predicting MB in humans. In 107 mother-child dyads, maternal OXT DNAm was serially analyzed in whole blood in early, mid and late pregnancy. MB was coded based on standardized mother-child interactions at six months postpartum. After controlling for cellular heterogeneity, race/ethnicity, age, and socioeconomic status, OXT-promoter DNAm exhibited a dynamic profile during pregnancy (b = 0.026, t=-3.37, p < .001), with decreases in DNAm from early to mid-pregnancy and no further change until late pregnancy. Moreover, dynamic DNAm trajectories of the OXT-promoter region predicted MB (intrusiveness) at six months postpartum (b = 0.006, t = 2.0, p < 0.05), with 6% higher OXT DNAm in late pregnancy in intrusive compared to non-intrusive mothers. We here demonstrate that OXT promoter DNAm changes significantly throughout gestation in peripheral blood and that these changes are associated with variability in MB, providing a novel potential biomarker predicting postnatal MB.