Genome-wide DNA Methylation Variation Research Articles

DNA methylation differences between stick insect ecotypes.

Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. Beginning to address this issue requires high-resolution sequencing studies of natural populations to pinpoint epigenetic regions of potential ecological and evolutionary significance. However, such studies are still relatively uncommon, especially in insects, and are mainly restricted to a few model organisms. Here, we characterize patterns of DNA methylation for natural populations of Timema cristinae adapted to two host plant species (i.e. ecotypes). By integrating results from sequencing of whole transcriptomes, genomes and methylomes, we investigate whether environmental, host and genetic differences of these stick insects are associated with methylation levels of cytosine nucleotides in the CpG context. We report an overall genome-wide methylation level for T. cristinae of ~14%, with methylation being enriched in gene bodies and impoverished in repetitive elements. Genome-wide DNA methylation variation was strongly positively correlated with genetic distance (relatedness), but also exhibited significant host-plant effects. Using methylome-environment association analysis, we pinpointed specific genomic regions that are differentially methylated between ecotypes, with these regions being enriched for genes with functions in membrane processes. The observed association between methylation variation and genetic relatedness, and with the ecologically important variable of host plant, suggests a potential role for epigenetic modification in T. cristinae adaptation. To substantiate such adaptive significance, future studies could test whether methylation can be transmitted across generations and the extent to which it responds to experimental manipulation in field and laboratory studies.

Developmental stress does not induce genome-wide DNA methylation changes in wild great tit (Parus major) nestlings.

The environment experienced during early life is a crucial factor in the life of many organisms. This early life environment has been shown to have profound effects on morphology, physiology and fitness. However, the molecular mechanisms that mediate these effects are largely unknown, even though they are essential for our understanding of the processes that induce phenotypic variation in natural populations. DNA methylation is an epigenetic mechanism that has been suggested to explain such environmentally induced phenotypic changes early in life. To investigate whether DNA methylation changes are associated with experimentally induced early developmental effects, we cross-fostered great tit (Parus major) nestlings and manipulated their brood sizes in a natural study population. We assessed experimental brood size effects on pre-fledging biometry and behaviour. We linked this to genome-wide DNA methylation levels of CpG sites in erythrocyte DNA, using 122 individuals and an improved epiGBS2 laboratory protocol. Brood enlargement caused developmental stress and negatively affected nestling condition, predominantly during the second half of the breeding season, when conditions are harsher. Brood enlargement, however, affected nestling DNA methylation in only one CpG site and only if the hatch date was taken into account. In conclusion, this study shows that nutritional stress in enlarged broods does not associate with direct effects on genome-wide DNA methylation. Future studies should assess whether genome-wide DNA methylation variation may arise later in life as a consequence of phenotypic changes during early development.

Genome-Wide Analysis of DNA Methylation in Buccal Cells of Children Conceived through IVF and ICSI.

Early life periconceptional exposures during assisted reproductive technology (ART) procedures could alter the DNA methylation profiles of ART children, notably in imprinted genes and repetitive elements. At the genome scale, DNA methylation differences have been reported in ART conceptions at birth, but it is still unclear if those differences remain at childhood. Here, we performed an epigenome-wide DNA methylation association study using Illumina InfiniumEPIC BeadChip to assess the effects of the mode of conception on the methylome of buccal cells from 7- to 8-year-old children (48 children conceived after ART or naturally (control, CTL)) and according to the embryo culture medium in which they were conceived. We identified 127 differentially methylated positions (DMPs) and 16 differentially methylated regions (DMRs) (FDR < 0.05) with low delta beta differences between the two groups (ART vs. CTL). DMPs were preferentially located inside promoter proximal regions and CpG islands and were mostly hypermethylated with ART. We highlighted that the use of distinct embryo culture medium was not associated with DNA methylation differences in childhood. Overall, we bring additional evidence that children conceived via ART display limited genome-wide DNA methylation variation compared with those conceived naturally.

Changes in DNA Methylation in Response to 6-Benzylaminopurine Affect Allele-Specific Gene Expression in Populus Tomentosa.

Cytokinins play important roles in the growth and development of plants. Physiological and photosynthetic characteristics are common indicators to measure the growth and development in plants. However, few reports have described the molecular mechanisms of physiological and photosynthetic changes in response to cytokinin, particularly in woody plants. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression in response to the external environment. In this study, we examined genome-wide DNA methylation variation and transcriptional variation in poplar (Populus tomentosa) after short-term treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA). We identified 460 significantly differentially methylated regions (DMRs) in response to 6-BA treatment. Transcriptome analysis showed that 339 protein-coding genes, 262 long non-coding RNAs (lncRNAs), and 15,793 24-nt small interfering RNAs (siRNAs) were differentially expressed under 6-BA treatment. Among these, 79% were differentially expressed between alleles in P. tomentosa, and 102,819 allele-specific expression (ASE) loci in 19,200 genes were detected showing differences in ASE levels after 6-BA treatment. Combined DNA methylation and gene expression analysis demonstrated that DNA methylation plays an important role in regulating allele-specific gene expression. To further investigate the relationship between these 6-BA-responsive genes and phenotypic variation, we performed SNP analysis of 460 6-BA-responsive DMRs via re-sequencing using a natural population of P. tomentosa, and we identified 206 SNPs that were significantly associated with growth and wood properties. Association analysis indicated that 53% of loci with allele-specific expression had primarily dominant effects on poplar traits. Our comprehensive analyses of P. tomentosa DNA methylation and the regulation of allele-specific gene expression suggest that DNA methylation is an important regulator of imbalanced expression between allelic loci.

Prenatal Growth Patterns and Birthweight Are Associated With Differential DNA Methylation and Gene Expression of Cardiometabolic Risk Genes in Human Placentas: A Discovery-Based Approach.

Inherent genetic programming and environmental factors affect fetal growth in utero. Epidemiologic data in growth-altered fetuses, either intrauterine growth restricted (IUGR) or large for gestational age (LGA), demonstrate that these newborns are at increased risk of cardiometabolic disease in adulthood. There is growing evidence that the in utero environment leads to epigenetic modification, contributing to eventual risk of developing heart disease or diabetes. In this study, we used reduced representation bisulfite sequencing to examine genome-wide DNA methylation variation in placental samples from offspring born IUGR, LGA, and appropriate for gestational age (AGA) and to identify differential methylation of genes important for conferring risk of cardiometabolic disease. We found that there were distinct methylation signatures for IUGR, LGA, and AGA groups and identified over 500 differentially methylated genes (DMGs) among these group comparisons. Functional and gene network analyses revealed expected relationships of DMGs to placental physiology and transport, but also identified novel pathways with biologic plausibility and potential clinical importance to cardiometabolic disease. Specific loci for DMGs of interest had methylation patterns that were strongly associated with anthropometric presentations. We further validated altered gene expression of these specific DMGs contributing to vascular and metabolic diseases (SLC36A1, PTPRN2, CASZ1, IL10), thereby establishing transcriptional effects toward assigning functional significance. Our results suggest that the gene expression and methylation state of the human placenta are related and sensitive to the intrauterine environment, as it affects fetal growth patterns. We speculate that these observed changes may affect risk for offspring in developing adult cardiometabolic disease.

Genome-wide DNA methylation variation in maternal and cord blood of gestational diabetes population.

Gestational diabetes mellitus (GDM) has always been a concerning issue for pregnant women. In recent studies, GDM was found to be related to epigenetic modifications, which would alter gene expressions, thus affecting the patients' and their offspring's health, leading to a higher probability of developing metabolic syndromes and diabetes later in life. In this study, we collected both maternal and cord blood samples from 16 pregnant women and their newborns, including eight exposed to GDM. GDM was diagnosed via a 75g oral glucose tolerance test (OGTT) at 24-28weeks of pregnancy. DNA methylation was measured at 841,573 CpG sites via the Infinium HumanMethylationEPIC BeadChip. An Ingenuity Pathway Analysis was conducted afterwards to identify genes and pathways epigenetically affected by GDM. We identified the top 200 loci and their corresponding genes in the maternal blood group (n=151) and cord blood group (n=167), both of which were methylated differently in the GDM and unexposed group. Metabolic disease-related pathways and molecules, such as interleukin-6 and interleukin-10 were identified in both groups. These results suggested that GDM has epigenetic effects on both mother and their offspring, which might result in future metabolic syndromes or diabetes. The high-throughput platform enabled us to analyze methylation sites throughout the genome and identify the most promising genes and pathways associated with GDM.

Abstract MP25: Adiposity-related DNA Methylation as a Predictor of Coronary Heart Disease in Adult African Americans: The Atherosclerosis Risk in Communities Study

Background: Epigenetic modifications such DNA methylation variation comprise a potentially useful new class of biomarkers that may improve coronary heart disease (CHD) risk stratification, or better capture early pathophysiological processes. However, replicated associations of DNA methylation and CHD are few, and existing studies are primarily cross-sectional and restricted to European ancestry populations. Given the strong association of excess adiposity with CHD risk, we tested 41 DNA methylation variants (CpG sites) that were previously reported to be associated with BMI in African Americans (AA), and tested their association with incident CHD in AA adults. Methods: Genome-wide DNA methylation variation was assayed at a single time point in stored frozen leukocyte samples using the Illumina HM450K chip in a subset of 1,797 AA participants in the Atherosclerosis Risk in Communities (ARIC) study, a prospective cohort study of cardiovascular disease risk conducted in four U.S. communities. Methylation beta values and other continuous covariates were winsorized prior to analysis to reduce outlier influence. Incident CHD cases were identified through annual telephone interviews and medical records review. Proportional hazards regression (frailty) models examined the relationship between DNA methylation beta values and incident CHD with separate models for each of the 41 CpGs, with a random effect specified for chip. Fully adjusted models included age, BMI, sex, center, education, household income, leisure time activity, alcohol and tobacco use, white blood cell count and imputed cell type differentials. To explore the relationship between DNA methylation and CHD risk accounting for major CHD risk factors, mediator models additionally contained prevalent hypertension status, blood glucose, and total and HDL cholesterol. A Bonferroni-corrected p value of 0.00122 was set as the threshold for statistical significance. Results: There were 224 cases of incident CHD out of 1,797 individuals at risk. One CpG, cg09664445 near CLUH was significantly associated with incident CHD in the full (HR=1.47, 95%CI=1.26, 1.72) and mediator model (HR=1.46, 95% CI=1.24, 1.71) while cg06500161 near ABCG1 was significant in the full model only (HR=1.34, 95% CI=1.15, 1.56). Conclusion: Two obesity-related DNA methylation variants were associated with incident CHD independent of known risk factors and potential confounders. In the literature, CLUH is involved in mitochondrial biogenesis while promoter hypermethylation of ABCG1 was previously found to increase CHD risk and atherosclerosis. Replication in additional cohorts is required to further investigate the predictive value of DNA methylation variants over established risk factors and biomarkers for CHD.

Maternal gestational diabetes is associated with genome-wide DNA methylation variation in placenta and cord blood of exposed offspring.

Exposure of a developing foetus to maternal gestational diabetes (GDM) has been shown to programme future risk of diabetes and obesity. Epigenetic variation in foetal tissue may have a mechanistic role in metabolic disease programming through interaction of the pregnancy environment with gene function. We aimed to identify genome-wide DNA methylation variation in cord blood and placenta from offspring born to mothers with and without GDM. Pregnant women of South Asian origin were studied and foetal tissues sampled at term delivery. The Illumina HumanMethylation450 BeadChip was used to assay genome-wide DNA methylation in placenta and cord blood from 27 GDM exposed and 21 unexposed offspring. We identified 1485 cord blood and 1708 placenta methylation variable positions (MVPs) achieving genome-wide significance (adjusted P-value <0.05) with methylation differences of >5%. MVPs were disproportionately located within first exons. A bioinformatic co-methylation algorithm was used to detect consistent directionality of methylation in 1000 bp window around each MVP was observed at 74% of placenta and 59% of cord blood MVPs. KEGG pathway analysis showed enrichment of pathways involved in endocytosis, MAPK signalling and extracellular triggers to intracellular metabolic processes. Replication studies should integrate genomics and transcriptomics with longitudinal sampling to elucidate stability, determine causality for translation into biomarker and prevention studies.