Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA231916 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparison between groups of monozygotic (MZ) and dizygotic (DZ) twins enables an estimation of the relative contribution of genetic, shared and non-shared environmental factors to phenotypic variability. Using DNA methylation profiling of ~20,000 CpG sites as a phenotype, we have examined discordance levels in multiple tissues in neonatal twins. MZ twins exhibit a wide range of within-pair differences at birth, but show discordance levels generally lower than DZ pairs. Within-pair methylation discordance was lowest in CpG islands in all twins and increased as a function of distance from islands. This was largely independent of distance from transcriptional start site in promoters without CpG islands. Variance component decomposition analysis of DNA methylation in MZ and DZ pairs revealed a low mean heritability across all tissues, although a wide range of heritabilities was detected for specific genomic CpG sites. The largest component of variation was attributed to the combined effects of non-shared intrauterine environment and stochastic factors. Regression analysis of methylation on birth weight revealed a general association between methylation of genes involved in metabolism and biosynthesis, providing further support for epigenetic change in the previously described link between low birth weight and increasing risk for cardiovascular, metabolic and other complex diseases. Finally, comparison of our data with that of several older twins, revealed little evidence for genome-wide epigenetic drift with increasing age. This is the first study to analyse DNA methylation on a genome scale in twins at birth, further highlighting the importance of the intrauterine environment on shaping the neonatal epigenome. Data from cord blood mononuclear cells (CBMCs), human umbilical vascular endothelial cells (HUVECs) and placenta from 22 MZ and 11 DZ pairs with one replicate sample
2012-07-17 | E-GEOD-36642 | biostudies-arrayexpress
Project description:Inter-individual variability in DNA methylation has been hypothesized to contribute to complex phenotypes through epigenetic modulation of gene expression levels. Population epigenetic studies have been examining differences in DNA methylation in a variety of accessible tissues for association with specific diseases or exposures, but relatively little is known about how this inter-individual variation differs between tissues. This study presents an analysis of global DNA methylation differences between matched peripheral blood mononuclear cells and buccal epithelial cells; specifically it examines differential DNA methylation, probe-wise DNA methylation variance, and how methylation relates to a number of demographic factors across the two tissues. We found that peripheral blood mononuclear cells have overall higher DNA methylation than buccal epithelial cells, and regions of the genome that are differently methylated between the tissues tend to have low CpG density. We also discovered that although both tissues show extensive probe-wise variability, the specific regions and magnitude of variability differed between tissues. Finally, we observed that while both buccal epithelial and peripheral mononuclear blood cell DNA methylation was associated with gender, only methylation of the latter was associated with body mass index. The work presented here offers insight into variability of DNA methylation between individuals and across tissues and the suitability of buccal epithelial and peripheral mononuclear cells for the biological questions explored by epigenome-wide association studies in human populations.
2014-05-31 | GSE53396 | GEO
Project description:DNA methylation distinguishes pathologically normal human tissues
| PRJNA122305 | ENA
Project description:Comparison between groups of monozygotic (MZ) and dizygotic (DZ) twins enables an estimation of the relative contribution of genetic, shared and non-shared environmental factors to phenotypic variability. Using DNA methylation profiling of ~20,000 CpG sites as a phenotype, we have examined discordance levels in multiple tissues in neonatal twins. MZ twins exhibit a wide range of within-pair differences at birth, but show discordance levels generally lower than DZ pairs. Within-pair methylation discordance was lowest in CpG islands in all twins and increased as a function of distance from islands. This was largely independent of distance from transcriptional start site in promoters without CpG islands. Variance component decomposition analysis of DNA methylation in MZ and DZ pairs revealed a low mean heritability across all tissues, although a wide range of heritabilities was detected for specific genomic CpG sites. The largest component of variation was attributed to the combined effects of non-shared intrauterine environment and stochastic factors. Regression analysis of methylation on birth weight revealed a general association between methylation of genes involved in metabolism and biosynthesis, providing further support for epigenetic change in the previously described link between low birth weight and increasing risk for cardiovascular, metabolic and other complex diseases. Finally, comparison of our data with that of several older twins, revealed little evidence for genome-wide epigenetic drift with increasing age. This is the first study to analyse DNA methylation on a genome scale in twins at birth, further highlighting the importance of the intrauterine environment on shaping the neonatal epigenome.
2012-07-18 | GSE36642 | GEO
Project description:Inter-individual variability in DNA methylation has been hypothesized to contribute to complex phenotypes through epigenetic modulation of gene expression levels. Population epigenetic studies have been examining differences in DNA methylation in a variety of accessible tissues for association with specific diseases or exposures, but relatively little is known about how this inter-individual variation differs between tissues. This study presents an analysis of global DNA methylation differences between matched peripheral blood mononuclear cells and buccal epithelial cells; specifically it examines differential DNA methylation, probe-wise DNA methylation variance, and how methylation relates to a number of demographic factors across the two tissues. We found that peripheral blood mononuclear cells have overall higher DNA methylation than buccal epithelial cells, and regions of the genome that are differently methylated between the tissues tend to have low CpG density. We also discovered that although both tissues show extensive probe-wise variability, the specific regions and magnitude of variability differed between tissues. Finally, we observed that while both buccal epithelial and peripheral mononuclear blood cell DNA methylation was associated with gender, only methylation of the latter was associated with body mass index. The work presented here offers insight into variability of DNA methylation between individuals and across tissues and the suitability of buccal epithelial and peripheral mononuclear cells for the biological questions explored by epigenome-wide association studies in human populations. This cohort consist of genomic DNA extracted from the peripheral blood mononuclear cells and buccal epithelial cells of 25 individuals, bisulphite converted and hybridized to the Illumina GoldenGate Methylation Cancer Panel for genome wide DNA methylation profiling
2014-05-31 | E-GEOD-53396 | biostudies-arrayexpress
Project description:Over two decades after the discovery of ROS1 as the first eukaryotic DNA demethylase, its genome-wide binding sites and functions beyond active DNA demethylation remain unknown. Here, using advanced ChIP-seq, we reveal that ROS1 specifically occupies nearly all accessible chromatin and dynamically correlates with changes in chromatin accessibility across tissues, establishing it as a marker of accessible chromatin. Furthermore, we demonstrate that ROS1 maintains DNA hypomethylation through an occupancy-based mechanism that prevents the recruitment of RNA-directed DNA methylation, distinct from its active DNA demethylation. Additionally, ROS1 plays a regulatory role in chromatin accessibility, both independently and in cooperation with other epigenetic regulators. This regulation occurs in both DNA methylation-dependent and independent contexts, with ROS1 functioning as a potential or actual protector of accessible chromatin, depending on the presence and targeting of DNA methylation systems. Our results provide a comprehensive understanding of the regulatory roles of ROS1 in chromatin accessibility and DNA methylation, highlighting the intricate crosstalk between these mechanisms.
2026-02-06 | GSE282075 | GEO
Project description:Over two decades after the discovery of ROS1 as the first eukaryotic DNA demethylase, its genome-wide binding sites and functions beyond active DNA demethylation remain unknown. Here, using advanced ChIP-seq, we reveal that ROS1 specifically occupies nearly all accessible chromatin and dynamically correlates with changes in chromatin accessibility across tissues, establishing it as a marker of accessible chromatin. Furthermore, we demonstrate that ROS1 maintains DNA hypomethylation through an occupancy-based mechanism that prevents the recruitment of RNA-directed DNA methylation, distinct from its active DNA demethylation. Additionally, ROS1 plays a regulatory role in chromatin accessibility, both independently and in cooperation with other epigenetic regulators. This regulation occurs in both DNA methylation-dependent and independent contexts, with ROS1 functioning as a potential or actual protector of accessible chromatin, depending on the presence and targeting of DNA methylation systems. Our results provide a comprehensive understanding of the regulatory roles of ROS1 in chromatin accessibility and DNA methylation, highlighting the intricate crosstalk between these mechanisms.
2026-02-06 | GSE282073 | GEO
Project description:Over two decades after the discovery of ROS1 as the first eukaryotic DNA demethylase, its genome-wide binding sites and functions beyond active DNA demethylation remain unknown. Here, using advanced ChIP-seq, we reveal that ROS1 specifically occupies nearly all accessible chromatin and dynamically correlates with changes in chromatin accessibility across tissues, establishing it as a marker of accessible chromatin. Furthermore, we demonstrate that ROS1 maintains DNA hypomethylation through an occupancy-based mechanism that prevents the recruitment of RNA-directed DNA methylation, distinct from its active DNA demethylation. Additionally, ROS1 plays a regulatory role in chromatin accessibility, both independently and in cooperation with other epigenetic regulators. This regulation occurs in both DNA methylation-dependent and independent contexts, with ROS1 functioning as a potential or actual protector of accessible chromatin, depending on the presence and targeting of DNA methylation systems. Our results provide a comprehensive understanding of the regulatory roles of ROS1 in chromatin accessibility and DNA methylation, highlighting the intricate crosstalk between these mechanisms.
2026-02-06 | GSE282071 | GEO
Project description:Over two decades after the discovery of ROS1 as the first eukaryotic DNA demethylase, its genome-wide binding sites and functions beyond active DNA demethylation remain unknown. Here, using advanced ChIP-seq, we reveal that ROS1 specifically occupies nearly all accessible chromatin and dynamically correlates with changes in chromatin accessibility across tissues, establishing it as a marker of accessible chromatin. Furthermore, we demonstrate that ROS1 maintains DNA hypomethylation through an occupancy-based mechanism that prevents the recruitment of RNA-directed DNA methylation, distinct from its active DNA demethylation. Additionally, ROS1 plays a regulatory role in chromatin accessibility, both independently and in cooperation with other epigenetic regulators. This regulation occurs in both DNA methylation-dependent and independent contexts, with ROS1 functioning as a potential or actual protector of accessible chromatin, depending on the presence and targeting of DNA methylation systems. Our results provide a comprehensive understanding of the regulatory roles of ROS1 in chromatin accessibility and DNA methylation, highlighting the intricate crosstalk between these mechanisms.
2026-02-06 | GSE282072 | GEO
Project description:Genome-wide analysis of DNA methylation between nasopharyngeal carcinoma tissues and normal nasopharyngeal epithelial tissues
| PRJNA226616 | ENA