DNA methylation landscapes of human fetal development
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Roderick Slieker
PROVIDER: E-GEOD-56515 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Here we assessed the genome-scale DNA methylation of 472,703 autosomal CpG sites in 4 tissues (muscle, amnion, pancreas and adrenal glands) on 3 time-points (9, 18 and 22 weeks) using the Illumina 450k array. We identified 52,134 CpG sites with dynamic DNA methylation during fetal development (gain or loss >20% from 9 to 22 weeks), where the period between 9 and 18 weeks was most dynamic. Loss in DNA methylation (25,579 CpGs), displayed clear tissue-specific patterns near genes enriched for a role in tissue-specific processes. Gain in DNA methylation (26,555 CpGs) occurred often near genes involved in (tissue-specific) developmental processes.
2015-09-22 | GSE56515 | GEO
Project description:In this study, we investigated the interaction between CpG methylation and genetic polymorphisms by taking the advantage of the family structure in 22 nuclear pedigrees. We have identified CpG sites that exhibit heritable methylation patterns, among which the majority are SNPs ditrectly disrupting CpG dinucleotides. We also identified 27.2% of the heritable non-SNP CpGs were associated with cis-regulatory SNPs. Additionally, we have identified hundreds of CpG clusters whose the degree of DNA methylation variation is associated with genetic polymorphism. Investigate the influence of genetic variances on blood DNA methylation patterns in the human genome of 96 subjects from 22 pedigrees by using different approaches, including mid-parent offspring analysis (MPO), methylation quantitative trait loci (mQTL) analysis and allele-specific DNA methylation (ASM) Raw data not provided since the files contain genetic information of the human subject that should be protected.
2013-06-20 | E-GEOD-47614 | biostudies-arrayexpress
Project description:In this study, we investigated the interaction between CpG methylation and genetic polymorphisms by taking the advantage of the family structure in 22 nuclear pedigrees. We have identified CpG sites that exhibit heritable methylation patterns, among which the majority are SNPs ditrectly disrupting CpG dinucleotides. We also identified 27.2% of the heritable non-SNP CpGs were associated with cis-regulatory SNPs. Additionally, we have identified hundreds of CpG clusters whose the degree of DNA methylation variation is associated with genetic polymorphism.
2013-06-20 | GSE47614 | GEO
Project description:We investigated the epigenetic landscape of benign prostatic hyperplasia (BPH) by defining the DNA methylation profile of 18 BPH samples and 5 controls from normal transitional zone. We identified 92,046 hypermethylated CpG and 10,117 hypomethylated CpG across different genomic regions in BPH, and hypermethylation was the dominant signal across all genomic regions, even when controlling for bias of CpG-rich loci. We defined a methylation signature for BPH that included 696 differentially methylated CpGs in promoter regions.
2020-03-18 | GSE123111 | GEO
Project description:Gender differences in the prevalence of psychiatric disorders are well documented in epidemiological studies. Exposure to stress during gestation impacts differentially between females and males. Environmental or biological factors can alter DNA methylation and affect the development of neurodevelopmental diseases. In this study, we explored gender-specific DNA methylation in regarding their potential connection to psychiatric outcomes. We assessed the methylation of cord blood of 39 females and 32 males born at term and with appropriate weight at birth. Mothers between 18 and 48 years of age (median: 28 years) were interviewed to gather information about environmental factors (gestational exposure) that can potentially interfere with the methylation profiles in the newborns. Bisulphite converted DNA was hybridized to Illumina HumanMethylation450 BeadChips. After exclusion of XYS probes, there were 2,332 differentially methylated CpG sites (DMS) between sexes, with an overlap of 890 (38%) CpG sites with an a cohort submitted to gestational stress exposition. Using externals datasets, we found that the DMSs were enriched within brain modules of co-methylated CpGs during gestation and were also differentially methylated in the brain comparing boys and girls during brain development. Genes associated to the DMSs were enriched for neurodevelopmental disorders. Accordingly, we described an enrichment of the DMSs among the differentially methylated CpG sites in brain tissue between schizophrenics and controls. Here, we suggest that gender changes methylation in the autosomes working as a primary driver to stress exposition which potentially contributes for gender differences found in psychiatric outcomes.
2017-05-01 | GSE85042 | GEO
Project description:Progressively longer regions of the gag gene sequence in HIV-1 were codon-optimized, which introduced 11, 18 or 26 CpGs (CM22-165: codon-optimized gag from nucleotide 22 to 165, adding 11 CpGs; CM22-261: 18 CpGs; CM22-378: 26 CpGs).
2019-11-07 | GSE134159 | GEO
Project description:Background: Researching the murine epigenome in disease models has been hampered by the lack of an appropriate and cost-effective DNA methylation array. Until recently, investigators have been limited to the relatively expensive and analysis intensive bisulphite sequencing methods. Here, we performed a comprehensive, comparative analysis between the new Mouse Methylation BeadChip (MMB) and reduced representation bisulphite sequencing (RRBS) in two murine models of colorectal carcinogenesis, providing insight into the utility to each platforms in a real world environment. Results: We captured 1.47x106 CpGs by RRBS and 2.64x105 CpGs by MMB, mapping to 13,778 and 13,365 CpG islands, respectively. RRBS captured significantly more CpGs per island (median 41 for RRBS versus 2 for MMB). We found that 64.4% of intra-island CpG methylation variability can be captured by measuring approximately one quarter of CpG island (CGI) CpGs. MMB was more precise in measuring DNA methylation, especially at sites that had low RRBS coverage. This impacted differential methylation analysis, with more statistically significantly differentially methylated CpG sites identified by MMB in all experimental conditions, however the difference was minute when appropriate thresholding for the magnitude of methylation change (0.2 beta value difference) was applied, providing confidence that both techniques can identify similar differential DNA methylation. Gene ontology enrichment analysis of differentially hypermethylated gene promoters identified similar biological processes and pathways by both RRBS and MMB across two murine model systems. Conclusion: MMB is an effective tool for profiling the murine methylome that performs comparably to RRBS, identifying similar differentially methylated pathways. Although MMB captures a similar proportion of CpG islands, it does so with fewer CpGs per island. We show that subsampling informative CpGs from CpG islands is an appropriate strategy to capture whole island variation. Choice of technology is experiment dependent and will be predicated on the underlying biology being probed.
2022-08-31 | E-MTAB-11985 | biostudies-arrayexpress
Project description:Background: Researching the murine epigenome in disease models has been hampered by the lack of an appropriate and cost-effective DNA methylation array. Until recently, investigators have been limited to the relatively expensive and analysis intensive bisulphite sequencing methods. Here, we performed a comprehensive, comparative analysis between the new Mouse Methylation BeadChip (MMB) and reduced representation bisulphite sequencing (RRBS) in two murine models of colorectal carcinogenesis, providing insight into the utility to each platforms in a real world environment. Results: We captured 1.47x106 CpGs by RRBS and 2.64x105 CpGs by MMB, mapping to 13,778 and 13,365 CpG islands, respectively. RRBS captured significantly more CpGs per island (median 41 for RRBS versus 2 for MMB). We found that 64.4% of intra-island CpG methylation variability can be captured by measuring approximately one quarter of CpG island (CGI) CpGs. MMB was more precise in measuring DNA methylation, especially at sites that had low RRBS coverage. This impacted differential methylation analysis, with more statistically significantly differentially methylated CpG sites identified by MMB in all experimental conditions, however the difference was minute when appropriate thresholding for the magnitude of methylation change (0.2 beta value difference) was applied, providing confidence that both techniques can identify similar differential DNA methylation. Gene ontology enrichment analysis of differentially hypermethylated gene promoters identified similar biological processes and pathways by both RRBS and MMB across two murine model systems. Conclusion: MMB is an effective tool for profiling the murine methylome that performs comparably to RRBS, identifying similar differentially methylated pathways. Although MMB captures a similar proportion of CpG islands, it does so with fewer CpGs per island. We show that subsampling informative CpGs from CpG islands is an appropriate strategy to capture whole island variation. Choice of technology is experiment dependent and will be predicated on the underlying biology being probed.
2022-10-15 | E-MTAB-12214 | biostudies-arrayexpress
Project description:Background DNA methylation has long been known to play an essential role in the epigenetic regulation of gene expression and other cellular functions, and has been in some cases linked to genetic variation. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood. Results We report the joint analysis of sequence variants, gene expression and DNA methylation in primary fibroblast samples derived from a set of 62 unrelated individuals. Approximately 2% of the most variable CpG sites are mappable in cis to sequence variation, usually within 5kb. However, only 5% of those mappable CpG sites also have methylation levels that correlate in cis with a gene's expression level. Methylation and gene expression are often correlated but not always in the expected direction (negative for promoter CpGs, positive for gene body CpGs). Population-level correlation between methylation and expression is strongest in a subset of developmentally significant genes, including all four HOX clusters. The presence and sign of this correlation are best predicted using specific histone marks or DNase hypersensitivity rather than position of the CpG site with respect to the gene, showing that other epigenetic markers are necessary to interpret downstream effects of individual methylation variants. Conclusion Our results indicate strong relationships between gene expression and DNA methylation in untransformed adult human fibroblasts, with considerable involvement of chromatin features and relatively modest involvement of sequence variation. 62 human skin fibroblast samples obtained from Coriell and McGill Cellbank, bisulfite converted DNA was hybridized to the Illumina Infinium 450K chip.
2013-12-10 | E-GEOD-52025 | biostudies-arrayexpress
Project description:Background DNA methylation has long been known to play an essential role in the epigenetic regulation of gene expression and other cellular functions, and has been in some cases linked to genetic variation. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood. Results We report the joint analysis of sequence variants, gene expression and DNA methylation in primary fibroblast samples derived from a set of 62 unrelated individuals. Approximately 2% of the most variable CpG sites are mappable in cis to sequence variation, usually within 5kb. However, only 5% of those mappable CpG sites also have methylation levels that correlate in cis with a gene's expression level. Methylation and gene expression are often correlated but not always in the expected direction (negative for promoter CpGs, positive for gene body CpGs). Population-level correlation between methylation and expression is strongest in a subset of developmentally significant genes, including all four HOX clusters. The presence and sign of this correlation are best predicted using specific histone marks or DNase hypersensitivity rather than position of the CpG site with respect to the gene, showing that other epigenetic markers are necessary to interpret downstream effects of individual methylation variants. Conclusion Our results indicate strong relationships between gene expression and DNA methylation in untransformed adult human fibroblasts, with considerable involvement of chromatin features and relatively modest involvement of sequence variation. Four human skin fibroblast samples obtained from Coriell. Bisulfite converted DNA was sequenced using the Illumina HiSeq 2000 system.
2014-01-25 | E-GEOD-54373 | biostudies-arrayexpress