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Detection of aberrant DNA methylation in undifferentiated and differentiated human ES cells compared to normal fetal tissues

ABSTRACT: Embryonic stem cells can be differentiated in vitro to produce a variety of somatic cell types. We have employed the mDIP method combined with hybridization to a tiling microarray to obtain a genome-wide methylation analysis of all UnMethylated Regions(UMRs). We show that this differentiation is accompanied by an intrinsic process of extensive aberrant CpG island de novo methylation that includes developmental and cancer target genes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE24270 | GEO | 2014/02/04

SECONDARY ACCESSION(S): PRJNA133005

REPOSITORIES: GEO

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Detection of aberrant DNA methylation in undifferentiated and differentiated human ES cells compared to normal fetal tissues

Project description:Embryonic stem cells can be differentiated in vitro to produce a variety of somatic cell types. We have employed the mDIP method combined with hybridization to a tiling microarray to obtain a genome-wide methylation analysis of all UnMethylated Regions(UMRs). We show that this differentiation is accompanied by an intrinsic process of extensive aberrant CpG island de novo methylation that includes developmental and cancer target genes. CpG-methylated genomic DNA was enriched using a methyl-DNA immunoprecipitation (mDIP) assay. DNA from the input and bound (enriched) DNA for each sample were labeled and hybridized on the array to define the methylation state of each region.

2014-02-04 | E-GEOD-24270 | biostudies-arrayexpress

Detection of aberrant DNA methylation in undifferentiated and differentiated mouse ES cells compared to normal tissues

Project description:Embryonic stem cells can be differentiated in vitro to produce a variety of somatic cell types. We have employed the mDIP method combined with hybridization to a CpG islend microarray . We show that this differentiation is accompanied by an intrinsic process of extensive aberrant CpG island de novo methylation that includes developmental and cancer target genes.

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Detection of aberrant DNA methylation in undifferentiated and differentiated mouse ES cells compared to normal tissues

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2014-02-05 | GSE54664 | GEO

Detection of aberrant DNA methylation in undifferentiated and differentiated mouse ES cells compared to normal tissues

Project description:Embryonic stem cells can be differentiated in vitro to produce a variety of somatic cell types. We have employed the mDIP method combined with hybridization to a CpG islend microarray . We show that this differentiation is accompanied by an intrinsic process of extensive aberrant CpG island de novo methylation that includes developmental and cancer target genes. CpG-methylated genomic DNA was enriched using a methyl-DNA immunoprecipitation (mDIP) assay. DNA from the input and bound (enriched) DNA for each sample were labeled and hybridized on the array to define the methylation state of each region.

2014-02-05 | E-GEOD-54664 | biostudies-arrayexpress

DNA methylome of Alpine Dingo

Project description:Using WGBS we investigated blood DNA methylation profiles of Cooinda the Alpine dingo and determined putative regulatory elements (unmethylated regions, UMRs, and lowly methylated regions, LMRs).

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Robust detection of undifferentiated iPSC among differentiated cells.

Project description:Recent progress in human induced pluripotent stem cells (iPSC) technologies suggest that iPSC application in regenerative medicine is a closer reality. Numerous challenges prevent iPSC application in the development of numerous tissues and for the treatment of various diseases. A key concern in therapeutic applications is the safety of the cell products to be transplanted into patients. Here, we present novel method for detecting residual undifferentiated iPSCs amongst directed differentiated cells of all three germ lineages. Marker genes, which are expressed specifically and highly in undifferentiated iPSC, were selected from single cell RNA sequence data to perform robust and sensitive detection of residual undifferentiated cells in differentiated cell products. ESRG (Embryonic Stem Cell Related), CNMD (Chondromodulin), and SFRP2 (Secreted Frizzled Related Protein 2) were well-correlated with the actual amounts of residual undifferentiated cells and could be used to detect residual cells in a highly sensitive manner using qPCR. In addition, such markers could be used to detect residual undifferentiated cells from various differentiated cells, including hepatic cells and pancreatic cells for the endodermal lineage, endothelial cells and mesenchymal cells for the mesodermal lineage, and neural cells for the ectodermal lineage. Our method facilitates robust validation and could enhance the safety of the cell products through the exclusion of undifferentiated iPSC.

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Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection

Project description:This SuperSeries is composed of the following subset Series: GSE15746: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 1 GSE15747: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 2 Refer to individual Series

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Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

Project description:The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. Thus, UMRs can provide powerful filters to distill large genomes down to the small fraction putative functional elements and facilitate the discovery of tens of thousands of novel candidate regulatory regions.

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Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

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Placental ischemia disrupts DNA methylation patterns of distal regulatory regions in rat

Project description:We carry out whole-genome bisulfite sequencing (WGBS) of rat placental DNA to investigate epigenome-wide alterations in a reduced uterine perfusion pressure (RUPP) PE model. The Hidden Markov Model (HMM) was applied to identify functional epigenetic structures including partially methylated domains (PMDs), low methylated regions (LMRs) and unmethylated regions (UMRs).

2023-08-12 | GSE211194 | GEO

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