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Title: The dynamics of DNA methylation fidelity during mouse embryonic stem cell renewal and differentiation      
dateReleased:
05-12-2014
description:
Purpose: we aimed to gain a genome-wide view of the dynamics in DNA methylation inheritance and define the factors associated with methylation fidelity. Methods: Using mouse embryonic stem cell (ES-E14TG2a) in both undifferentiated and differentiated states as a model system, we exploited the hairpin bisulfite sequencing approach to generate methylation data for DNA double strands simultaneously at single-base resolution. We generated the genome-wide hairpin bisulfite sequencing data to capture the methylation pattern variation during the stem cell transition from self-renewal to commitment, and integrated with various “omics” data to scrutinize the relationships among DNA methylation inheritance, gene expression, histone modification, transcriptional factor binding and distribution of 5-hydroxylmethylation cytosine. Results and conclusion: Our results indicated that DNA methylation fidelity increases globally during early mouse embryonic stem cell differentiation. Methylation fidelity is remarkably high in promoter regions of actively expressed genes and positively correlated with active histone modification marks and binding of transcriptional factors. Strikingly, methylation fidelity follows a bimodal distribution for the intermediately methylated CpG dyads. In addition, the methylation difference in between two DNA strands rather than different DNA molecules is a major source of the intermediate DNA methylation. Lastly, while 5-hmC and 5-mC tend to coexist, no significant increase in the pairing with unmethylated cytosine was observed. For mouse embryonic stem cell of undifferentiated and spontaneous differentiated states, we determined DNA double strands methylation pattern by hairpin bisulfite sequencing approach and determined gene expression profiles using RNA-seq.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-48229
refinement:
raw
alternateIdentifiers:
48229
keywords:
functional genomics
dateModified:
06-19-2014
availability:
available
types:
gene expression
name:
Mus musculus
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-48229/E-GEOD-48229.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-48229/E-GEOD-48229.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48229
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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