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Series GSE47893 Query DataSets for GSE47893
Status Public on Jun 03, 2014
Title Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO Methyl-Seq)
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary During mammalian development DNA methylation patterns need to be reset in primordial germ cells (PGC) and preimplantation embryos. However, many retro-transposons and imprinted genes are resistant to such global epigenetic reprogramming via hitherto undefined mechanisms. Here, we report that some of these sequences are immune to widespread erasure of DNA methylation in the mouse embryonic stem cells (mESCs) lacking de novo DNA methyltransferases. Persistence of DNA methylation at these loci in mESCs depends on the histone H3K9 methyltransferase Setdb1, as deletion of Setdb1 results in reduction of H3K9me3 and DNA methylation levels concomitant with an increase in 5-hydroxymethylation (5hmC). In addition, depletion of H3K9 methyltransferase G9a leads to genome-wide reduction of DNA methylation but to a lesser extent at the above sequences. Taken together, these data reveal that Setdb1 ensures the fidelity of DNA methylation at specific loci in mESCs, which may reflect mechanisms functioning in vivo during key developmental stages.
Overall design Examination of genome-wide DNA methylation status in 2 cell types.
Contributor(s) Leung D, Du T, Wagner U, Xie W, Lee AY, Goyal P, Li Y, Szulwach KE, Jin P, Lorincz M, Ren B
Citation(s) 24757056
Submission date Jun 12, 2013
Last update date May 15, 2019
Contact name Ulrich Wagner
Organization name Uiversity Hospital Zurich
Street address Schmelzbergstrasse 12
City Zurich
ZIP/Postal code 8091
Country Switzerland
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (6)
GSM1162043 methyl-C-seq_WT_rep1
GSM1162044 methyl-C-seq_WT_rep2
GSM1162045 methyl-C-seq_WT_rep2 paired end
This SubSeries is part of SuperSeries:
GSE47894 Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases
BioProject PRJNA208367
SRA SRP025996

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Supplementary file Size Download File type/resource 81.3 Mb (ftp)(http) BW 79.0 Mb (ftp)(http) BW
GSE47893_RAW.tar 330.5 Mb (http)(custom) TAR (of BW)
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Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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