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Series GSE49178 Query DataSets for GSE49178
Status Public on Sep 27, 2013
Title Dnmt3L-dependent regulation of DNA methylation promotes stem cells differentiation toward primitive germinal cells [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The de novo DNA methyltransferase 3-like (Dnmt3L) is a catalytically inactive DNA methylase that has been previously shown to cooperate with Dnmt3a and Dnmt3b to methylate DNA. Dnmt3L is highly expressed in mouse embryonic stem cells (ESC) but its function in these cells is unknown. We here report that Dnmt3L is required for the differentiation of ESC into primordial germ cells (PGC) through activation of the homeotic gene Rhox5. By genome-wide analysis we found that Dnmt3L is a positive regulator of methylation at gene bodies of housekeeping genes and a negative regulator of methylation at promoters of bivalent genes. We demonstrate that Dnmt3L interacts with the Polycomb PRC2 complex in competition with the DNA methyltransferases Dnmt3a and Dnmt3b to maintain low the methylation level at H3H27me3 regions. Thus, in ESC, Dnmt3L counteracts the activity of de novo DNA methylases to keep low the level of DNA methylation at developmental gene promoters.
 
Overall design Examination of Ezh2 ChIP-Seq in shGFP and shDnmt3L ESC. Examination of Dnmt3L ChIP-Seq in shGFP and shSuz12 ESC.
 
Contributor(s) Neri F, Oliviero S
Citation(s) 24074865
Submission date Jul 24, 2013
Last update date Dec 09, 2016
Contact name Francesco Neri
E-mail francesco.neri@hugef-torino.org
Organization name HuGeF
Street address Via Nizza 52
City Torino
State/province Italy
ZIP/Postal code 10126
Country Italy
 
Platforms (1)
GPL16173 Illumina HiScanSQ (Mus musculus)
Samples (4)
GSM1195114 Ezh2_ESC_shGFP
GSM1195115 Ezh2_ESC_shDnmt3L
GSM1195116 BioDnmt3L_ESC_shGFP
This SubSeries is part of SuperSeries:
GSE44644 Dnmt3L-dependent regulation of DNA methylation promotes stem cells differentiation toward primitive germinal cells
Relations
BioProject PRJNA213234
SRA SRP028244

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE49178_RAW.tar 2.4 Mb (http)(custom) TAR (of BED)
Raw data are available in SRA
Processed data provided as supplementary file

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