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Series GSE68733 Query DataSets for GSE68733
Status Public on Apr 12, 2017
Title DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells
Organisms Mus musculus; Mus musculus musculus x Mus musculus castaneus
Experiment type Methylation profiling by high throughput sequencing
Summary Blastocyst-derived embryonic stem cells (ESCs) and gonad-derived embryonic germ cells (EGCs) represent two classic types of pluripotent cell lines, yet their molecular equivalence remains incompletely understood. Here, we compare genome-wide methylation patterns between isogenic ESC and EGC lines to define epigenetic similarities and differences. Surprisingly, we find that sex rather than cell type drives methylation patterns in ESCs and EGCs. Cell fusion experiments further reveal that the ratio of X chromosomes to autosomes dictates methylation levels, with female hybrids being hypomethylated and male hybrids being hypermethylated. We show that the X-linked MAPK phosphatase DUSP9 is upregulated in female compared to male ESCs, and its heterozygous loss in female ESCs leads to male-like methylation levels. However, male and female blastocysts are similarly hypomethylated, indicating that sex-specific methylation differences arise in culture. Collectively, our data demonstrate the epigenetic similarity of sex-matched ESCs and EGCs and identify DUSP9 as a regulator of female-specific hypomethylation.
Overall design Genetically matched mouse EGC and ESC lines were collected for DNA methylation analysis via mRRBS
Contributor(s) Choi J, Webster J, Boyle P, Clement K, Meissner A, Hochedlinger K, Gu H
Citation(s) 28366588, 28746311
Submission date May 11, 2015
Last update date May 15, 2019
Contact name Kendell Clement
Organization name Harvard University
Lab Meissner Lab
Street address 7 Divinity Ave.
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL22270 Illumina HiSeq 2500 (Mus musculus musculus x M. m. castaneus)
Samples (32)
GSM1679861 J-17 EGC
GSM1679862 J-20 EGC
GSM1679863 J-23 EGC
BioProject PRJNA283520
SRA SRP058183

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Supplementary file Size Download File type/resource
GSE68733_RAW.tar 382.1 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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