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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 28, 2008 |
| Title |
Mapping Promoter CpG Methylation in mESCs |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
Methylation profiling by genome tiling array
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| Summary |
DNA methylation and histone modifications influence gene activities in a variety of mammalian cells. We report here the large scale mapping of DNA methylation patterns at proximal promoter regions in mouse embryonic stem cells (mESCs). A majority of methylated genes represent cell differentiation-associated genes that are repressed in mESCs. In contrast, unmethylated genes include many housekeeping and pluripotency genes such as STAT3 and Oct4/Nanog/Sox2, which are essential for ESC self-renewal. By comparing methylation patterns to the binding domains of Oct4/Nanog, Polycomb proteins, and histone H3 lysine (K) 4/27 trimethylation on gene promoters, we found that promoter DNA methylation is frequently the only epigenetic marker associated with a subset of silenced genes in mESCs that do not possess H3 K4/K27 trimethylation marks and are free from the binding of Polycomb proteins and the Oct4/Nanog transcription factors. Gene expression profiling of demethylated mESCs showed that a majority of up-regulated genes, including a subset of X-linked genes and many development genes, represent a distinct population of genes that are neither targeted by Polycomb and Oct4/Nanog, nor carry H3 K4/K27 trimethylation marks. Our data suggest that promoter methylation patterns in mESCs represent a unique epigenetic program that complements other regulatory mechanisms to allow the expression of pluripotency genes, but represses a subset of genes that will only be activated in specific cell lineages upon cell differentiation.
Keywords: DNA Methylation, methylated DNA immunoprecipitation
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| Overall design |
We compared DNA methylation patterns in Wildtype (J1) and DNA methylation deficient (TKO) mouse ES cells. We performed 7 replicates using different passages of mouse ES cells. For gene expression analysis, we used the same cultures and performed 3 replicates. The supplied table is the average log ratio for the 3 replicates and takes into account the dye swap of replicate 2.
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| Contributor(s) |
Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G |
| Citation(s) |
18371437 |
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| Submission date |
Sep 26, 2007 |
| Last update date |
Jan 18, 2013 |
| Contact name |
Yin Shen |
| E-mail(s) |
yshen@mednet.ucla.edu
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| Organization name |
UCLA
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| Street address |
695 Charles E. Young Dr.
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (3) |
| GPL2872 |
Agilent-012694 Whole Mouse Genome G4122A (Feature Number version) |
| GPL5805 |
Agilent-013276 Mouse Promoter ChIP-on-Chip Set 44k, Microarray 2 of 2 |
| GPL5806 |
Agilent-013275 Mouse Promoter ChIP-on-Chip Set 44k, Microarray 1 of 2 |
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| Samples (15)
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| GSM227260 |
Promoter CpG Methylation in Mouse ES cells (1/2) replicate 1 |
| GSM227261 |
Promoter CpG Methylation in Mouse ES Cells (1/2) replicate 2 |
| GSM227262 |
Promoter CpG Methylation in Mouse ES Cells (1/2) replicate 4 |
| GSM227263 |
Promoter CpG Methylation in Mouse ES Cells (1/2) replicate 5 |
| GSM227264 |
Promoter CpG Methylation in Mouse ES Cells (1/2) replicate 6 |
| GSM227266 |
Promoter CpG Methylation in Mouse ES Cells (1/2) replicate 7 |
| GSM227267 |
Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 1 |
| GSM227268 |
Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 2 |
| GSM227269 |
Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 3 |
| GSM227270 |
Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 4 |
| GSM227271 |
Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 5 |
| GSM227272 |
Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 6 |
| GSM227273 |
Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 7 |
| GSM231736 |
Promoter CpG Methylation in Mouse ES cells (1/2) replicate 3 |
| GSM231739 |
Wildtype vs DNA Methylation Deficient mESC Gene Expression |
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| Relations |
| BioProject |
PRJNA102733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9172_RAW.tar |
191.1 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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