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Series GSE20551 Query DataSets for GSE20551
Status Public on Oct 14, 2010
Title ChIP-chip from mouse embryonic stem (mES) cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary c-Myc (Myc) is an important transcriptional regulator in embryonic stem (ES) cells, somatic cell reprogramming, and cancer, yet functionally differs from the core pluripotency transcription factors, such as Oct4, Sox, and Nanog. Here, we identify a Myc-centered regulatory network in ES cells by combining protein-protein interaction and protein-DNA interaction studies, and show that Myc interacts with the NuA4 histone acetyltransferase complex, previously identified as a critical regulator in ES cell identity. In combination with previously studied transcriptional regulatory network information, we construct three ES cell modules (Core, Polycomb, and Myc) and show that these modules are functionally separable in ES, iPS, MEFs, and partial iPS cells, suggesting that the overall ES cell transcription program is comprised of distinct functional units. With these regulatory modules as an analytical tool, we have reassessed data suggesting that cancer cells reactivate an ES cell-like transcriptional program. We find that the Myc module, independent of the Core module, is active in various cancers and predicts cancer outcome. These observations argue against the hypothesis linking an embryonic gene expression signature with cancer or cancer stem cells. The apparent similarity of cancer and ES cell signatures reflects in large part the pervasive nature of Myc regulatory network.
Keywords: Biotin-mediated Chip-chip, Antibody ChIP-chip, Mouse embryonic stem cells
Overall design Genomic targets of 5 transcription factors (Max, Dmap1, Tip60, Gcn5, and E2F4) and 2 histone modification signatures (AcH3, AcH4) were identified by biotin-mediated ChIP-chip (bioChIP-chip) in mouse ES cells.
Contributor(s) Kim J, Woo AJ, Chu J, Snow J, Fujiwara Y, Kim CG, Cantor AB, Orkin SH
Citation(s) 20946988
Submission date Feb 26, 2010
Last update date Oct 14, 2014
Contact name Jonghwan Kim
Phone 607-919-2051
Organization name HMS/CHB
Lab Stuart H Orkin lab
Street address 1 Blackfan circle Karp-7
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL5811 [Mm_PromPR] Affymetrix Mouse Promoter 1.0R Array
Samples (7)
GSM516404 bioMax
GSM516405 bioDmap1
GSM516406 bioTip60
BioProject PRJNA125311

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
GSE20551_RAW.tar 1.0 Gb (http)(custom) TAR (of BAR, BED, CEL)
Processed data provided as supplementary file

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