|
| Status |
Public on Nov 01, 2009 |
| Title |
SetDB1 Contributes to Repression of Genes Encoding Developmental Regulators and Maintenance of ES Cell State |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Transcription factors that play key roles in regulating embryonic stem (ES) cell state have been identified, but the chromatin regulators that help maintain ES cells are less well understood. A high-throughput shRNA screen was used to identify novel chromatin regulators that influence ES cell state. Loss of histone H3K9 methyltransferases, particularly SetDB1, had the most profound effects on ES cells. ChIP-Seq and functional analysis revealed that SetDB1 and histone H3K9 methylated nucleosomes occupy and repress genes encoding developmental regulators. These SetDB1-occupied genes are a subset of the “bivalent” genes, which contain nucleosomes with H3K4me3 and H3K27me3 modifications catalyzed by trithorax and polycomb group proteins, respectively. These genes are subjected to repression by both polycomb group proteins and SetDB1, and loss of either regulator can destabilize ES cell state.
|
| |
|
| Overall design |
ChIP-seq data for SetDB1 and H3K9me3 in mouse ES cells.
|
| |
|
| Contributor(s) |
Bilodeau S, Kagey MH, Frampton GM, Rahl PB, Young RA |
| Citation(s) |
19884255 |
| Submission date |
Oct 01, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Garrett M Frampton |
| E-mail(s) |
frampton@mit.edu
|
| Organization name |
Whitehead Instute - MIT
|
| Department |
Biology
|
| Lab |
Richard Young
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
|
| Samples (11)
|
|
| Relations |
| SRA |
SRP001533 |
| BioProject |
PRJNA118137 |
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