|
| Status |
Public on Dec 30, 2012 |
| Title |
The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Enhancers play a central role in precisely regulating the spatiotemporal expression of developmentally regulated genes. The molecular mechanisms and factors required for controlling the inactive or poised enhancers and their function in future gene activation remain elusive. Here, we have identified that Ell3, a member of the Ell (Eleven-nineteen Lysine-rich Leukemia gene) family of RNA Pol II elongation factors, predominately occupies active and inactive enhancers of many developmentally regulated genes in mouse embryonic stem cells. Ell3 localizes to active enhancers of key stem cell renewal genes, but is not required for maintaining the undifferentiated state. Instead, Ell3 binding to inactive or poised enhancers is essential for marking them for stem cell specification through regulating the activation of key lineage-specific genes throughout differentiation. Ell3’s association with enhancers is required for setting up proper Pol II occupancy at the proximal promoter regions of neighboring genes. This functional interaction between Ell3 and proximal promoter Pol II is dependent on cohesin. The depletion of cohesin subunits removes Ell3 from the enhancers and results in reduction in the levels of promoter proximally paused Pol II. Our study demonstrates that Ell3 is required for stem cell fate specification through regulating Pol II pausing on key developmental genes in the undifferentiated state and for their proper expression during differentiation.
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| Overall design |
ChIP-seq of Ell3 in mES cells. ChIP-seq of Pol II in mES cells after Ell3 shRNA and non-targeting shRNA. RNA-seq of mES cells after Ell3 shRNA and non-targeting shRNA. RNA-seq of mouse embryoid bodies at day five after non-targeting shRNA.
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| Contributor(s) |
Garruss AS, Lin C, Shilatifard A |
| Citation(s) |
23273992 |
| |
| Submission date |
May 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander (Garrett) Garruss |
| E-mail(s) |
[email protected]
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Shilatifard
|
| Street address |
1000 East 50th Street
|
| City |
Kansas CIty |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (12)
|
| GSM935894 |
ChIP-seq of WCE in mES after non-targeting shRNA |
| GSM935895 |
ChIP-seq of Pol2 in mES after Ell3 shRNA |
| GSM935896 |
ChIP-seq of WCE in mES after Ell3 shRNA |
| GSM935897 |
RNA-seq of mES total RNA after non-targeting shRNA replicate 1 |
| GSM935898 |
RNA-seq of mES total RNA after non-targeting shRNA replicate 2 |
| GSM935899 |
RNA-seq of mES total RNA after Ell3 shRNA replicate 1 |
| GSM935900 |
RNA-seq of mES total RNA after Ell3 shRNA replicate 2 |
| GSM935901 |
RNA-seq of embryoid bodies at day 5 total RNA after non-targeting shRNA replicate 1 |
| GSM935902 |
RNA-seq of embryoid bodies at day 5 total RNA after non-targeting shRNA replicate 2 |
|
| Relations |
| BioProject |
PRJNA167281 |
| SRA |
SRP013333 |
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