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Series GSE38148 Query DataSets for GSE38148
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.
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.
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
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)
GSM935891 ChIP-seq of Ell3 in mES
GSM935892 ChIP-seq of WCE in mES
GSM935893 ChIP-seq of Pol2 in mES after non-targeting shRNA
BioProject PRJNA167281
SRA SRP013333

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Supplementary file Size Download File type/resource
GSE38148_RAW.tar 3.4 Gb (http)(custom) TAR (of BED, TAB)
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Raw data are available in SRA
Processed data provided as supplementary file

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