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| Status |
Public on Jan 23, 2015 |
| Title |
Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes accumulation of local H3K9me2, and subsequent Dnmt3a-mediated DNA methylation. Upon binding DNA, Oct4 recruits the histone lysine demethylase Jmjd1c. ChIP timecourse experiments identify a stepwise Oct4 mechanism involving Jmjd1c recruitment and H3K9me2 demethylation, transient FACT complex recruitment, and nucleosome depletion. Genome-wide and targeted ChIP confirms binding of newly-synthesized Oct4, together with Jmjd1c and FACT, to the Pou5f1 enhancer and a small number of other Oct4 targets, including the Nanog promoter. Histone demethylation is required for both FACT recruitment and H3 depletion. Jmjd1c is required to induce endogenous Oct4 expression and fully reprogram fibroblasts to pluripotency, indicating that the assay system identifies functional Oct4 cofactors. These findings indicate that Oct4 sequentially recruits activities that catalyze histone demethylation and depletion.
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| Overall design |
Examination of transcription factor occupancy in cells with newly synthesized Oct4.
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| Contributor(s) |
Shakya A, Callister C, Goren A, Yosef N, Garg N, Khoddami V, Nix D, Regev A, Tantin D |
| Citation(s) |
25582194 |
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| Submission date |
Jan 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Dean Tantin |
| E-mail(s) |
dean.tantin@path.utah.edu
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| Phone |
(801) 587-3035
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| Organization name |
University of Utah
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| Department |
Department of Pathology
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| Street address |
15 North Medical Drive East
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platforms (1) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA273378 |
| SRA |
SRP052745 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE65192_RAW.tar |
969.7 Mb |
(http)(custom) |
TAR (of TDF) |
| GSE65192_Shakya_et_al_Supp_Table_1.xlsx |
123.1 Kb |
(ftp)(http) |
XLSX |
| GSE65192_Shakya_et_al_Supp_Table_2.xlsx |
488.1 Kb |
(ftp)(http) |
XLSX |
| GSE65192_Shakya_et_al_Supp_Table_3.xlsx |
52.4 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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