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| Status |
Public on Mar 07, 2016 |
| Title |
SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells[ChIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The transcription factor SOX2 is central in establishing and maintaining pluripotency. The processes that modulate SOX2 activity to promote pluripotency are not well understood. Here, we show SOX2 is O-GlcNAc modified in its transactivation domain during reprogramming and in mouse embryonic stem cells (mESCs). Upon induction of differentiation SOX2 O-GlcNAcylation at serine 248 is decreased. Replacing wild type with an O-GlcNAc-deficient SOX2 (S248A) increases reprogramming efficiency. ESCs with O-GlcNAc-deficient SOX2 exhibit alterations in gene expression. This change correlates with altered protein-protein interactions and genomic occupancy of the O-GlcNAc-deficient SOX2 compared to wild type. In addition, SOX2 O-GlcNAcylation impairs the SOX2-PARP1 interaction, which has been shown to regulate ESC self-renewal. These findings show that SOX2 activity is modulated by O-GlcNAc modification, and provide a novel regulatory mechanism for this crucial pluripotency transcription factor.
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| Overall design |
We performed FLAG chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) to compare SOX2 genomic distribution in fSOX2-Tg and fS248A-Tg mouse embryonic stem cells. We had two biological replicates for ChIP DNA and one input DNA per cell line. We had two sets of chromatin due to differences in fragment size distribution generated after sonication of the chromatin (long and short) and we decided to use both for library preparation. Long chromatin library was generated from chromatin that still had high molecular weight fragments (1-2Kb-500bp) even after sonication. Short chromatin library was generated using sheared chromatin that had majority of fragments under small molecular weight range (500-200 bp). We sequenced two biological replicates (long and short) and two technical replicates per sonication condition (two longs and two shorts) and one input per cell line. We multiplexed five samples. Sequences were generated using HiSeq 2000.
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| Contributor(s) |
Panning B, Peddada S |
| Citation(s) |
26949256 |
| |
| Submission date |
Jun 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Barbara Panning |
| E-mail(s) |
barbara.panning@gmail.com
|
| Phone |
415-514-0884
|
| Organization name |
University of California, San Francisco
|
| Department |
Biochemistry and Molecular biology
|
| Lab |
Panning Lab
|
| Street address |
600, 16TH STREET, S374 - Genentech Hall,
|
| City |
San Francisco |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE69594 |
SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells |
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| Relations |
| BioProject |
PRJNA285924 |
| SRA |
SRP059152 |
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