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Series GSE69592 Query DataSets for GSE69592
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
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.
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.
Contributor(s) Panning B, Peddada S
Citation(s) 26949256
Submission date Jun 04, 2015
Last update date May 15, 2019
Contact name Barbara Panning
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
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (10)
GSM1704272 R1a_fSOX2_long
GSM1704273 R1b_fSox2_long
GSM1704274 R2a_fSox2_short
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
BioProject PRJNA285924
SRA SRP059152

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE69592_RAW.tar 3.0 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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