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Series GSE39513 Query DataSets for GSE39513
Status Public on Oct 26, 2012
Title Regulation of pluripotency and self-renewal of ES cells through epigenetic-threshold modulation and mRNA pruning
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The core pluripotency factors (Oct4, Sox2, and Nanog), the Myc network, and the chromatin-modifying complexes such as PRC2 ensure the pluripotency and self-renewal of ES cells (ESC). How these factors coordinate with one another remains poorly understood. We report that Utf1, a target of Oct4 and Sox2, is a new bivalent chromatin component that buffers poised states of bivalent genes. By limiting PRC2 loading and Histone 3 lysine-27 trimethylation, Utf1 sets proper activation thresholds for bivalent genes. It also promotes nuclear tagging of mRNAs transcribed from insufficiently silenced bivalent genes for cytoplasmic degradation through mRNA de-capping. Whereas these opposing functions of Utf1 allow proper execution of ESC pluripotency, the mRNA pruning function also ensures rapid cell proliferation by blocking the Myc-Arf feedback regulation. Thus, Utf1 is an important regulator that couples the core pluripotency factors with Myc and PRC2 networks to promote proliferation and pluripotency execution of ESCs.
Overall design First we mapped Utf1 binding sites in ESCs using the biotin-mediated and cross-linked ChIP-sequencing. To investigate how Utf1 might regulate gene expression, we did RNA-seq on WT and Utf1-KO ES cells. Then we did ChIP-seq of Suz12 and H3K27me3 on WT and Utf1-KO ES cells to study whether Utf1 affects PRC2 loading and H3K27me3 modofication, using H3 as control. Finally, we did RNAseq on WT and Dcp1a-KD ES cells to confirm Utf1 repress gene expression by recruiting Dcp1a complex.
Contributor(s) Jia J, Zheng X, Hu G, Cui K, Zhao K, Zheng Y
Citation(s) 23101626
Submission date Jul 19, 2012
Last update date May 15, 2019
Contact name Yixian Zheng
Organization name Carnegie Institution for Science
Department Embryology
Lab Yixian Zheng
Street address 3520 San Martin Drive
City Baltimore
State/province MD
ZIP/Postal code 21218
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (21)
GSM970523 Input
GSM970524 Utf1
GSM970525 BirA-Control
BioProject PRJNA171100
SRA SRP014645

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Supplementary file Size Download File type/resource
GSE39513_RAW.tar 6.9 Gb (http)(custom) TAR (of BED, BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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