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Series GSE31006 Query DataSets for GSE31006
Status Public on Sep 15, 2011
Title An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Alternative splicing (AS) is a key process underlying the expansion of proteomic diversity and the regulation of gene expression. However, the contribution of AS to the control of embryonic stem cell (ESC) pluripotency is not well understood. Here, we identify an evolutionarily conserved ESC-specific AS event that changes the DNA binding preference of the forkhead family transcription factor FOXP1. We show that the ESC-specific isoform of FOXP1 stimulates the expression of transcription factor genes required for pluripotency including OCT4, NANOG, NR5A2 and GDF3, while concomitantly repressing genes required for ESC differentiation. Remarkably, this isoform also promotes the maintenance of ESC pluripotency and the efficient reprogramming of somatic cells to induced pluripotent stem cells. These results thus reveal that an AS switch plays a pivotal role in the regulation of pluripotency and functions by controlling critical ESC-specific transcriptional programs.
Overall design To identify genes potentially directly regulated by FOXP1-ES and FOXP1 in H9 ESCs, we performed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq). Using an antibody capable of efficiently immunoprecipitating both isoforms, >3400 significant ChIP-Seq peaks were detected across the human genome. To assess if these peaks are sites of FOXP1 and FOXP1-ES occupancy, we determined whether they are significantly enriched in individual PBM-derived 8-mers that bind to either or both isoforms.
Contributor(s) Gabut M, Samavarchi-Tehrani P, Wang X, Slobodeniuc V, O'Hanlon D, Sung H, Alvarez M, Talukder S, Pan Q, Woltjen K, Mazzoni EO, Nedelec S, Wichterle H, Hughes TR, Zandstra P, Nagy A, Wrana JL, Blencowe BJ
Citation(s) 21924763
Submission date Jul 28, 2011
Last update date May 15, 2019
Contact name Xinchen Wang
Organization name MIT
Street address 32 Vassar St, D514
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (4)
GSM768310 FOXP1_ChIP-Seq_1
GSM768311 FOXP1_ChIP-Seq_2
GSM768312 WCE_1
This SubSeries is part of SuperSeries:
GSE30992 An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming
SRA SRP008254
BioProject PRJNA154619

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

Supplementary file Size Download File type/resource
GSE31006_RAW.tar 1020.0 Kb (http)(custom) TAR (of FA)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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