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Series GSE30538 Query DataSets for GSE30538
Status Public on Oct 11, 2011
Title Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors comprising retinoic acid (RARa,b,g) and retinoid X (RXRa,b,g) receptors. How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes is unclear. Using an RA-inducible differentiation model we defined the temporal changes in the genome-wide binding patterns of RARg and RXRa and correlated them with transcription regulation. Unexpectedly, both receptors displayed a highly dynamic binding, with different RXRa heterodimers targeting identical loci. Comparison of RARg and RXRa co-binding at RA-regulated genes identified putative RXRa-RARg target genes that were validated with subtype-selective agonists. Gene regulatory decisions during differentiation were inferred from transcription factor target gene information and temporal gene expression. This analysis revealed 6 distinct co-expression paths of which RXRa-RARg is associated with transcription activation, while Sox2 and Egr1 were predicted to regulate repression. Finally, RXRa-RARg regulatory networks were reconstructed through integration of functional co-citations. Our analysis provides a dynamic view of RA signalling during cell differentiation, reveals RA heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs.
 
Overall design RXRa; RARg and RNA Polymerase II chromatin binding has been assessed at five time points; in addition an input control for F9 cells as well as a RXRa ChIP-seq assay from a rxra-/- ko strain has been performed.
 
Contributor(s) Mendoza-Parra MA, Walia M, Sankar M, Gronemeyer H
Citation(s) 21988834
Submission date Jul 10, 2011
Last update date May 15, 2019
Contact name Marco Antonio Mendoza-Parra
E-mail(s) marco@igbmc.fr
Organization name IGBMC
Street address 1, rue Laurent Fries
City Illkirch; Strasbourg
ZIP/Postal code 67400
Country France
 
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (20)
GSM757794 RXRa_48h-EtOH_ChIP-seq
GSM757795 RXRa_2h-ATRA_ChIP-seq
GSM757796 RXRa_6h-ATRA_ChIP-seq
This SubSeries is part of SuperSeries:
GSE30539 Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics
Relations
SRA SRP007613
BioProject PRJNA154779

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
GSE30538_RAW.tar 1.0 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data not provided for this record
Processed data included within Sample table
Raw data are available in SRA

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