Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells [Affymetrix]

We have integrated dynamic RXRa binding, chromatin accessibility and promoter epigenetic status with the transcriptional activity inferred from RNA polymerase II mapping and transcription profiling. This demonstrated a temporal organization structure, in which early events are preferentially enriched for common GRNs, while cell fate specification is reflected by the activation of late programs in a cell-type specific manner. Furthermore, significant differences in cell lines' promoter status of genes associated with cell-line specific programs were inferred. Finally, a variety of transcription factors (TFs) playing a direct role in the signal transduction cascade downstream of the RXR/RAR initiated wiring were identified, several of them commonly regulated in both model systems, but in addition cell-type specific TF drivers were also identified. time series gene expression assessed over the retinoic acide induced differentiation in P19 and F9 embryonal carcinoma cells. 5 timepoints over four different treatment conditions (ATRA; RARa agonist BMS753; RARb agonist BMS641 and the RARg agonist BMS961) assessed in P19 cells and compared with those assessed in F9 cells described in a previous study: GSE30537