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

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. Overall design: profiling of time series ChIP-seq datasets in two related embryonic stem cells. 5 different factors assessed in 5 timepoints in 2 different cell lines. In addition two input control samples (one per cell line): Total=52 datasets.