Mapping of transcription factor binding sites in mouse embryonic stem cells

Transcription factors and their specific interactions with targets are crucial in specifying gene expression programs. To gain insights into the transcriptional regulatory networks in embryonic stem cells, we use chromatin immunoprecipitation coupled to ultra-high-throughput DNA sequencing (ChIP-seq) to map the locations of thirteen sequence specific transcription factors (Nanog, Oct4, STAT3, Smad1, Sox2, Zfx, c-Myc, n-Myc, Klf4, Esrrb, Tcfcp2l1, E2f1 and CTCF) and two transcription regulators (p300 and Suz12). These factors are known to play different roles in ES cell biology as components of the LIF and BMP signaling pathways, self-renewal regulators and key reprogramming factors. Our study provides insights into the integration of the signaling pathways to the ES cell-specific transcription circuitries. Intriguingly, we find specific genomic regions extensively targeted by different transcription factors. Collectively, the comprehensive mapping of transcription factor binding sites identifies important features of the transcriptional regulatory networks that define ES cell identity. Keywords: Transcription factor binding sites in undifferentiated mouse embryonic stem cells ChIP-enriched DNA from pooled ChIP samples were analyzed by Solexa sequencing.