Introduction

Transcription factors (TFs) and their specific interactions with targets are crucial for specifying gene-expression programs. To gain insights into the transcriptional regulatory networks in embryonic stem (ES) cells, we use chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequencing (ChIP-seq) to map the locations of 13 sequence-specific TFs (Nanog, Oct4, STAT3, Smad1, Sox2, Zfx, c-Myc, n-Myc, Klf4, Esrrb, Tcfcp2l1, E2f1, and CTCF) and 2 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 into the ES-cell-specific transcription circuitries. Intriguingly, we find specific genomic regions extensively targeted by different TFs. Collectively, the comprehensive mapping of TF-binding sites identifies important features of the transcriptional regulatory networks that define ES-cell identity.

Publications

  1. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.
    Cite this
    Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH, 2008-06-01 - Cell

Credits

  1. Xi Chen
    Developer

  2. Han Xu
    Developer

  3. Ping Yuan
    Developer

  4. Fang Fang
    Developer

  5. Mikael Huss
    Developer

  6. Vinsensius B Vega
    Developer

  7. Eleanor Wong
    Developer

  8. Yuriy L Orlov
    Developer

  9. Weiwei Zhang
    Developer

  10. Jianming Jiang
    Developer

  11. Yuin-Han Loh
    Developer

  12. Hock Chuan Yeo
    Developer

  13. Zhen Xuan Yeo
    Developer

  14. Vipin Narang
    Developer

  15. Kunde Ramamoorthy Govindarajan
    Developer

  16. Bernard Leong
    Developer

  17. Atif Shahab
    Developer

  18. Yijun Ruan
    Developer

  19. Guillaume Bourque
    Developer

  20. Wing-Kin Sung
    Developer

  21. Neil D Clarke
    Developer

  22. Chia-Lin Wei
    Developer

  23. Huck-Hui Ng
    Investigator

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Summary
AccessionBT006537
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByHuck-Hui Ng