Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

@article{Chen2008IntegrationOE,
  title={Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells},
  author={X. Chen and Han Xu and Ping Yuan and Fang Fang and Mikael Huss and Vinsensius B. Vega and Eleanor Wong and Yuriy L. Orlov and Weiwei Zhang and Jianming Jiang and Yuin Han Loh and Hock Chuan Yeo and Zhen Xuan Yeo and Vipin Narang and Kunde Ramamoorthy Govindarajan and Bernard Leong and Atif Shahab and Yijun Ruan and Guillaume Bourque and Wing-Kin Sung and Neil D. Clarke and Chia-Lin Wei and Huck-Hui Ng},
  journal={Cell},
  year={2008},
  volume={133},
  pages={1106-1117}
}
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… 
Transcriptional regulatory networks in embryonic stem cells.
  • X. Chen, V. Vega, H. Ng
  • Biology, Medicine
    Cold Spring Harbor symposia on quantitative biology
  • 2008
TLDR
Studying the properties of ES-cell-specific enhanceosomes in different pluripotent cells will shed light on the composition and regulation of their activity and help to distinguish the core and peripheral parts of the networks.
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Computer and Statistical Analysis of Transcription Factor Binding and Chromatin Modifications by ChIP-seq data in Embryonic Stem Cell
TLDR
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Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell.
TLDR
Computer program is developed to filter out noise signals and find significant association between binding site affinity and number of sequence reads in genome ChIP-sequencing maps, which provide new insights into the function of chromatin organization and regulation in stem cells.
Examination of transcriptional networks reveals an important role for TCFAP2C, SMARCA4, and EOMES in trophoblast stem cell maintenance.
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Through genome-wide mapping and global expression analysis of five TF target genes, the data provide a comprehensive analysis of transcriptional networks that regulate TS cell self-renewal.
Systematic identification of transcriptional regulatory modules from protein–protein interaction networks
TLDR
The prediction and experimental validation of the co-factors that endow master regulatory TFs with the capacity to select specific genomic sites, modulate the local epigenetic profile and integrate multiple signals will provide important mechanistic insights not only into how such TFs operate, but also into abnormal transcriptional states leading to disease.
The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells
TLDR
The authors show that TF Nanog utilises multiple molecular strategies to enhance embryonic stem cell self-renewal, which include regulation of chromatin accessibility in the presence of LIF or maintenance of H3K27me3 at developmental regulators in its absence.
Stat3 and c-Myc Genome-Wide Promoter Occupancy in Embryonic Stem Cells
TLDR
Investigation of genome-wide chromatin immunoprecipitation and microarray analysis reveals transcriptional targets of two key pluripotency-related genes in ES cells – Stat3 and c-Myc, thus providing further insight into the ES cell transcriptional network.
A central role for TFIID in the pluripotent transcription circuitry
TLDR
This work shows that knockdown of the transcription factor IID (TFIID) complex affects the pluripotent circuitry in mouse ES cells and inhibits reprogramming of fibroblasts, and shows that TFIID is critical for transcription-factor-mediated reprograming.
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