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  A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells

Jung, M., Peterson, H., Chavez, L., Kahlem, P., Lehrach, H., Vilo, J., et al. (2010). A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PLoS ONE, 5(5), e10709-e10709. doi:10.1371/journal.pone.0010709.

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Jung, M.1, Author
Peterson, H., Author
Chavez, L.2, Author              
Kahlem, P., Author
Lehrach, H.2, Author              
Vilo, J., Author
Adjaye, J.3, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
2Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
3Molecular Embryology and Aging (James Adjaye), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479654              

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Free keywords: Algorithms; Amino Acid Motifs; Base Sequence; Computational Biology/methods; Conserved Sequence; Databases, Genetic; Embryonal Carcinoma Stem Cells/metabolism; Embryonic Stem Cells/metabolism; Evolution, Molecular; Gene Regulatory Networks/genetics; Genome, Human/genetics; Humans; Models, Genetic; Molecular Sequence Data; Octamer Transcription Factor-3/*genetics; Promoter Regions, Genetic/genetics; Protein Binding; Quality Control; Reproducibility of Results; SOXB1 Transcription Factors/metabolism; Sequence Alignment; Statistics as Topic
 Abstract: It is essential to understand the network of transcription factors controlling self-renewal of human embryonic stem cells (ESCs) and human embryonal carcinoma cells (ECs) if we are to exploit these cells in regenerative medicine regimes. Correlating gene expression levels after RNAi-based ablation of OCT4 function with its downstream targets enables a better prediction of motif-specific driven expression modules pertinent for self-renewal and differentiation of embryonic stem cells and induced pluripotent stem cells.We initially identified putative direct downstream targets of OCT4 by employing CHIP-on-chip analysis. A comparison of three peak analysis programs revealed a refined list of OCT4 targets in the human EC cell line NCCIT, this list was then compared to previously published OCT4 CHIP-on-chip datasets derived from both ES and EC cells. We have verified an enriched POU-motif, discovered by a de novo approach, thus enabling us to define six distinct modules of OCT4 binding and regulation of its target genes.A selection of these targets has been validated, like NANOG, which harbours the evolutionarily conserved OCT4-SOX2 binding motif within its proximal promoter. Other validated targets, which do not harbour the classical HMG motif are USP44 and GADD45G, a key regulator of the cell cycle. Over-expression of GADD45G in NCCIT cells resulted in an enrichment and up-regulation of genes associated with the cell cycle (CDKN1B, CDKN1C, CDK6 and MAPK4) and developmental processes (BMP4, HAND1, EOMES, ID2, GATA4, GATA5, ISL1 and MSX1). A comparison of positively regulated OCT4 targets common to EC and ES cells identified genes such as NANOG, PHC1, USP44, SOX2, PHF17 and OCT4, thus further confirming their universal role in maintaining self-renewal in both cell types. Finally we have created a user-friendly database (http://biit.cs.ut.ee/escd/), integrating all OCT4 and stem cell related datasets in both human and mouse ES and EC cells.In the current era of systems biology driven research, we envisage that our integrated embryonic stem cell database will prove beneficial to the booming field of ES, iPS and cancer research.

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Language(s): eng - English
 Dates: 2010-05-21
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: eDoc: 556501
DOI: 10.1371/journal.pone.0010709
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Title: PLoS ONE
Source Genre: Journal
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Pages: - Volume / Issue: 5 (5) Sequence Number: - Start / End Page: e10709 - e10709 Identifier: ISSN: 1932-6203 (Electronic)