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name: Chickarmane2008 - Stem cell lineage - NANOG GATA-6 switch
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notes: Chickarmane2008 - Stem cell lineage - NANOG GATA-6 switch In this work, a dynamical model of lineage determination based upon a minimal circuit, as discussed in PMID: 17215298 , which contains the Oct4/Sox2/Nanog core as well its interaction with a few other key genes is discussed. This model is described in the article: A computational model for understanding stem cell, trophectoderm and endoderm lineage determination. Chickarmane V, Peterson C PloS one. 2008, 3(10):e3478 Abstract: BACKGROUND: Recent studies have associated the transcription factors, Oct4, Sox2 and Nanog as parts of a self-regulating network which is responsible for maintaining embryonic stem cell properties: self renewal and pluripotency. In addition, mutual antagonism between two of these and other master regulators have been shown to regulate lineage determination. In particular, an excess of Cdx2 over Oct4 determines the trophectoderm lineage whereas an excess of Gata-6 over Nanog determines differentiation into the endoderm lineage. Also, under/over-expression studies of the master regulator Oct4 have revealed that some self-renewal/pluripotency as well as differentiation genes are expressed in a biphasic manner with respect to the concentration of Oct4. METHODOLOGY/ PRINCIPAL FINDINGS: We construct a dynamical model of a minimalistic network, extracted from ChIP-on-chip and microarray data as well as literature studies. The model is based upon differential equations and makes two plausible assumptions; activation of Gata-6 by Oct4 and repression of Nanog by an Oct4-Gata-6 heterodimer. With these assumptions, the results of simulations successfully describe the biphasic behavior as well as lineage commitment. The model also predicts that reprogramming the network from a differentiated state, in particular the endoderm state, into a stem cell state, is best achieved by over-expressing Nanog, rather than by suppression of differentiation genes such as Gata-6. CONCLUSIONS: The computational model…
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ORG:
  orgname: EMBL-EBI
n:
  given: Lukas
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ORG:
  orgname: Keck Graduate Institute, California
n:
  given: Vijay
  family: Chickarmane

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

W3 CDTF: Fri Dec 05 15:38:48 GMT 2008

W3 CDTF: Wed Jun 05 17:41:07 BST 2013

ORG:
  orgname: Lund Strategic Research Centre for Stem Cell Biology and Cell Therapy, Lund University, Sweden.
n:
  given: Carsten
  family: Peterson