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Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives

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Item Type:Article
Title:Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives
Creators Name:Trouillas, M. and Saucourt, C. and Guillotin, B. and Gauthereau, X. and Ding, L. and Buchholz, F. and Doss, M.X. and Sachinidis, A. and Hescheler, J. and Hummel, O. and Huebner, N. and Kolde, R. and Vilo, J. and Schultz, H. and Boeuf, H.
Abstract:BACKGROUND: Mouse embryonic stem (ES) cells remain pluripotent in vitro when grown in the presence of the cytokine Leukemia Inhibitory Factor (LIF). Identification of LIF targets and of genes regulating the transition between pluripotent and early differentiated cells is a critical step for understanding the control of ES cell pluripotency. RESULTS: By gene profiling studies carried out with mRNAs from ES cells and their early derivatives treated or not with LIF, we have identified i) LIF-dependent genes, highly expressed in pluripotent cells, whose expression level decreases sharply upon LIF withdrawal [Pluri genes], ii) LIF induced genes [Lifind genes] whose expression is differentially regulated depending upon cell context and iii) genes specific to the reversible or irreversible committed states. In addition, by hierarchical gene clustering, we have identified, among eight independent gene clusters, two atypical groups of genes, whose expression level was highly modulated in committed cells only. Computer based analyses led to the characterization of different sub-types of Pluri and Lifind genes, and revealed their differential modulation by Oct4 or Nanog master genes. Individual knock down of a selection of Pluri and Lifind genes leads to weak changes in the expression of early differentiation markers, in cell growth conditions in which these master genes are still expressed. CONCLUSIONS: We have identified different sets of LIF-regulated genes depending upon the cell state (reversible or irreversible commitment) which allowed us to present a novel global view of LIF responses. We are also reporting on the identification of genes whose expression is strictly regulated during the commitment step. Furthermore, our studies identify sub-networks of genes with a restricted expression in pluripotent ES cells, whose down regulation occurs while the master knot (composed of OCT4, SOX2 and NANOG) is still expressed and which might be down-regulated together for driving cells towards differentiation.
Keywords:Cell Differentiation, Cell Line, Cluster Analysis, Embryonic Stem Cells, Gene Expression Profiling, Developmental Gene Expression Regulation, Homeodomain Proteins, Leukemia Inhibitory Factor, Octamer Transcription Factor-3, Oligonucleotide Array Sequence Analysis, Pluripotent Stem Cells, Animals, Mice
Source:BMC Genomics
ISSN:1471-2164
Publisher:BioMed Central (U.K.)
Volume:10
Number:1
Page Range:73
Date:9 February 2009
Official Publication:https://doi.org/10.1186/1471-2164-10-73
PubMed:View item in PubMed

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