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Open Access Highly Accessed Research article

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

Marina Trouillas123, Claire Saucourt12, Bertrand Guillotin12, Xavier Gauthereau12, Li Ding4, Frank Buchholz4, Michael Xavier Doss5, Agapios Sachinidis5, Jurgen Hescheler5, Oliver Hummel6, Norbert Huebner6, Raivo Kolde7, Jaak Vilo7, Herbert Schulz6 and Hélène Bœuf12*

Author Affiliations

1 Université Bordeaux, Bordeaux, France

2 CNRS-UMR-5164-CIRID, Bordeaux, France

3 CTSA, Département Recherches et Thérapies Cellulaires, Clamart, France

4 MPI-CBG, Pfotenhauer Str. 108, 01307 Dresden, Germany

5 Center of physiology and Pathophysiology, Institute of Neurophysiology and Center of Molecular Medecine, University of Cologne (CMMC), Robert Koch Strasse 39, 50931 Cologne, Germany

6 Max-Delbrück Center for Molecular Medecine, MDC Berlin, Buch Robert Roessle, Strasse 10, D13125- Berlin, Germany

7 Institute of Computer Science, University of Tartu, Liivi 2, 50409 Tartu, Estonia and Quretec Ltd, Ulikooli 6a, Tartu, Estonia

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BMC Genomics 2009, 10:73  doi:10.1186/1471-2164-10-73

Published: 9 February 2009

Abstract

Background

Mouse embryonic stem (ES) cells remain pluripotent in vitro when grown in the presence of the cytokine Leukaemia 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.

Conclusion

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.