Characterization of the phosphoinositide 3-kinase-dependent transcriptome in murine embryonic stem cells

identification of novel regulators of pluripotency

Michael P. Storm, Benjamin Kumpfmueller, Belinda Thompson, Raivo Kolde, Jaak Vilo, Oliver Hummel, Herbert Schulz, Melanie J. Welham

Research output: Contribution to journalArticle

41 Citations (Scopus)

Abstract

Phosphoinositide 3-kinase (PI3K)-dependent signaling has been implicated in the regulation of embryonic stem (ES) cell fate. To gain further insight into the mechanisms regulated by PI3Ks in murine ES cells, we have performed expression pro. ling using Affymetrix GeneChips to characterize the transcriptional changes that arise as a result of inhibition of PI3K-dependent signaling. Using filtering of greater than 1.5-fold change in expression and an analysis of variance significance level of p < .05, we have defined a dataset comprising 646 probe sets that detect changes in transcript expression (469 down and 177 up) on inhibition of PI3Ks. Changes in expression of selected genes have been validated by quantitative reverse transcription polymerase chain reaction. Gene ontology analyses reveal significant over-representation of transcriptional regulators within our dataset. In addition, several known regulators of ES cell pluripotency, for example, Nanog, Esrrb, Tbx3, and Tcl-1, are among the downregulated genes. To evaluate the functional involvement of selected genes in regulation of ES cell self-renewal, we have used short interfering RNA-mediated knockdown. These studies identify genes not previously associated with control of ES cell fate that are involved in regulating ES cell pluripotency, including the protein tyrosine phosphatase Shp-1 and the Zscan4 family of zinc finger proteins. Further gain-of-function analyses demonstrate the importance of Zscan4c in regulation of ES cell pluripotency.
Original languageEnglish
Pages (from-to)764-775
Number of pages12
JournalStem Cells
Volume27
Issue number4
Early online date15 Jan 2009
DOIs
Publication statusPublished - Apr 2009

Fingerprint

1-Phosphatidylinositol 4-Kinase
Embryonic Stem Cells
Transcriptome
Phosphatidylinositol 3-Kinases
Genes
Gene Ontology
Protein Tyrosine Phosphatases
Zinc Fingers
Small Interfering RNA
Reverse Transcription
Analysis of Variance
Down-Regulation
Gene Expression
Polymerase Chain Reaction

Keywords

  • Embryonic stem cells
  • Microarray analysis
  • Shp-1 protein tyrosine phosphatase
  • 1-Phosphoinositol 3-kinase
  • Zscan4
  • Pluripotent

Cite this

Characterization of the phosphoinositide 3-kinase-dependent transcriptome in murine embryonic stem cells : identification of novel regulators of pluripotency. / Storm, Michael P.; Kumpfmueller, Benjamin; Thompson, Belinda; Kolde, Raivo; Vilo, Jaak; Hummel, Oliver; Schulz, Herbert; Welham, Melanie J.

In: Stem Cells, Vol. 27, No. 4, 04.2009, p. 764-775.

Research output: Contribution to journalArticle

Storm, Michael P. ; Kumpfmueller, Benjamin ; Thompson, Belinda ; Kolde, Raivo ; Vilo, Jaak ; Hummel, Oliver ; Schulz, Herbert ; Welham, Melanie J. / Characterization of the phosphoinositide 3-kinase-dependent transcriptome in murine embryonic stem cells : identification of novel regulators of pluripotency. In: Stem Cells. 2009 ; Vol. 27, No. 4. pp. 764-775.
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