TY - JOUR
T1 - Characterization of the phosphoinositide 3-kinase-dependent transcriptome in murine embryonic stem cells
T2 - identification of novel regulators of pluripotency
AU - Storm, Michael P.
AU - Kumpfmueller, Benjamin
AU - Thompson, Belinda
AU - Kolde, Raivo
AU - Vilo, Jaak
AU - Hummel, Oliver
AU - Schulz, Herbert
AU - Welham, Melanie J.
PY - 2009/4
Y1 - 2009/4
N2 - 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.
AB - 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.
KW - Embryonic stem cells
KW - Microarray analysis
KW - Shp-1 protein tyrosine phosphatase
KW - 1-Phosphoinositol 3-kinase
KW - Zscan4
KW - Pluripotent
UR - http://dx.doi.org/10.1002/stem.3
UR - http://www.scopus.com/inward/record.url?scp=65649127710&partnerID=8YFLogxK
U2 - 10.1002/stem.3
DO - 10.1002/stem.3
M3 - Article
SN - 1066-5099
VL - 27
SP - 764
EP - 775
JO - Stem Cells
JF - Stem Cells
IS - 4
ER -