Open AccessCharacterization of the Phosphoinositide 3‐Kinase‐Dependent Transcriptome in Murine Embryonic Stem Cells: Identification of Novel Regulators of Pluripotency
Author(s) -
Storm Michael P.,
Kumpfmueller Benjamin,
Thompson Belinda,
Kolde Raivo,
Vilo Jaak,
Hummel Oliver,
Schulz Herbert,
Welham Melanie J.
Publication year - 2009
Publication title -
stem cells
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.159
H-Index - 229
eISSN - 1549-4918
pISSN - 1066-5099
DOI - 10.1002/stem.3
Subject(s) - biology , homeobox protein nanog , rex1 , embryonic stem cell , microbiology and biotechnology , gene knockdown , transcriptome , stem cell , gene expression profiling , regulation of gene expression , gene expression , gene , induced pluripotent stem cell , genetics
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 profiling 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. S TEM C ELLS 2009;27:764–775