Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment

Emily Walker; Minako Ohishi; Ryan E Davey; Wen Zhang; Paul A Cassar; Tetsuya S Tanaka; Sandy D Der; Quaid Morris; Timothy R Hughes; Peter W Zandstra; William L Stanford

doi:10.1016/j.stem.2007.04.002

Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment

Cell Stem Cell. 2007 Jun 7;1(1):71-86. doi: 10.1016/j.stem.2007.04.002.

Authors

Affiliations

¹ Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
² Department of Molecular and Medical Genetics, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
³ Institute of Medical Science, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
⁴ Laboratory Medicine and Pathobiology, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
⁵ Banting and Best Department of Medical Research, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
⁶ Department of Molecular and Medical Genetics, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada; Banting and Best Department of Medical Research, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
⁷ Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
⁸ Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada; Department of Molecular and Medical Genetics, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada. Electronic address: william.stanford@utoronto.ca.

PMID: 18371337
DOI: 10.1016/j.stem.2007.04.002

Abstract

Stem cell fate is governed by the integration of intrinsic and extrinsic positive and negative signals upon inherent transcriptional networks. To identify novel embryonic stem cell (ESC) regulators and assemble transcriptional networks controlling ESC fate, we performed temporal expression microarray analyses of ESCs after the initiation of commitment and integrated these data with known genome-wide transcription factor binding. Effects of forced under- or overexpression of predicted novel regulators, defined as differentially expressed genes with potential binding sites for known regulators of pluripotency, demonstrated greater than 90% correspondence with predicted function, as assessed by functional and high-content assays of self-renewal. We next assembled 43 theoretical transcriptional networks in ESCs, 82% (23 out of 28 tested) of which were supported by analysis of genome-wide expression in Oct4 knockdown cells. By using this integrative approach, we have formulated novel networks describing gene repression of key developmental regulators in undifferentiated ESCs and successfully predicted the outcomes of genetic manipulation of these networks.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Lineage
DNA-Binding Proteins / genetics
Electroporation
Embryonic Stem Cells / cytology*
HMGB Proteins / genetics
Humans
Octamer Transcription Factor-3 / genetics
Pluripotent Stem Cells / cytology
Polymerase Chain Reaction
RNA, Small Interfering
SOXB1 Transcription Factors
Transcription Factors / genetics
Transcription, Genetic*

Substances

DNA-Binding Proteins
HMGB Proteins
Octamer Transcription Factor-3
Pou5f1 protein, mouse
RNA, Small Interfering
SOX2 protein, human
SOXB1 Transcription Factors
Sox2 protein, mouse
Transcription Factors

Associated data

GEO/GSE7506
GEO/GSE7520