Transcriptomics,Multiomics

Dataset Information

4

Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression


ABSTRACT: POU transcription factor Pou5f1 (Oct3/4) is required to maintain ES cells in an undifferentiated state. Here we show that global expression profiling of Oct3/4-manipulated ES cells delineates the downstream target genes of Oct3/4. Combined with data from genome-wide chromatin-immunoprecipitation assays, this analysis identifies not only primary downstream targets of Oct3/4, but also secondary or tertiary targets. Furthermore, the analysis also reveals that downstream target genes are regulated either positively or negatively by Oct3/4. Identification of a group of genes that show both activation and repression depending on Oct3/4 expression levels provides a possible mechanism for the requirement of appropriate Oct3/4 expression to maintain undifferentiated ES cells. As a proof-of-principle study, one of the downstream genes, Tcl1, has been analyzed in detail. We show that Oct3/4 binds to the promoter region of Tcl1 and activates its transcription. We also show that Tcl1 is involved in the regulation of proliferation, but not differentiation, in ES cells. These findings suggest that the global expression profiling of gene-manipulated ES cells can help to delineate the structure and dynamics of gene regulatory networks. Keywords: development or differentiation design,time series design ZHBTc4, ZHTc6, and EB5 ES cells were cultured without feeder cells in LIF-supplemented medium as described . For differentiation, ZHTc6 cells were cultured in the absence of Tet, which induced the overexpression of Oct3/4. ZHBTc4 cells were cultured in the presence of Tet, repressing Oct3/4 expression. Trophoblast stem (TS) cells and another ES cell line (R1) were cultured as previously described . Three independent samples were prepared for each time point. Microarray experiments were carried out as described using the NIA Mouse 22K Microarray v1.0.

OTHER RELATED OMICS DATASETS IN: PRJNA97383

SUBMITTER: Minoru S.H. Ko   Shinji Masui  Mark G Carter  Hitoshi Niwa  Satoshi Ohtsuka  Minoru S Ko  Alexei A Sharov  Ryo Matoba 

PROVIDER: E-GEOD-5936 | ArrayExpress | 2010-06-30

SECONDARY ACCESSION(S): GSE5936PRJNA97383

REPOSITORIES: GEO, ArrayExpress

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E-GEOD-5936.README.txt Txt
E-GEOD-5936.idf.txt Idf
E-GEOD-5936.processed.1.zip Processed
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Publications

Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression profiling.

Matoba Ryo R   Niwa Hitoshi H   Masui Shinji S   Ohtsuka Satoshi S   Carter Mark G MG   Sharov Alexei A AA   Ko Minoru S H MS  

PloS one 20061220


POU transcription factor Pou5f1 (Oct3/4) is required to maintain ES cells in an undifferentiated state. Here we show that global expression profiling of Oct3/4-manipulated ES cells delineates the downstream target genes of Oct3/4. Combined with data from genome-wide chromatin-immunoprecipitation (ChIP) assays, this analysis identifies not only primary downstream targets of Oct3/4, but also secondary or tertiary targets. Furthermore, the analysis also reveals that downstream target genes are regu  ...[more]

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