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Stem Cells Dev 2006 Jun;15(3):315-23

Comparisons between transcriptional regulation and RNA expression in human embryonic stem cell lines.

Player A, Wang Y, Bhattacharya B, Rao M, Puri RK, Kawasaki ES

Player A, NCI, Ctr Adv Technol, NIH, Microarray Facil, 8717 Grovemont Circle, Bethesda, MD 20892 USA NCI, Ctr Adv Technol, NIH, Microarray Facil, Bethesda, MD 20892 USA SAIC Frederick Inc, NCI Frederick, Frederick, MD 21702 USA US FDA, Ctr Biol & Evaluat & Res, Tumor Vaccines & Biotechnol Branch, Bethesda, MD 20892 USA NIA, Neurosci Lab, Baltimore, MD 21224 USA


Recent studies have focused on transcriptional regulation and gene expression profiling of human embryonic stem cells (hESCs). However, little information is available regarding the relationship between RNA expression and transcriptional regulation, which is critical in the complete understanding of pluripotency and differentiation of hESCs. In the current study, we determined RNA expression of three different hESC lines compared to Human universal reference RNA expression (HuU-RNA) using a full genome expression microarray, and compared our results to target genes previously identified using ChIP-on-chip analysis. The objective was to identify genes common between the two methods, and generate a more reliable list of embryonic signature genes. Even though hESCs were obtained from different sources and maintained under different conditions, a considerable number of genes could be identified as common between RNA expression and transcriptional regulation analyses. As an example, results from ChIP-on-chip studies show that OCT4, SOX2, and NANOG co-occupy SOX2, OCT4, TDGF1, GJA1, SET, and DPPA4 genes. The results are consistent with RNA expression analyses that demonstrate these genes as differently expressed in our hESC lines, further substantiating their role across cell types and confirming their importance as embryonic signatures. In addition, we report the differential expression of growth arrest-specific (GAS) family of genes in hESC. GAS2L1 and GAS3 members of this family appear to be transcriptionally regulated by OCT4, SOX2, or NANOG, whereas GAS5 and GAS6 are not; all of the genes are differentially expressed, as determined by microarray and validated via quantitative (Q)- PCR. Collectively, these data provide insight into the relationship between gene expression and transcriptional regulation, resulting in a reliable list of genes associated with hESCs.

Category: Journal Article
PubMed ID: #16846370
Includes FDA Authors from Scientific Area(s): Biologics
Entry Created: 2011-10-04 Entry Last Modified: 2012-08-29