Abstract
BackgroundLittle is known about the genes that drive embryonic stem cell differentiation. However, such knowledge is necessary if we are to exploit the therapeutic potential of stem cells. To uncover the genetic determinants of mouse embryonic stem cell (mESC) differentiation, we have generated and analyzed 11-point time-series of DNA microarray data for three biologically equivalent but genetically distinct mESC lines (R1, J1, and V6.5) undergoing undirected differentiation into embryoid bodies (EBs) over a period of two weeks.ResultsWe identified the initial 12 hour period as reflecting the early stages of mESC differentiation and studied probe sets showing consistent changes of gene expression in that period. Gene function analysis indicated significant up-regulation of genes related to regulation of transcription and mRNA splicing, and down-regulation of genes related to intracellular signaling. Phylogenetic analysis indicated that the genes showing the largest expression changes were more likely to have originated in metazoans. The probe sets with the most consistent gene changes in the three cell lines represented 24 down-regulated and 12 up-regulated genes, all with closely related human homologues. Whereas some of these genes are known to be involved in embryonic developmental processes (e.g. Klf4, Otx2, Smn1, Socs3, Tagln, Tdgf1), our analysis points to others (such as transcription factor Phf21a, extracellular matrix related Lama1 and Cyr61, or endoplasmic reticulum related Sc4mol and Scd2) that have not been previously related to mESC function. The majority of identified functions were related to transcriptional regulation, intracellular signaling, and cytoskeleton. Genes involved in other cellular functions important in ESC differentiation such as chromatin remodeling and transmembrane receptors were not observed in this set.ConclusionOur analysis profiles for the first time gene expression at a very early stage of mESC differentiation, and identifies a functional and phylogenetic signature for the genes involved. The data generated constitute a valuable resource for further studies. All DNA microarray data used in this study are available in the StemBase database of stem cell gene expression data [1] and in the NCBI's GEO database.
Highlights
Little is known about the genes that drive embryonic stem cell differentiation
Our results showed a significant abundance of proteins related to transcription regulation, intracellular signaling, and the cytoskeleton; and enrichment in protein sequences whose phylogenetic distribution of homologs indicated that their evolutionary origin occurred along the metazoan lineage
Broad functional analysis To confirm that the gene expression data of the first 12 hours of the time series can be used to detect genes related to mouse embryonic stem cell (mESC) differentiation, we studied the properties of genes related to large or small expression changes in that period using a heuristic approach
Summary
Little is known about the genes that drive embryonic stem cell differentiation Such knowledge is necessary if we are to exploit the therapeutic potential of stem cells. Relatively few genes have been identified as associated with stem cell generation or maintenance [2] Such genes are likely to be important in deriving methods to control and direct the differentiation of stem cells for therapy, for example by expanding a stem cell culture or by directing differentiation towards a targeted cell type. To confirm that the gene expression data of the first 12 hours of the time series pinpoints to genes related to mESC differentiation, we performed a heuristic method for the analysis of the DNA microarray data that yielded the genes with the largest changes in expression in that period in two or three of the cell lines analyzed. Our results showed a significant abundance of proteins related to transcription regulation, intracellular signaling, and the cytoskeleton; and enrichment in protein sequences whose phylogenetic distribution of homologs indicated that their evolutionary origin occurred along the metazoan lineage
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