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Gene function in early mouse embryonic stem cell differentiation.

Hailesellasse Sene K, Porter CJ, Palidwor G, Perez-Iratxeta C, Muro EM, Campbell PA, Rudnicki MA, Andrade-Navarro MA - BMC Genomics (2007)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ontario Genomics Innovation Centre, Ottawa Health Research Institute, Ottawa, ON, Canada. kagnewab@yahoo.com <kagnewab@yahoo.com>

ABSTRACT

Background: Little 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.

Results: We 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.

Conclusion: Our 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.

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Signal values of 42 selected MOE430A probe sets in the three time series (R1, J1, and V6.5). Gene names and probe set identifiers are indicated on the left. Relative to their signal value at time 0 h, top 15 probe sets displayed a significant signal decrease at 6 h, next 13 displayed a significant signal decrease at 12 h, next 7 displayed a significant signal increase at 12 h, and bottom 7 displayed a significant signal increase at 6 h, in at least two of the three cell lines analyzed.
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Figure 5: Signal values of 42 selected MOE430A probe sets in the three time series (R1, J1, and V6.5). Gene names and probe set identifiers are indicated on the left. Relative to their signal value at time 0 h, top 15 probe sets displayed a significant signal decrease at 6 h, next 13 displayed a significant signal decrease at 12 h, next 7 displayed a significant signal increase at 12 h, and bottom 7 displayed a significant signal increase at 6 h, in at least two of the three cell lines analyzed.

Mentions: We compared the top 100 lists for the three cell lines to select probe sets present in at least two out of three lists with fold changes in the same direction for each of the 6 h/0 h and 12 h/0 h analyses. This condition was fulfilled by 15 probe sets corresponding to 11 genes down-regulated at 6 h, for 13 probe sets (13 genes) down-regulated at 12 h, for 7 probe sets (7 genes) up-regulated at 12 h, and for 7 probe sets (5 genes) up-regulated at 6 h (see Figure 5 and Table 1). In total, we selected 42 probe sets corresponding to 36 genes for further analysis. When these probe sets were highlighted on the expression fold change graph (Figure 3), they were found towards the extremes of the distribution, indicating a degree of agreement between the two methods.


Gene function in early mouse embryonic stem cell differentiation.

Hailesellasse Sene K, Porter CJ, Palidwor G, Perez-Iratxeta C, Muro EM, Campbell PA, Rudnicki MA, Andrade-Navarro MA - BMC Genomics (2007)

Signal values of 42 selected MOE430A probe sets in the three time series (R1, J1, and V6.5). Gene names and probe set identifiers are indicated on the left. Relative to their signal value at time 0 h, top 15 probe sets displayed a significant signal decrease at 6 h, next 13 displayed a significant signal decrease at 12 h, next 7 displayed a significant signal increase at 12 h, and bottom 7 displayed a significant signal increase at 6 h, in at least two of the three cell lines analyzed.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1851713&req=5

Figure 5: Signal values of 42 selected MOE430A probe sets in the three time series (R1, J1, and V6.5). Gene names and probe set identifiers are indicated on the left. Relative to their signal value at time 0 h, top 15 probe sets displayed a significant signal decrease at 6 h, next 13 displayed a significant signal decrease at 12 h, next 7 displayed a significant signal increase at 12 h, and bottom 7 displayed a significant signal increase at 6 h, in at least two of the three cell lines analyzed.
Mentions: We compared the top 100 lists for the three cell lines to select probe sets present in at least two out of three lists with fold changes in the same direction for each of the 6 h/0 h and 12 h/0 h analyses. This condition was fulfilled by 15 probe sets corresponding to 11 genes down-regulated at 6 h, for 13 probe sets (13 genes) down-regulated at 12 h, for 7 probe sets (7 genes) up-regulated at 12 h, and for 7 probe sets (5 genes) up-regulated at 6 h (see Figure 5 and Table 1). In total, we selected 42 probe sets corresponding to 36 genes for further analysis. When these probe sets were highlighted on the expression fold change graph (Figure 3), they were found towards the extremes of the distribution, indicating a degree of agreement between the two methods.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ontario Genomics Innovation Centre, Ottawa Health Research Institute, Ottawa, ON, Canada. kagnewab@yahoo.com <kagnewab@yahoo.com>

ABSTRACT

Background: Little 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.

Results: We 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.

Conclusion: Our 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.

Show MeSH