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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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12 h/0 h versus 6 h/0 h signal ratios for MOE430A/B probe sets. Values are m6, the median of the three 6 h/0 h signal ratios, and m12, the median of the three 12 h/0 h signal ratios, in the three time series (section 2.2). Marked data points correspond to the 42 probe sets selected from the MOE430A data using SAM (section 2.4). Green squares: 15 probe sets down-regulated at 6 h; green circles: 13 probe sets down-regulated at 12 h; red circles: 7 probe sets up-regulated at 12 h; red squares: 7 probe sets up-regulated at 6 h. The data underlying this table are available [see Additional file 1].
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Figure 3: 12 h/0 h versus 6 h/0 h signal ratios for MOE430A/B probe sets. Values are m6, the median of the three 6 h/0 h signal ratios, and m12, the median of the three 12 h/0 h signal ratios, in the three time series (section 2.2). Marked data points correspond to the 42 probe sets selected from the MOE430A data using SAM (section 2.4). Green squares: 15 probe sets down-regulated at 6 h; green circles: 13 probe sets down-regulated at 12 h; red circles: 7 probe sets up-regulated at 12 h; red squares: 7 probe sets up-regulated at 6 h. The data underlying this table are available [see Additional file 1].

Mentions: Next, we computed the ratios of the signal of these probe sets at 6 h and 12 h relative to the initial time point (6 h/0 h and 12 h/0 h) in the three time series. Defining m6 and m12, as the median of the 6 h/0 h ratios and of the 12 h/0 h ratios for a given probe set in the three time series, respectively, we plotted m6 against m12 for each probe set (Figure 3). The distribution of the values indicated a small number of probe sets with particularly large fold changes.


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)

12 h/0 h versus 6 h/0 h signal ratios for MOE430A/B probe sets. Values are m6, the median of the three 6 h/0 h signal ratios, and m12, the median of the three 12 h/0 h signal ratios, in the three time series (section 2.2). Marked data points correspond to the 42 probe sets selected from the MOE430A data using SAM (section 2.4). Green squares: 15 probe sets down-regulated at 6 h; green circles: 13 probe sets down-regulated at 12 h; red circles: 7 probe sets up-regulated at 12 h; red squares: 7 probe sets up-regulated at 6 h. The data underlying this table are available [see Additional file 1].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: 12 h/0 h versus 6 h/0 h signal ratios for MOE430A/B probe sets. Values are m6, the median of the three 6 h/0 h signal ratios, and m12, the median of the three 12 h/0 h signal ratios, in the three time series (section 2.2). Marked data points correspond to the 42 probe sets selected from the MOE430A data using SAM (section 2.4). Green squares: 15 probe sets down-regulated at 6 h; green circles: 13 probe sets down-regulated at 12 h; red circles: 7 probe sets up-regulated at 12 h; red squares: 7 probe sets up-regulated at 6 h. The data underlying this table are available [see Additional file 1].
Mentions: Next, we computed the ratios of the signal of these probe sets at 6 h and 12 h relative to the initial time point (6 h/0 h and 12 h/0 h) in the three time series. Defining m6 and m12, as the median of the 6 h/0 h ratios and of the 12 h/0 h ratios for a given probe set in the three time series, respectively, we plotted m6 against m12 for each probe set (Figure 3). The distribution of the values indicated a small number of probe sets with particularly large fold changes.

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