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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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Correspondence between down-regulated genes from this study with two previous studies of mESC differentiation. Venn diagram showing the genes found in at least two studies. We note that the cell lines, conditions, and gene selection procedures for these three studies are very different. Palmqvist et al.: 48 genes from Table 3 in [7]. Sekkai et al.: 143 genes from Table S1 of [6]. This study: 24 genes down-regulated in at least two cell lines at 6 hr or 12 hr.
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Figure 8: Correspondence between down-regulated genes from this study with two previous studies of mESC differentiation. Venn diagram showing the genes found in at least two studies. We note that the cell lines, conditions, and gene selection procedures for these three studies are very different. Palmqvist et al.: 48 genes from Table 3 in [7]. Sekkai et al.: 143 genes from Table S1 of [6]. This study: 24 genes down-regulated in at least two cell lines at 6 hr or 12 hr.

Mentions: In summary, our study provides for the first time a functional and phylogenetic signature associated with gene expression patterns in early differentiating mESC. This is not surprising since this study differs from previous studies in cell types and time frame analyzed. To contrast our results to those from previous studies, we compared our list of 24 down-regulated genes at 6 and 12 hours from MOE430A (Table 1) with the list of 143 down-regulated genes at 16, 24, and 48 hours from Sekkai et al (Gs2 hESC; Supplementary Table 1 from [6]) and the list of 48 down-regulated genes at 18 and 72 hours from Palmqvist et al (H9 mESC; Table 3 in [7]) (Figure 8). Only one gene, Bcl3, was identified by all three analyses, although the importance of this gene for embryo development is doubtful since knock-out mice for this gene are viable only showing immunological defects [58]. Our list has five genes in common with the other two studies, more than they share in common with each other. However, differences in experimental design and analyses complicate the comparison to previous studies, especially since we focused on an earlier time frame.


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)

Correspondence between down-regulated genes from this study with two previous studies of mESC differentiation. Venn diagram showing the genes found in at least two studies. We note that the cell lines, conditions, and gene selection procedures for these three studies are very different. Palmqvist et al.: 48 genes from Table 3 in [7]. Sekkai et al.: 143 genes from Table S1 of [6]. This study: 24 genes down-regulated in at least two cell lines at 6 hr or 12 hr.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Correspondence between down-regulated genes from this study with two previous studies of mESC differentiation. Venn diagram showing the genes found in at least two studies. We note that the cell lines, conditions, and gene selection procedures for these three studies are very different. Palmqvist et al.: 48 genes from Table 3 in [7]. Sekkai et al.: 143 genes from Table S1 of [6]. This study: 24 genes down-regulated in at least two cell lines at 6 hr or 12 hr.
Mentions: In summary, our study provides for the first time a functional and phylogenetic signature associated with gene expression patterns in early differentiating mESC. This is not surprising since this study differs from previous studies in cell types and time frame analyzed. To contrast our results to those from previous studies, we compared our list of 24 down-regulated genes at 6 and 12 hours from MOE430A (Table 1) with the list of 143 down-regulated genes at 16, 24, and 48 hours from Sekkai et al (Gs2 hESC; Supplementary Table 1 from [6]) and the list of 48 down-regulated genes at 18 and 72 hours from Palmqvist et al (H9 mESC; Table 3 in [7]) (Figure 8). Only one gene, Bcl3, was identified by all three analyses, although the importance of this gene for embryo development is doubtful since knock-out mice for this gene are viable only showing immunological defects [58]. Our list has five genes in common with the other two studies, more than they share in common with each other. However, differences in experimental design and analyses complicate the comparison to previous studies, especially since we focused on an earlier time frame.

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
Related in: MedlinePlus