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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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Phylogenetic distribution of proteins associated with probe sets. Percentage of proteins with homologues in a given organism: Homo sapiens (human), Brachydanio rerio (fish), Xenopus laevis (frog), Drosophila melanogaster (fly), Caenorhabditis elegans (worm), and Saccharomyces cerevisiae (yeast). For each organism, the leftmost column indicates homologues found for proteins from the 1,675 probe sets with largest gene expression changes, the middle column those from the complete set of 16,752 probe sets, and the rightmost column those from the 1,675 probe sets with smallest gene expression changes. In each column, the dark bottom part indicates the percentage of proteins aligned along their full length (less than 30 amino acids unmatched at the N- and C-termini of both sequences), and the lighter upper part is the percentage of proteins with sequence similarity (no length restriction). Proteins were considered similar with a BLAST E-value < 1e-6.
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Figure 4: Phylogenetic distribution of proteins associated with probe sets. Percentage of proteins with homologues in a given organism: Homo sapiens (human), Brachydanio rerio (fish), Xenopus laevis (frog), Drosophila melanogaster (fly), Caenorhabditis elegans (worm), and Saccharomyces cerevisiae (yeast). For each organism, the leftmost column indicates homologues found for proteins from the 1,675 probe sets with largest gene expression changes, the middle column those from the complete set of 16,752 probe sets, and the rightmost column those from the 1,675 probe sets with smallest gene expression changes. In each column, the dark bottom part indicates the percentage of proteins aligned along their full length (less than 30 amino acids unmatched at the N- and C-termini of both sequences), and the lighter upper part is the percentage of proteins with sequence similarity (no length restriction). Proteins were considered similar with a BLAST E-value < 1e-6.

Mentions: We used NetAffx [13] to identify mouse protein sequences associated with each of the probe sets, and for each mouse protein identified the most similar protein sequence in the SPtrEMBL database [14] for six model eukaryotic organisms: Homo sapiens, Danio rerio, Xenopus laevis, Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae (see Figure 4). C. elegans is considered to have stem cells [15] as are the other metazoan organisms considered in this analysis.


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)

Phylogenetic distribution of proteins associated with probe sets. Percentage of proteins with homologues in a given organism: Homo sapiens (human), Brachydanio rerio (fish), Xenopus laevis (frog), Drosophila melanogaster (fly), Caenorhabditis elegans (worm), and Saccharomyces cerevisiae (yeast). For each organism, the leftmost column indicates homologues found for proteins from the 1,675 probe sets with largest gene expression changes, the middle column those from the complete set of 16,752 probe sets, and the rightmost column those from the 1,675 probe sets with smallest gene expression changes. In each column, the dark bottom part indicates the percentage of proteins aligned along their full length (less than 30 amino acids unmatched at the N- and C-termini of both sequences), and the lighter upper part is the percentage of proteins with sequence similarity (no length restriction). Proteins were considered similar with a BLAST E-value < 1e-6.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Phylogenetic distribution of proteins associated with probe sets. Percentage of proteins with homologues in a given organism: Homo sapiens (human), Brachydanio rerio (fish), Xenopus laevis (frog), Drosophila melanogaster (fly), Caenorhabditis elegans (worm), and Saccharomyces cerevisiae (yeast). For each organism, the leftmost column indicates homologues found for proteins from the 1,675 probe sets with largest gene expression changes, the middle column those from the complete set of 16,752 probe sets, and the rightmost column those from the 1,675 probe sets with smallest gene expression changes. In each column, the dark bottom part indicates the percentage of proteins aligned along their full length (less than 30 amino acids unmatched at the N- and C-termini of both sequences), and the lighter upper part is the percentage of proteins with sequence similarity (no length restriction). Proteins were considered similar with a BLAST E-value < 1e-6.
Mentions: We used NetAffx [13] to identify mouse protein sequences associated with each of the probe sets, and for each mouse protein identified the most similar protein sequence in the SPtrEMBL database [14] for six model eukaryotic organisms: Homo sapiens, Danio rerio, Xenopus laevis, Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae (see Figure 4). C. elegans is considered to have stem cells [15] as are the other metazoan organisms considered in this analysis.

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