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Differences in the Early Development of Human and Mouse Embryonic Stem Cells.

Gabdoulline R, Kaisers W, Gaspar A, Meganathan K, Doss MX, Jagtap S, Hescheler J, Sachinidis A, Schwender H - PLoS ONE (2015)

Bottom Line: Many development features were found to be conserved, and a majority of differentially regulated genes have similar expression change in both organisms.However, we also found that some biological processes develop differently; this can clearly be shown, for example, for neuron and sensory organ development.We also detected a larger number of upregulated genes during development of mESCs as compared to hESCs.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics and Biostatistics, Biological Medical Research Center, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.

ABSTRACT
We performed a systematic analysis of gene expression features in early (10-21 days) development of human vs mouse embryonic cells (hESCs vs mESCs). Many development features were found to be conserved, and a majority of differentially regulated genes have similar expression change in both organisms. The similarity is especially evident, when gene expression profiles are clustered together and properties of clustered groups of genes are compared. First 10 days of mESC development match the features of hESC development within 21 days, in accordance with the differences in population doubling time in human and mouse ESCs. At the same time, several important differences are seen. There is a clear difference in initial expression change of transcription factors and stimulus responsive genes, which may be caused by the difference in experimental procedures. However, we also found that some biological processes develop differently; this can clearly be shown, for example, for neuron and sensory organ development. Some groups of genes show peaks of the expression levels during the development and these peaks cannot be claimed to happen at the same time points in the two organisms, as well as for the same groups of (orthologous) genes. We also detected a larger number of upregulated genes during development of mESCs as compared to hESCs. The differences were quantified by comparing promoters of related genes. Most of gene groups behave similarly and have similar transcription factor (TF) binding sites on their promoters. A few groups of genes have similar promoters, but are expressed differently in two species. Interestingly, there are groups of genes expressed similarly, although they have different promoters, which can be shown by comparing their TF binding sites. Namely, a large group of similarly expressed cell cycle-related genes is found to have discrepant TF binding properties in mouse vs human.

No MeSH data available.


Related in: MedlinePlus

Relation between expression and promoter similarities.The x-axis is for Pearson correlation coefficients of average gene expression profiles of human vs mouse gene group pairs. The y-axis is for p-value of overlap of their TFBS-s lists.
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pone.0140803.g006: Relation between expression and promoter similarities.The x-axis is for Pearson correlation coefficients of average gene expression profiles of human vs mouse gene group pairs. The y-axis is for p-value of overlap of their TFBS-s lists.

Mentions: We see almost all possible scenarios, indicating that the correlation of gene expression profiles is not directly related to the similarities or dissimilarities of promoter sequences, quantified by the list of TFBSs on them. In majority of cases, the similarity in expression is accompanied by the similarity of promoters (right-bottom of Fig 6). It should be kept in mind, however, that the similarity of the promoters is not sufficient to ensure similar expression. Additional requirement is that the activity of relevant transcription factors is similar in mESCs and hESCs. Thus in majority of cases both requirements are met. There are few cases when hESCs and mESCs promoters have apparently the same TFBSs, but their expression profiles are not correlated, and even anti-correlated (left-bottom in Fig 6). These are likely the cases when differences in the activity of relevant transcription factors can be expected.


Differences in the Early Development of Human and Mouse Embryonic Stem Cells.

Gabdoulline R, Kaisers W, Gaspar A, Meganathan K, Doss MX, Jagtap S, Hescheler J, Sachinidis A, Schwender H - PLoS ONE (2015)

Relation between expression and promoter similarities.The x-axis is for Pearson correlation coefficients of average gene expression profiles of human vs mouse gene group pairs. The y-axis is for p-value of overlap of their TFBS-s lists.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4608779&req=5

pone.0140803.g006: Relation between expression and promoter similarities.The x-axis is for Pearson correlation coefficients of average gene expression profiles of human vs mouse gene group pairs. The y-axis is for p-value of overlap of their TFBS-s lists.
Mentions: We see almost all possible scenarios, indicating that the correlation of gene expression profiles is not directly related to the similarities or dissimilarities of promoter sequences, quantified by the list of TFBSs on them. In majority of cases, the similarity in expression is accompanied by the similarity of promoters (right-bottom of Fig 6). It should be kept in mind, however, that the similarity of the promoters is not sufficient to ensure similar expression. Additional requirement is that the activity of relevant transcription factors is similar in mESCs and hESCs. Thus in majority of cases both requirements are met. There are few cases when hESCs and mESCs promoters have apparently the same TFBSs, but their expression profiles are not correlated, and even anti-correlated (left-bottom in Fig 6). These are likely the cases when differences in the activity of relevant transcription factors can be expected.

Bottom Line: Many development features were found to be conserved, and a majority of differentially regulated genes have similar expression change in both organisms.However, we also found that some biological processes develop differently; this can clearly be shown, for example, for neuron and sensory organ development.We also detected a larger number of upregulated genes during development of mESCs as compared to hESCs.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics and Biostatistics, Biological Medical Research Center, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.

ABSTRACT
We performed a systematic analysis of gene expression features in early (10-21 days) development of human vs mouse embryonic cells (hESCs vs mESCs). Many development features were found to be conserved, and a majority of differentially regulated genes have similar expression change in both organisms. The similarity is especially evident, when gene expression profiles are clustered together and properties of clustered groups of genes are compared. First 10 days of mESC development match the features of hESC development within 21 days, in accordance with the differences in population doubling time in human and mouse ESCs. At the same time, several important differences are seen. There is a clear difference in initial expression change of transcription factors and stimulus responsive genes, which may be caused by the difference in experimental procedures. However, we also found that some biological processes develop differently; this can clearly be shown, for example, for neuron and sensory organ development. Some groups of genes show peaks of the expression levels during the development and these peaks cannot be claimed to happen at the same time points in the two organisms, as well as for the same groups of (orthologous) genes. We also detected a larger number of upregulated genes during development of mESCs as compared to hESCs. The differences were quantified by comparing promoters of related genes. Most of gene groups behave similarly and have similar transcription factor (TF) binding sites on their promoters. A few groups of genes have similar promoters, but are expressed differently in two species. Interestingly, there are groups of genes expressed similarly, although they have different promoters, which can be shown by comparing their TF binding sites. Namely, a large group of similarly expressed cell cycle-related genes is found to have discrepant TF binding properties in mouse vs human.

No MeSH data available.


Related in: MedlinePlus