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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

Mouse clusters.23 clustered expression profile sets are shown. The right part of each graph is the expression profile of (clustered) mouse genes and the left–for corresponding human genes. A line on the graphs is an average expression and grey areas indicate standard deviation of individual expression values with respect to average. Before clustering the standard deviation of expression profiles was set to 1, in order to make the results independent of specific probe set properties.
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pone.0140803.g002: Mouse clusters.23 clustered expression profile sets are shown. The right part of each graph is the expression profile of (clustered) mouse genes and the left–for corresponding human genes. A line on the graphs is an average expression and grey areas indicate standard deviation of individual expression values with respect to average. Before clustering the standard deviation of expression profiles was set to 1, in order to make the results independent of specific probe set properties.

Mentions: Various comparisons were performed. First, correlation of profiles in each orthologous gene pair is calculated. In the second approach, we cluster expression profiles in one case and then look at the expression profiles of orthologous genes of the other case (i.e. human and then mouse, or mouse and then human). Different clustering methods were tried as well to ensure that the conclusions do not depend on selected clustering method. Detailed descriptions of the calculated clusters are available in the supporting information. Gross pictures of similarities and dissimilarities are shown in the Fig 2. Some remarkable similarities and dissimilarities are presented in Fig 3.


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)

Mouse clusters.23 clustered expression profile sets are shown. The right part of each graph is the expression profile of (clustered) mouse genes and the left–for corresponding human genes. A line on the graphs is an average expression and grey areas indicate standard deviation of individual expression values with respect to average. Before clustering the standard deviation of expression profiles was set to 1, in order to make the results independent of specific probe set properties.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0140803.g002: Mouse clusters.23 clustered expression profile sets are shown. The right part of each graph is the expression profile of (clustered) mouse genes and the left–for corresponding human genes. A line on the graphs is an average expression and grey areas indicate standard deviation of individual expression values with respect to average. Before clustering the standard deviation of expression profiles was set to 1, in order to make the results independent of specific probe set properties.
Mentions: Various comparisons were performed. First, correlation of profiles in each orthologous gene pair is calculated. In the second approach, we cluster expression profiles in one case and then look at the expression profiles of orthologous genes of the other case (i.e. human and then mouse, or mouse and then human). Different clustering methods were tried as well to ensure that the conclusions do not depend on selected clustering method. Detailed descriptions of the calculated clusters are available in the supporting information. Gross pictures of similarities and dissimilarities are shown in the Fig 2. Some remarkable similarities and dissimilarities are presented in Fig 3.

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