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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

Number of upregulated (compared to day 0) genes and enrichment p-values for several organ development categories and TFs.Gene numbers (left two columns) and enrichment p-values (-log10(p), right two columns) for up-regulated genes of GO Biological Processes: (1) kidney development, (2) lung development, (3) skeletal system development, (4) neuron development, (5) sensory organ development, (6) vascular development, (7) muscle tissue development. Notation MU stands for mESC and HS for hESC data. (8) Down- and (9) upregulated genes, annotated as transcription factors.
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pone.0140803.g001: Number of upregulated (compared to day 0) genes and enrichment p-values for several organ development categories and TFs.Gene numbers (left two columns) and enrichment p-values (-log10(p), right two columns) for up-regulated genes of GO Biological Processes: (1) kidney development, (2) lung development, (3) skeletal system development, (4) neuron development, (5) sensory organ development, (6) vascular development, (7) muscle tissue development. Notation MU stands for mESC and HS for hESC data. (8) Down- and (9) upregulated genes, annotated as transcription factors.

Mentions: We compare early development of human vs mouse ESCs (hESCs vs mESCs). hESCs are quantified by gene expression microarrays at development days 0, 3, 6, 9, 12, 15, 18 and 21, with 0 corresponding to undifferentiated state. mESCs gene expression is measured on days 0, 1, 2, 3, 4, 5, 6, 7 and 10. Every time point is represented by 3 replicates. At each development time point, we extract genes that are upregulated with respect to undifferentiated state and classified as relevant to specific organ development GO Biological Process. The number of genes and enrichment p-values are calculated and presented in Fig 1. In certain cases the p-values give another picture than the number of genes because of differences in the total number of classified genes in human and mouse.


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)

Number of upregulated (compared to day 0) genes and enrichment p-values for several organ development categories and TFs.Gene numbers (left two columns) and enrichment p-values (-log10(p), right two columns) for up-regulated genes of GO Biological Processes: (1) kidney development, (2) lung development, (3) skeletal system development, (4) neuron development, (5) sensory organ development, (6) vascular development, (7) muscle tissue development. Notation MU stands for mESC and HS for hESC data. (8) Down- and (9) upregulated genes, annotated as transcription factors.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0140803.g001: Number of upregulated (compared to day 0) genes and enrichment p-values for several organ development categories and TFs.Gene numbers (left two columns) and enrichment p-values (-log10(p), right two columns) for up-regulated genes of GO Biological Processes: (1) kidney development, (2) lung development, (3) skeletal system development, (4) neuron development, (5) sensory organ development, (6) vascular development, (7) muscle tissue development. Notation MU stands for mESC and HS for hESC data. (8) Down- and (9) upregulated genes, annotated as transcription factors.
Mentions: We compare early development of human vs mouse ESCs (hESCs vs mESCs). hESCs are quantified by gene expression microarrays at development days 0, 3, 6, 9, 12, 15, 18 and 21, with 0 corresponding to undifferentiated state. mESCs gene expression is measured on days 0, 1, 2, 3, 4, 5, 6, 7 and 10. Every time point is represented by 3 replicates. At each development time point, we extract genes that are upregulated with respect to undifferentiated state and classified as relevant to specific organ development GO Biological Process. The number of genes and enrichment p-values are calculated and presented in Fig 1. In certain cases the p-values give another picture than the number of genes because of differences in the total number of classified genes in human and mouse.

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