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. 2014 Dec;66(6):967-78.
doi: 10.1007/s10616-013-9649-0. Epub 2013 Oct 16.

Bioinformatic analysis of the four transcription factors used to induce pluripotent stem cells

Yuzhen Ma  1 , Xinmin Zhang, Heping Ma, Yu Ren, Yangyang Sun, Qinglian Wang, Jingyu Shi
Affiliations

Bioinformatic analysis of the four transcription factors used to induce pluripotent stem cells

Yuzhen Ma et al. Cytotechnology. 2014 Dec.

Abstract

Induced pluripotent stem (iPS) cells are a type of pluripotent stem cell artificially derived from non-pluripotent cells by overexpressing the transcription factors Oct4, Sox2, Klf4 and Nanog. These transcription factors play a pivotal role in stem cells; however, the function of these factors are not fully characterized. In this study, we analyzed Oct4, Sox2, Klf4 and Nanog in ten different species using bioinformatics, to provide more knowledge of the function of these genes. Nanog does not exist in the invertebrates Caenorhabditis elegans and Drosophila melanogaster, indicating that the absence of Nanog may be responsible for the developmental differences between vertebrates and invertebrates. Construction of phylogenetic trees confirmed that the function of Nanog is conserved from fish to mammals. The effect of alternative splicing on the protein domains present in Oct4, Sox2, Klf4 and Nanog were also analyzed. Examination of the expression patterns in human stem cells, iPS cells and normal tissues showed that Oct4, Sox2, Klf4 and Nanog are expressed at similar levels in iPS cells and embryonic stem cells, and expression of all four transcription factors decreases after differentiation. Expression of Klf4 reduced to the least during differentiation, and Klf4 was found to be specifically expressed in several normal tissues, especially the salivary gland. In this paper, we systematically indentified the family proteins of the four transcription factors used to induce pluripotent stem cells, and then analyzed their evolution status, composed of those protein domains, alternative splicing translation, expression status and interaction networks. Those analysis could shed a light for further research of iPS.

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Figures

Fig. 1
Fig. 1
The ten species investigated in this study
Fig. 2
Fig. 2
Phylogenetic tree of the Nanog proteins in eight species
Fig. 3
Fig. 3
Phylogenetic tree of the Oct4 proteins in ten species
Fig. 4
Fig. 4
Phylogenetic tree of the Sox2 proteins in nine species
Fig. 5
Fig. 5
Phylogenetic tree of the Klf4 proteins in nine species
Fig. 6
Fig. 6
Alternative splicing of the transcription factors Oct4 (a), Klf4 (b), Sox2 (c) and Nanog (d) in ten species. Each line represents an individual transcript; exons are indicated by blocks, introns are represented by lines. Red exons have at least one different alternative splicing method. A black bold bar represent an exon that had no change in every different transcription
Fig. 7
Fig. 7
Protein domains in the transcription factors Oct4, Klf4, Sox2 and Nanog
Fig. 8
Fig. 8
Protein domains present in the isoforms of the four transcription factors generated by alternative splicing. a Oct4 human, mouse and D. melanogaster isoforms. b human Klf4 isoforms, mouse Nanog isoforms and C. elegans Sox2 isoforms
Fig. 9
Fig. 9
Expression levels of the transcription factors Oct4, Nanog, Sox2, and Klf4 during human embryonic stem cell differentiation. Three types of human embryonic stem cells and their derived cells (the undifferentiated human embryonic stem cell line hES-T3 (T3ES), hES-T3 derived embryoid bodies (T3EB) and hES-T3 differentiated fibroblast-like cells (T3DF)) were selected for RNA extraction. Expression data were treated with the log2 method. RNA extraction was used from cultured and differentiated cells: the methods have been described in the materials and methods section
Fig. 10
Fig. 10
Expression levels of the transcription factors Oct4, Klf4, Sox2 and Nanog in 36 types of normal tissue. Each tissue RNA sample was pooled from several donors. Results identify tissue specific genes and provide baselines for interpreting gene expression in cancer. Expression data were treated with the RMA (Robust Multi-array Average) method. Each transcription factor was painted by a certain color in the Fig. The method used for the extraction of RNA have been presented in the materials and methods section
Fig. 11
Fig. 11
Human Oct4, Nanog, Klf4 and Sox2 regulatory network
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