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. 2015 May 22;290(21):13605-21.
doi: 10.1074/jbc.M114.601401. Epub 2015 Apr 6.

Crucial genes and pathways in chicken germ stem cell differentiation

Zhentao Zhang  1 , Ahmed Kamel Elsayed  2 , Qingqing Shi  1 , Yani Zhang  3 , Qisheng Zuo  1 , Dong Li  1 , Chao Lian  1 , Beibei Tang  1 , Tianrong Xiao  1 , Qi Xu  1 , Guobin Chang  1 , Guohong Chen  1 , Lei Zhang  1 , Kehua Wang  4 , Yingjie Wang  1 , Kai Jin  1 , Yilin Wang  1 , Jiuzhou Song  5 , Hengmi Cui  1 , Bichun Li  6
Affiliations

Crucial genes and pathways in chicken germ stem cell differentiation

Zhentao Zhang et al. J Biol Chem. .

Abstract

Male germ cell differentiation is a subtle and complex regulatory process. Currently, its regulatory mechanism is still not fully understood. In our experiment, we performed the first comprehensive genome and transcriptome-wide analyses of the crucial genes and signaling pathways in three kinds of crucial cells (embryonic stem cells, primordial germ cell, and spermatogonial stem cells) that are associated with the male germ cell differentiation. We identified thousands of differentially expressed genes in this process, and from these we chose 173 candidate genes, of which 98 genes were involved in cell differentiation, 19 were involved in the metabolic process, and 56 were involved in the differentiation and metabolic processes, like GAL9, AMH, PLK1, and PSMD7 and so on. In addition, we found that 18 key signaling pathways were involved mainly in cell proliferation, differentiation, and signal transduction processes like TGF-β, Notch, and Jak-STAT. Further exploration found that the candidate gene expression patterns were the same between in vitro induction experiments and transcriptome results. Our results yield clues to the mechanistic basis of male germ cell differentiation and provide an important reference for further studies.

Keywords: bioinformatics; cell differentiation; gene expression; microarray; stem cells.

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Figures

FIGURE 1.
FIGURE 1.
Cell sorting and culture. a, the purity of FAC-sorted ESCs, PGCs, and SSCs. b, the morphological characters of the three types of cells.
FIGURE 2.
FIGURE 2.
DEGs in microarry.
FIGURE 3.
FIGURE 3.
KEGG classification of DEGs in microarray. A, ESCs versus PGCs. B, ESCs versus SSCs. C, PGCs versus SSCs.
FIGURE 4.
FIGURE 4.
DEGs in RNA-seq.
FIGURE 5.
FIGURE 5.
KEGG classification of DEGs in RNA-seq. A, ESCs versus PGCs. B, ESCs versus SSCs. C, PGCs versus SSCs.
FIGURE 6.
FIGURE 6.
Venn diagram comparing DEGs among the three analyses.
FIGURE 7.
FIGURE 7.
Heat map representation (left) and GO classification (right) of differentiation-related genes among ESCs, PGCs, and SSCs.
FIGURE 8.
FIGURE 8.
Gene regulatory network analysis.
FIGURE 9.
FIGURE 9.
KEGG pathway enrichment analysis of the DEGs.
FIGURE 10.
FIGURE 10.
Screening of the candidate pathways involved in male germ cell development. a, classification of the 13 enriched pathways related to cellular processes regulation. b, distribution of the participating 19 pathways in environmental information regulatory process. c, percentages of the related pathways to the regulation of metabolism.
FIGURE 11.
FIGURE 11.
Signaling regulate different stages of male germ cell.
FIGURE 12.
FIGURE 12.
Validation of RNA-seq results by quantitative PCR.
FIGURE 13.
FIGURE 13.
Express trend of mark genes during differentiation.
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