Comparative analysis of single‐cell RNA sequencing data from mouse spermatogonial and mesenchymal stem cells to identify differentially expressed genes and transcriptional regulators of germline cells

Abstract

Identifying effective internal factors for regulating germline commitment during development and for maintaining spermatogonial stem cells (SSCs) self-renewal is important to understand the molecular basis of spermatogenesis process, and to develop new protocols for the production of the germline cells from other cell sources. Therefore, this study was designed to investigate single-cell RNA-sequencing data for identification of differentially expressed genes (DEGs) in 12 mouse-derived single SSCs (mSSCs) in compare with 16 mouse-derived single mesenchymal stem cells. We also aimed to find transcriptional regulators of DEGs. Collectively, 1,584 up-regulated DEGs were identified that are associated with 32 biological processes. Moreover, investigation of the expression profiles of genes including in spermatogenesis process revealed that Dazl, Ddx4, Sall4, Fkbp6, Tex15, Tex19.1, Rnf17, Piwil2, Taf7l, Zbtb16, and Cadm1 are presented in the first 30 up-regulated DEGs. We also found 12 basal transcription factors (TFs) and three sequence-specific TFs that control the expression of DEGs. Our findings also indicated that MEIS1, SMC3, TAF1, KAT2A, STAT3, GTF3C2, SIN3A, BDP1, PHC1, and EGR1 are the main central regulators of DEGs in mSSCs. In addition, we collectively detected two significant protein complexes in the protein-protein interactions network for DEGs regulators. Finally, this study introduces the major upstream kinases for the main central regulators of DEGs and the components of core protein complexes. In conclusion, this study provides a molecular blueprint to uncover the molecular mechanisms behind the biology of SSCs and offers a list of candidate factors for cell type conversion approaches and production of germ cells.

Dynamic and regulated TAF gene expression during mouse embryonic germ cell development

“…Although basal transcription components such as TFIID are not widely studied in the context of reproduction, Sisakhtnezhad and Heshmati [38] found that Taf7l (with Dazl, Mael, etc.) was one of the 30 most significantly SSC-enriched genes in comparison to mesenchymal stem cells in PND7 mice.…”

“…was one of the 30 most significantly SSC-enriched genes in comparison to mesenchymal stem cells in PND7 mice. In addition, Taf1, Taf2, Taf4b, Taf7, Taf7l2, and Taf9b were also significantly enriched in SSCs along with other basal transcription machinery such as RNA-PII subunits [38]. Soh et al found that Taf4b, Taf5, Taf7l, Taf7l2, and Taf9b were "ovarian germ cell enriched", of which Taf7l, Taf7l2, and Taf9b are also highlighted as "meiotic prophase" genes [25].…”

The shared KEGG pathways between icariin-targeted genes and osteoporosis

“…Bioinformatics has the potential to identify genes differentially expressed in patients with osteoporosis, predict hub genes based on protein interactions and gene enrichment analyses, and identify the responsible molecular mechanisms [9,10]. Bioinformatics analysis has been widely used to identify disease mechanisms and search for target genes [11,12].…”

Recent Research Advances in Mitosis during Mammalian Gametogenesis

“…In mammalian somatic cells, there are at least four different Cdks to regulate the interphase of mitosis: Cdk2, Cdk3, Cdk4, and Cdk6. After interphase, Cdk1 drive cells through mitosis (Figure 2A) [60,61]. To perform kinase activity, CDK must bind to a cyclin as a regulatory protein.…”