Single-cell transcriptomics reveal temporal dynamics of critical regulators of germ cell fate during mouse sex determination

Despite the importance of germ cell (GC) differentiation for sexual reproduction, the gene networks underlying their fate remain unclear. Here, University of Geneva researchers comprehensively characterize the gene expression dynamics during sex determination based on single‐cell RNA sequencing of 14 914 XX and XY mouse GCs between embryonic days (E) 9.0 and 16.5. The researchers found that XX and XY GCs diverge transcriptionally as early as E11.5 with upregulation of genes downstream of the bone morphogenic protein (BMP) and nodal/Activin pathways in XY and XX GCs, respectively. They also identified a sex‐specific upregulation of genes associated with negative regulation of mRNA processing and an increase in intron retention consistent with a reduction in mRNA splicing in XY testicular GCs by E13.5. Using computational gene regulation network inference analysis, they identified sex‐specific, sequential waves of putative key regulator genes during GC differentiation and revealed that the meiotic genes are regulated by positive and negative master modules acting in an antagonistic fashion. Finally, the researchers found that rare adrenal GCs enter meiosis similarly to ovarian GCs but display altered expression of master genes controlling the female and male genetic programs, indicating that the somatic environment is important for GC function. These data are available on a web platform and provide a molecular roadmap of GC sex determination at single‐cell resolution, which will serve as a valuable resource for future studies of gonad development, function, and disease.

Generation of the germ cell sex determination atlas


A, Schematic representation of developing testis and ovary highlighting the major events of male and female GC differentiation as well as the time points used in the study. B, Illustration of the experimental workflow using the 10x Genomics Chromium platform. UMAP projection of 14 914 GCs colored by time (C), sex (D), and pseudotime (PT) going from 0 (E9.5 cells) to 100 (E16.5 cells) (E). F, Mirror heatmap of 63 known genes involved in GC differentiation. Cells were ordered along a pseudotime. Cells with lowest PT (E10.5) are in the center of the figure and those with highest PT (E16.5) are on the left side for XX cells and on the right side for XY cells. Gene expression was smoothed to reduce dropout effect and obtain a better visualization of expression tendencies (expression scale: log normalized counts normalized per gene). The relevant processes regulated by these genes (cell cycle, male sex determination, meiosis, pluripotency, and others) are indicated on the left side of the heatmap. G, Barplot representing the number of significantly overexpressed genes in XX or XY cells at each stage. The numbers above the bars indicate the number of genes

Availability – An interactive website is availabel at:

Mayère C, Neirijnck Y, Sararols P, Rands CM, Stévant I, Kühne F, Chassot AA, Chaboissier MC, Dermitzakis ET, Nef S. (2021) Single-cell transcriptomics reveal temporal dynamics of critical regulators of germ cell fate during mouse sex determination. FASEB J 35(4):e21452. [article]

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