Dissecting the initiation of female meiosis in the mouse at single-cell resolution


Meiosis is one of the most finely orchestrated events during gametogenesis with distinct developmental patterns in males and females. However, the molecular mechanisms involved in this process remain not well known. Here, we report detailed transcriptome analyses of cell populations present in the mouse female gonadal ridges (E11.5) and the embryonic ovaries from E12.5 to E14.5 using single-cell RNA sequencing (scRNA seq). These periods correspond with the initiation and progression of meiosis throughout the first stage of prophase I. We identified 13 transcriptionally distinct cell populations and 7 transcriptionally distinct germ cell subclusters that correspond to mitotic (3 clusters) and meiotic (4 clusters) germ cells. By analysing cluster-specific gene expression profiles, we found four cell clusters correspond to different cell stages en route to meiosis and characterized their detailed transcriptome dynamics. Our scRNA seq analysis here represents a new important resource for deciphering the molecular pathways driving female meiosis initiation.

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Primordial germ cells


Retinoic acid


Bone morphogenetic protein


Single-cell RNA sequencing


t-Distributed Stochastic Neighbor Embedding


Differentially expressed genes


Gene ontology


Principal component analysis


Gene regulatory networks


Single-cell regulatory network inference and clustering


Embryonic stem


Gel-bead in emulsions


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We would like to thank all members of the Institute of Reproductive Sciences, Qingdao Agricultural University for their kind help during preparing single-cell samples and suggestions for preparing the manuscript. This work was supported by the National Key Research and Development Program of China (2018YFC1003400), National Nature Science Foundation (31671554 and 31970788) and Taishan Scholar Construction Foundation of Shandong Province (ts20190946).

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WG and WS: conceived and designed the experiments; WG, JW, RZ, ST, FZ, WL, LL, XS and SC: performed the experiments; WG, PD, MDF and WS: wrote and edited the manuscript.

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Correspondence to Wei Shen.

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Supplementary Figure 1

Supplementary material 1 Quality control of the data set and representative cell marker gene expression analysis. a The summary metrics describe sequencing quality and various characteristics of the detected cells. b Barcode rank plot of all samples. c Violin plot demonstrating the number of genes (nGene), unique molecular identifier (nUMI) and percentage of mitochondria genes (percent.mito) in the different data sets. d tSNE plot of all single-cells coloured by sample information. e Marker gene expression projected into the tSNE plot. Mesothelial: Lhx9, Upk3b; Interstitial: Col1a2, Bgn;Endothelial: Pecam1, Kdr; Pluripotent genes: Utf1, Sall4, Pou5f1, Sox2; Meiotic genes: Sycp1, Rec8, Tex14, Mael; Pregranulosa genes: Wnt4, Wnt6; Erythroid genes: Alas2, Alad; Immune genes: Cd52, Car2. Supplementary Figure 2 Interpreting cellular diversity in the gonads. a The cell population dynamics during four different developmental time-points. The cells were colored coded with the same color as in Figure 1d. b Heatmap of top 10 expressed DEGs in each cluster. Each color bar in the column represents one cell cluster, and each row represents one gene. c Dot plot illustrating marker gene expression across all cell types. The dot size represents the percentage of cells expressing the indicated genes in each cluster and the dot colour intensity represents the average expression level of the indicated genes. d Immunofluorescence analysis of the mitotic GC marker UTF1 in E12.5, E13.5 and E14.5 ovarian cells. Scale bars = 25 μm. e GO enrichment of DEGs in germ cell clusters 1, 8, and 9. f GO enrichment of DEGs in granulosa precursor clusters. g GO enrichment of DEGs in interstitial cell clusters. h GO enrichment of DEGs in mesothelial cell clusters. i GO enrichment of DEGs in endothelial cell clusters. Supplementary Figure 3 Dissecting germ cell subclusters. a PCA plot labeled with tSNE identified clusters in Figure 2b. b Heatmap illustrating germ cell subcluster top 5 expressed genes. c Violin plot illustrating mitosis germ cell, early meiotic and late meiotic marker genes expression in each germ cell clusters. d Western blot analysis of STK31 expression in E12.5, E13.5 and E14.5 fetus ovaries. e Circos plot displaying shared DEGs and shared GO terms between different germ cell clusters. Shared DEGs were labeled with purple lines and shared GO terms were labeled with light blue lines. f Heatmap demonstrating the enrichment of GO terms in each germ cell cluster. Each row represents GO terms and each column represents a cell cluster. Supplementary Figure 4 SCENIC binary regulon activity matrix displaying all enriched regulons across different germ cell clusters. Each column represents one single cell and each row represents one regulon. Supplementary Figure 5 Pseudotime ordering of germ cells. a Visualization of variable genes used for Pseudotime ordering. b Expression profiles of representative marker genes identified by Monocle. The x-axis represents pseudotime. Supplementary Figure 6 Interpreting granulosa cell lineage cell fate using Monocle. a Pregranulosa cell lineage subclusters dynamics along developmental time point. b Heatmap of top 5 expressed DEGs in each cluster. Each column represents one cell cluster, and each row represents one gene. c Pseudotime ordering of all granulosa cell lineage clusters colored by cell identity, cell clusters, and cellular states. d GO enrichment of DEGs in different gene sets in Figure 5f. e Expression profile representative genes corresponding to each gene sets in Figure 5f. Supplementary Figure 7 Interpreting endothelial, interstitial and mesothelial cellular heterogeneity. a tSNE plot of endothelial, interstitial, and mesothelial cell clusters. Cells were labeled with sample identity. b Heatmap of top 5 expressed DEGs in each cluster corresponding to endothelial, interstitial and mesothelial cells. Each column represents one cell cluster, and each row represents one gene. c Expression of cell cycle-related marker genes in tSNE projection of endothelial, interstitial and mesothelial cells. (PDF 14812 kb)

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Ge, W., Wang, JJ., Zhang, RQ. et al. Dissecting the initiation of female meiosis in the mouse at single-cell resolution. Cell. Mol. Life Sci. 78, 695–713 (2021). https://doi.org/10.1007/s00018-020-03533-8

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  • Single-cell RNA seq
  • Meiosis initiation
  • Female germ cells