MicroRNAs-wide analysis of primordial germ and somatic cells reveals sexual and developmental differential functional regulation in mouse embryonic gonads
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE98713 | GEO | 2018/02/28
REPOSITORIES: GEO
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Project description:Purpose: To identify molecular pathways underlying epigenetic reprogramming in early germ cell precursors, we examined global gene expression of wild type primordial germ cells using mRNA sequencing. Methods: Given the limited number of PGCs collected from E9.5 to E13.5 (ranging from 300 to 5000), we used a low-input RNA sequencing method, Smart-Seq. RNA libraries were pooled and sequenced by Illumina Hiseq. Results: We generated >22 million uniquely mapped reads per sample and identified >10 thousand transcripts per genotype (RPKM>0.1). Hierarchical clustering and correlation analysis on gene expression indicates samples were clearly separated according to their genotypes with Spearman correlation coefficient of 0.98/0.99 within biological replicates. Compared with E9.5 PGCs, 479 genes were significantly up-regulated and 248 genes were down-regulated in E11.5 PGCs. When compared with E11.5 PGCs, male E13.5 PGCs had 362 up-regulated, and 239 down-regulated genes, whereas female E13.5 PGCs had 1163 up-regulated and 333 down-regulated genes. Overall, the number of up-regulated genes was greater than that of the down-regulated genes in every comparison, suggesting that gene expression is generally activated during PGC reprogramming. mRNA profiles of primordial germ cells derived from developmental embryos stages (E9.5, E11.5 and E13.5) were generated by deep sequencing, in duplicates (E9.5 and E11.5) or triplicates (E13.5f and E13.5m), using Illumina Hiseq.
2012-10-31 | E-GEOD-41908 | biostudies-arrayexpress
Project description:Primordial germ cells (PGCs) are the foundation of totipotency and vital for reproduction and heredity. PGCs in mice arise from the epiblast around Embryonic Day (E) 7.0, migrate through the hindgut endoderm, and colonize and proliferate in the embryonic gonads until around E13.5 prior to their differentiation either into pro-spermatogonia or oogonia. PRDM1, a transcriptional repressor, plays an essential role in PGC specification that includes robustly repressing a somatic mesodermal program. Using an inducible conditional knockout system, we show here that PRDM1 is critically required throughout PGC development. When Prdm1 was deleted in migrating PGCs at E9.5/E10.5 or in male gonadal PGCs at E11.5, PGCs were eliminated by apoptosis from around E10/5/E11.5 or E13.5, respectively. When Prdm1 was deleted in female gonadal PGCs at E11.5, PGCs progressed into the first meiotic prophase in an apparently normal fashion, but the oogonia exhibited an aberrant pachytene phenotype, undergoing abrupt apoptosis from around E16.5. The escape of a fraction of PGCs (~10%) from the Prdm1 deletion was sufficient to recover fairly normal germ-cell pools both in male and female adults. The key targets of PRDM1 in migrating/gonadal PGCs, including genes for development, apoptosis, and pro-spermatogonial differentiation, showed only a modest overlap with those upon PGC specification and were enriched with histone H3 lysine 27 tri-methylation (H3K27me3). Our findings provide a critical insight into the mechanism for maintaining the transcriptional integrity of PGCs.
2015-12-02 | GSE74094 | GEO
Project description:Purpose: To identify molecular pathways underlying epigenetic reprogramming in early germ cell precursors, we examined global gene expression of wild type primordial germ cells using mRNA sequencing. Methods: Given the limited number of PGCs collected from E9.5 to E13.5 (ranging from 300 to 5000), we used a low-input RNA sequencing method, Smart-Seq. RNA libraries were pooled and sequenced by Illumina Hiseq. Results: We generated >22 million uniquely mapped reads per sample and identified >10 thousand transcripts per genotype (RPKM>0.1). Hierarchical clustering and correlation analysis on gene expression indicates samples were clearly separated according to their genotypes with Spearman correlation coefficient of 0.98/0.99 within biological replicates. Compared with E9.5 PGCs, 479 genes were significantly up-regulated and 248 genes were down-regulated in E11.5 PGCs. When compared with E11.5 PGCs, male E13.5 PGCs had 362 up-regulated, and 239 down-regulated genes, whereas female E13.5 PGCs had 1163 up-regulated and 333 down-regulated genes. Overall, the number of up-regulated genes was greater than that of the down-regulated genes in every comparison, suggesting that gene expression is generally activated during PGC reprogramming.
2012-10-31 | GSE41908 | GEO
Project description:We profiled a time-course single-cell RNA-seq on C57BL/6 mouse ovary from E11.5 to E14.5 to study the cell population heterogeneity and regulation of meiosis initiation. We collected single cell from XX gonads at E11.5, E12.5, E13.5 and E14.5, and were further captured with 10x Genomics based single-cell system. By using single-cell RNA seq, we recapitulated the progression of meiosis using pseudotime ordering of all germ cells and delineated key molecular network among all germ cell clusters. Besides, we provide candidate meiosis stage-specific master regulons along the progression of meiosis and provide detailed transcriptome profile information for controversial Xist+ PGCs. Our data here offers the opportunity for exploring mechanisms underlying germ cell meiosis progression at single cell resolution.
2020-06-30 | GSE128553 | GEO
Project description:Reconstitution of female germ-cell development in vitro is a key challenge in reproductive biology and medicine. We show here that female (XX) embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) in mice are induced into primordial germ cell-like cells (PGCLCs), which, when aggregated with female gonadal somatic cells as reconstituted ovaries, develop pre-meiotic germ cell characteristics, including X-reactivation, imprint erasure, and cyst formation. Upon transplantation under ovarian bursa, PGCLCs in the reconstituted ovaries mature into germinal vesicle-stage oocytes, which, through in vitro maturation and fertilization, contribute to fertile offspring. Our culture system serves as a robust foundation for the investigation of key properties of female germ cells, including the acquisition of totipotency, and for the reconstitution of whole female germ-cell development in vitro. We performed expression analysis of female PGC-like cells [PGCLCs; day 3 (d3), day 6 (d6), and day 3 followed by day 6 in aggregation with female embryonic day (E) 12.5 gonadal somatic cells (d3ag6)] in comparison to in vivo embryonic PGCs (E12.5 female PGCs and E9.5 PGCs) and male d6 PGCLCs. PGCLCs were marked with fluorescence of Blimp1-mVenus, stella-ECFP transgenic reporters (BVSC). PGCs were marked with fluorescence of the stella-EGFP transgenic reporter.
2012-11-05 | E-GEOD-40716 | biostudies-arrayexpress
Project description:Primordial germ cells (PGCs) are precursors of both male and female gametes as fundamental materials for organism development. The transcriptome, methylome and chromatin accessibility profiles of PGCs in both mice and humans have been recently reported. However, little is known about the characteristics of PGCs at the protein levels, which directly exert cellular functions. Here, we construct landscapes of both proteome of mouse PGCs at E11.5, E13.5 and E16.5 days, the three critical developmental windows for PGCs’ sex differentiation, female meiosis initiation and male mitotic arrest. In each developmental stage of PGCs nearly 2000-3000 proteins are identified, among which specific functional pathways such as oxidative phosphorylation, DNA damage repair, and meiotic cell cycle are involved for different events during PGCs development. Thus, our work offers a valuable resource for the systematic investigations of PGC development at protein level.
2020-05-18 | PXD019222 |
Project description:We used microarrays to profile global gene expression changes of Pou5f1-GFP-positive germ cells between E11.5 to E15.5. Germ cells were FACS-purified from gonadal single cell suspension based on Pou5f1-GFP expression. Three timepoints were included in this study: E11.5 (male/female), E13.5 (male) and E15.5 (male). For each timepoint, three biological replicates were analyzed. The Pou5f1-GFP-negative (non-germ cell) fraction of E13.5 (male) gonads was also included as a control.
2013-01-25 | E-GEOD-38126 | biostudies-arrayexpress
Project description:This experiment depicts RNA-Seq datasets from wild type XY male and XX female, as well as sex chromosomally abnormal XO female (Turner syndrome) and XX male (Klinefelter variant syndrome) mouse germ cells before, during and after germline reprogramming. This range from E6.5 epiblasts, fluorescence activated cell sorted (FACS) highly purified populations of germ cells (EGFP-positive) and gonadal somatic cells (EGFP-negative) from both sexes at E9.5, E11.5, E12.5, E14.5, E15.5, E16.5 and E18.5, as well as purified spermatogonia and leptotene / zygotene spermatocytes from P2 and P11 males, respectively. Non-gonadal somatic cell control datasets were generated from male and female E14.5 liver and tail. Germ cells from individual embryos were processed to make cDNA libraries and served as biological replicates. We generated in total 184 libraries for our analysis from 60 separate conditions.
2017-02-06 | E-MTAB-4616 | biostudies-arrayexpress
Project description:Epigenetic reprogramming, characterized by loss of cytosine methylation and histone modifications, occurs during mammalian development in primordial germ cells (PGCs). Here we provide a detailed map of cytosine methylation on a large portion of the genome in developing male and female PGCs isolated from mouse embryos. We mapped DNA methylation in E13.5 PGCs isolated by FACS sorting from Oct4-GFP male and female embryos. As a control, we also mapped DNA methylation in E7.5 epiblasts from wich PGCs derive from. MeDIP and Input samples were hybridized to Nimblegen HD2 MM8 promoter deluxe arrays covering 12 kb of all gene promoters. Experiments were performed in duplicates for E7.5 epiblasts and triplicates for E13.5 PGCs.
2012-01-31 | E-GEOD-31572 | biostudies-arrayexpress
Project description:Although mitochondria are widely studied organelles, the recent interest in the role of mitochondrial small non-coding RNAs (sncRNA) is providing new functional perspectives in germ cell development and differentiation. PIWI-interacting RNAs (piRNAs) are single-stranded sncRNAs of 20-35 nt generated from the processing of pre-piRNAs longer molecules to be functionally bound to PIWI proteins. Initially ascribed to germ cells, as protectors against transposons, we now know that they are also expressed in somatic cells. In mammals, germ cells differentiate at early stages of embryonic development in the primitive gonads as primordial germ cells (PGCs), initiating divergent pathways in both sexes, accompanied by somatic cells (SCs) of the ovary or testis. Previously, we identified mitochondrial piRNAs (mito-piRNAs) in mouse germ and somatic cells. However, a comparative analysis of mito-piRNAs between PGCs and SCs, between sexes and during early gonadal development has not been performed. We leverage NGS data obtained from PGCs and SCs purified from early differentiating embryonic ovaries and testis from E11.5 to E13.5. Using bioinformatic tools, here we unravel: the origin (from nuclear or mitochondrial genome), the levels of expression, the potential role of mito-piRNAs, as well as their association with genomic regions encoding other sncRNAs (such as tRNAs and rRNAs) and the mitochondrial regulatory region (D-loop). Finally, our results indicate nucleo-mitochondrial communication at both anterograde and retrograde signaling, mediated by mito-piRNAs.
2021-07-01 | GSE179299 | GEO