Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA789855 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17262950_1.fastq.gz | Fastqsanger.gz | |||
| SRR17262950_2.fastq.gz | Fastqsanger.gz | |||
| SRR17262951_1.fastq.gz | Fastqsanger.gz | |||
| SRR17262951_2.fastq.gz | Fastqsanger.gz | |||
| SRR17262952_1.fastq.gz | Fastqsanger.gz |
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Project description:Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development, yet there are still significant gaps in our understanding of the genes that regulate gonad development, sex, and reproduction. Unlike the development of many organs, such as the brain and heart that form during the first few days of development, zebrafish gonads do not begin to form until the larval stage ( ≥5 dpf). Thus, forward genetic screens have identified very few genes required for gonad development. In addition, bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations, we have used single-cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10,658 germ cells and 14,431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, for select examples, we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies.
2021-12-19 | GSE191137 | GEO
Project description:Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development, yet there are still significant gaps in our understanding of the genes that regulate gonad development, sex, and reproduction. Unlike the development of many organs, such as the brain and heart that form during the first few days of development, zebrafish gonads do not begin to form until the larval stage (≥5 days post-fertilization). Thus, forward genetic screens have identified very few genes required for gonad development. In addition, bulk RNA-sequencing studies that identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in the development and function of these organs. To overcome these limitations, we have used single-cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10,658 germ cells and 14,431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells, and ovarian stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, we used gene knockout experiments to determine the roles of foxl2l and wnt9b for oocyte development and sex determination and/or differentiation, respectively. Our results reveal novel insights into zebrafish ovarian development and function, and the transcriptome profiles will provide a valuable resource for future studies.
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Project description:Goal of this study is the gene expression analysis of the zebrafish adult germline (ovary, oocyte, testis)
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Project description:The commercially available zebrafish (Danio rerio) gene expression microarray (4x44K format, Agilent G2519F-026437) was used to characterise the changes in gene expression levels in the ovary and brain of adult female zebrafish after exposure to 55, 553 and 5442 ng/L DRS for 14 days. Also, the transcriptional response in the brain of adult female zebrafish was characterised after exposure to mixtures of DRS and P4 at concentrations of 27+0.8, 277+8, 3119+123 (ng/L), respectively. This study was designed to achieve an understanding of the mode of action of DRS and steroid mixtures in zebrafish.
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Project description:Ddx4 (DEAD-box helicase 4) is a well-established marker gene for early-stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary-specific transcript (ddx4-L) remains unclear. In this study, using the ddx4-L knockout zebrafish model, we found that elimination of ddx4-L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4-L knockout ovaries. A total of 1134 differentially expressed genes were identified, of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization, sperm-egg recognition process, and oocyte meiosis might be affected by elimination of ddx4-L. Furthermore, we found that Sycp1, a synaptonemal complex protein involved in meiosis and fertility, was dramatically decreased in the ddx4-L knockout ovaries at both mRNA and protein levels. Moreover, the activities of transposable elements were analyzed based on the RNA-seq data. The result showed that elimination of ddx4-L causes the derepression of DNA transposons, a subclass of transposable elements, in zebrafish ovaries. In conclusion, the aforementioned findings indicate that the ovary-specific transcript of ddx4 plays an important role in oocyte development and egg quality, possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis.
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Project description:The germ cells are vital for reproduction and heredity. However, the mechanisms for female germ cell development in primates, especially in late embryonic stage, has remained elusive. Here, we performed single-cell RNA sequencing of 12471 cells from fetal ovaries. We identified five cell types (germ cell, granulosa cell, theca cell, endothelial cell, macrophage cell), and explored the interactions between germ cells and niche cells. Interestingly, we demonstrated that two waves of oogenesis occur during fetal ovary development and ZGLP1 could activate oogenic program and is essential for meiosis initiation. Furthermore, late formed double strand breaks (DSBs) mediated by PRDM9 may lead to the apoptosis of germ cells during cyst breakdown process. Moreover, our study identified the origin of theca cells that may derive from Leydig cell like cells in fetal ovaries. Overall, our work provides new insights into the molecular and cellular basis of fetal ovary development at single-cell resolution.
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