A single-cell multiomics roadmap of zebrafish spermatogenesis reveals conserved regulatory principles of male germline formation [scRNA-Seq]
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PROVIDER: PRJNA1195601 | ENA |
REPOSITORIES: ENA
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Project description:A single-cell multiomics roadmap of zebrafish spermatogenesis reveals conserved regulatory principles of male germline formation [scATAC-Seq]
| PRJNA1195600 | ENA
Project description:Spermatogenesis is a highly complex biological process through which male sperm cells, or spermatozoa, are produced in the testes. Besides enabling the flow of genetic information, spermatogenesis also creates a potential template for inter- and transgenerational inheritance of gene-regulatory states. While extensively studied in mammals, current knowledge of anamniote spermatogenesis remains limited. Here we provide a comprehensive resource consisting of single-cell gene expression and chromatin accessibility data complemented by base-resolution DNA methylome profiling of sorted germ cell populations, obtained from zebrafish (Danio rerio) testes. We identify major germ and somatic cell types implicated in zebrafish spermatogenesis as well as transcriptional drivers associated with each cell type. Moreover, we describe a localised DNA methylome reconfiguration event associated with the spermatocyte stage, and both local and global changes in chromatin accessibility leading to chromatin compaction in spermatids. Finally, we identify loci that escape global chromatin compaction, and which remain accessible thus forming a potential template for the intergenerational transmission of epigenetic states. In summary, our high-resolution cellular atlas of zebrafish spermatogenesis constitutes a major community resource that will enable further studies of germ cell development, evolution, and that will deepen our understanding of diverse molecular mechanisms implicated in genetic and epigenetic inheritance.
2025-07-16 | GSE283804 | GEO
Project description:Spermatogenesis is a highly complex biological process through which male sperm cells, or spermatozoa, are produced in the testes. Besides enabling the flow of genetic information, spermatogenesis also creates a potential template for inter- and transgenerational inheritance of gene-regulatory states. While extensively studied in mammals, current knowledge of anamniote spermatogenesis remains limited. Here we provide a comprehensive resource consisting of single-cell gene expression and chromatin accessibility data complemented by base-resolution DNA methylome profiling of sorted germ cell populations, obtained from zebrafish (Danio rerio) testes. We identify major germ and somatic cell types implicated in zebrafish spermatogenesis as well as transcriptional drivers associated with each cell type. Moreover, we describe a localised DNA methylome reconfiguration event associated with the spermatocyte stage, and both local and global changes in chromatin accessibility leading to chromatin compaction in spermatids. Finally, we identify loci that escape global chromatin compaction, and which remain accessible thus forming a potential template for the intergenerational transmission of epigenetic states. In summary, our high-resolution cellular atlas of zebrafish spermatogenesis constitutes a major community resource that will enable further studies of germ cell development, evolution, and that will deepen our understanding of diverse molecular mechanisms implicated in genetic and epigenetic inheritance.
2025-07-16 | GSE283803 | GEO
Project description:Continuous sperm production is not necessary for the survival of the organism, but is essential to maintain a species. The process of spermatogenesis is comprised of three phases: mitotic proliferation, meiosis, and spermiogenesis. To illuminate germline intrinsic and extrinsic programs, we performed single-cell RNA sequencing on ~35K cells from the adult mouse testis. This analysis provides a comprehensive molecular atlas of the testis, identifying both known and novel cell types. We demonstrate for the first time the continuous nature of germ cell differentiation, provide molecular signatures and subtype-specific molecular markers, and identify several novel candidate regulators of spermatogenesis. Finally, we demonstrate in vivo using spatial mapping that germ and somatic cell molecular subtypes correspond to previously defined histological cell types residing at different stages of seminiferous epithelial cycle. Taken together, our results unveil the complexity of the testis, and provide a global, unbiased roadmap of the in vivo gametogenesis program.
2018-08-24 | GSE112393 | GEO
Project description:A comprehensive roadmap of spermatogenesis and testis niche from single-cell RNA-seq
| PRJNA445877 | ENA
Project description:Single-cell RNA sequencing uncovers dynamic roadmap and cell-cell communication during buffalo spermatogenesis
| PRJNA787261 | ENA
Project description:Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis, the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single-cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia, but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis.
2024-10-04 | GSE275361 | GEO
Project description:Spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the production of mature spermatozoa. If recent genome-wide studies have contributed to the in-depth analysis of the male germline protein-coding transcriptome, little effort has yet been devoted to the systematic identification of lncRNAs expressed during spermatogenesis in human. We report high-resolution expression profiling of human male germ cells using Illumina next-generation sequencing technology and highly enriched testicular cell populations. 25,161 high-confidence transcripts were reconstructed and classified into eleven expression patterns. Our study provides new insights in transcriptional profiling of the male germline and represents a high-quality resource of novel loci expressed during spermatogenesis that significantly contributes to the human genome annotation. A graphical display of the data is conveniently accessible through the ReproGenomics Viewer (RGV) at http://rgv.genouest.org.
2017-11-24 | GSE74896 | GEO
Project description:Spermatogenesis carries the task of precise intergenerational transmission of genetic information from the paternal genome and involves complex developmental processes regulated by the testicular microenvironment. Studies performed mainly in mouse models have established the theoretical basis for spermatogenesis, yet the wide inter-species differences preclude direct translation of the findings, and farm animal studies are progressing slowly. More than 32,000 cells from prepubertal (3-month-old) and pubertal (24-month-old) buffalo testes were analyzed using single-cell RNA sequencing (scRNA-seq), and dynamic gene expression roadmaps of germ cell and somatic cell development were generated. In addition to identifying the dynamic processes of sequential cell fate transitions, the global cell-cell communication essential to maintain regular spermatogenesis in the buffalo testicular microenvironment was uncovered. The findings provide the theoretical basis for establishing buffalo germline stem cells in vitro or culturing organoids and facilitating the expansion of superior livestock breeding.
2022-11-24 | GSE190477 | GEO
Project description:Roadmap Epigenomics Program - Broad
| PRJNA233641 | ENA