Single-cell RNA sequencing reveals dynamic process and novel markers in porcine spermatogenesis
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ABSTRACT:
PROVIDER: PRJNA731514 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14607445_1.fastq.gz | Fastqsanger.gz | |||
| SRR14607445_2.fastq.gz | Fastqsanger.gz | |||
| SRR14607446_1.fastq.gz | Fastqsanger.gz | |||
| SRR14607446_2.fastq.gz | Fastqsanger.gz | |||
| SRR14607447_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: To understand the overall transcriptional profile changes in porcine spermatogenesis.
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Project description:BackgroundSpermatogenesis is the process by which male gametes are formed from spermatogonial stem cells and it is essential for the reliable transmission of genetic information between generations. To date, the dynamic transcriptional changes of defined populations of male germ cells in pigs have not been reported.ResultsTo characterize the atlas of porcine spermatogenesis, we profiled the transcriptomes of ~ 16,966 testicular cells from a 150-day-old pig testis through single-cell RNA-sequencing (scRNA-seq). The scRNA-seq analysis identified spermatogonia, spermatocytes, spermatids and three somatic cell types in porcine testes. The functional enrichment analysis demonstrated that these cell types played diverse roles in porcine spermatogenesis. The accuracy of the defined porcine germ cell types was further validated by comparing the data from scRNA-seq with those from bulk RNA-seq. Since we delineated four distinct spermatogonial subsets, we further identified CD99 and PODXL2 as novel cell surface markers for undifferentiated and differentiating spermatogonia, respectively.ConclusionsThe present study has for the first time analyzed the transcriptome of male germ cells and somatic cells in porcine testes through scRNA-seq. Four subsets of spermatogonia were identified and two novel cell surface markers were discovered, which would be helpful for studies on spermatogonial differentiation in pigs. The datasets offer valuable information on porcine spermatogenesis, and pave the way for identification of key molecular markers involved in development of male germ cells.
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Project description:Transcriptome-wide dynamics of m6A mRNA methylation during porcine spermatogenesis
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Project description:A systematic interrogation of male germ cells is key to complete understanding of molecular mechanisms governing spermatogenesis and the development of new strategies for infertility therapies and male contraception. Here we develop an approach to purify all types of homogeneous spermatogenic cells by combining transgenic labelling and synchronization of the cycle of the seminiferous epithelium, and subsequent single-cell RNA-sequencing. We reveal extensive and previously uncharacterized dynamic processes and molecular signatures in gene expression, as well as specific patterns of alternative splicing, and novel regulators for specific stages of male germ cell development. Our transcriptomics analyses led us to discover discriminative markers for isolating specific stages of round spermatids, and identify different embryo developmental potential between early and late stage spermatids, providing evidence that maturation of round spermatids impacts on embryo development. This work provides valuable insights into mammalian spermatogenesis, and a comprehensive resource for the complete elucidation of gametogenesis.
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Project description:To evaluate the roles of gene regulation in porcine liver, dynamic profiles of transcriptome were investigated in swine breeds with different traits of commercial interest, we sampled liver tissues from a Chinese well-known elite native breed of Enshi black pig, a Large White pig, and a Chinese wild boar living within the same environment at the same day-old(90d).
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Project description:To evaluate the roles of miRNA in porcine liver, dynamic profiles of microRNAome were investigated in swine breeds with different traits of commercial interest, we sampled liver tissues from a Chinese well-known elite native breed of Enshi black pig, a Large White pig, and a Chinese wild boar living within the same environment at the same day-old(90d).
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Project description:A detailed understanding of the gene regulation mechanisms in premeiosis cells is germane to understanding normal spermatogenesis. The genome-wide expression profiles of type B spermatogonia and primary spermatocytes in mouse were investigated using Solexa/Illumina’s digital gene expression (DGE) system, a tag based high-throughput transcriptome sequencing method, and the developmental process of early spermatogenesis was analyzed systematically. The results suggested that the expression pattern of mouse type B spermatogonia and primary spermatocytes was changed dramatically, especially the genes related to junction assembly, regulation of actin cytoskeleton and pluripotency. The change of the expression levels of these pathways’ main components may be affected by corresponding miRNAs through post-transcriptional regulation. The analysis results will benefit for better understanding the molecular mechanism of early spermatogenesis process. Using DGE technology to examine gene expression pattern's change between mouse type B spermatogonia and primary spermatocytes cell types.
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Project description:Sertoli cells (SCs), the only somatic cells within seminiferous tubules, associate intimately with developing germ cells. They not only provide physical and nutritional support but also secrete factors essential to the complex developmental processes of germ cell proliferation and differentiation. The SC transcriptome must therefore adapt rapidly during the different stages of spermatogenesis. We report comprehensive genome-wide expression profiles of pure populations of SCs isolated at 5 distinct stages of the first wave of mouse spermatogenesis, using RNA sequencing technology. We were able to reconstruct about 13 901 high-confidence, nonredundant coding and noncoding transcripts, characterized by complex alternative splicing patterns with more than 45% comprising novel isoforms of known genes. Interestingly, roughly one-fifth (2939) of these genes exhibited a dynamic expression profile reflecting the evolving role of SCs during the progression of spermatogenesis, with stage-specific expression of genes involved in biological processes such as cell cycle regulation, metabolism and energy production, retinoic acid synthesis, and blood-testis barrier biogenesis. Finally, regulatory network analysis identified the transcription factors endothelial PAS domain-containing protein 1 (EPAS1/Hif2α), aryl hydrocarbon receptor nuclear translocator (ARNT/Hif1β), and signal transducer and activator of transcription 1 (STAT1) as potential master regulators driving the SC transcriptional program. Our results highlight the plastic transcriptional landscape of SCs during the progression of spermatogenesis and provide valuable resources to better understand SC function and spermatogenesis and its related disorders, such as male infertility. Genome-wide expression profiling analysis using Illumina next-generation sequencing technology
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Project description:Human spermatogenesis is a well-ordered dynamic process, which ensures the long-term production of functional spermatozoa; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here, by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes of human spermatogenesis using the modified single-cell chromatin overall omic-scale landscape sequencing approach (Modified scCOOL-seq), we revealed that the transcriptional changes throughout human spermatogenesis were correlated with the dynamic alternations of chromatin accessibility; particularly, several potential transcription factors and a set of regulatory elements involved in such process were identified. Remarkably, a round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. And aberrant DNA hypermethylation at recombination hotspots could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination. Collectively, this study provides multi-omics landscapes of human spermatogenesis at single-cell resolution, and offers insights into the association between DNA demethylation and male meiotic recombination.
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