DNA methylation dynamics of oocyte in follicular maturation (RNA-Seq data set)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA438031 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6825260_1.fastq.gz | Fastqsanger.gz | |||
| SRR6825260_2.fastq.gz | Fastqsanger.gz | |||
| SRR6825270_1.fastq.gz | Fastqsanger.gz | |||
| SRR6825270_2.fastq.gz | Fastqsanger.gz | |||
| SRR6825280_1.fastq.gz | Fastqsanger.gz |
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Project description:DNA methylation dynamics of oocyte in follicular maturation
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Project description:Folliculogenesis in mammals is a cyclic and hierarchical process that the ovarian follicles undergo dramatic changes in the shape and number of granulosa cells accompanied by gradually enlarged immature oocyte. Here we show a thorough and high-resolution view of DNA methylation maps in oocyte free of somatic cells present at each distinct follicular development stages. We found that global DNA establishment occurs in Type5b follicles, the final stage of pre-antral follicles, and that the acquisition of DNA methylation at different trans-regulatory elements couples with different chromatin modifiers. Besides, we showed that Dnmt1 as well as Uhrf1 also play critical roles in requiring and retaining of de novo methylation statue, typically at LINE and LTR elements, in these immature oocytes, which successfully escape DNA replication. Our study thus refined the current knowledge on the establishment of unique DNA methylation profile in mammalian oocytes, and provide a valuable resource for further studies on female gametogenesis.
2020-12-25 | GSE111685 | GEO
Project description:Folliculogenesis in mammals is a cyclic and hierarchical process that the ovarian follicles undergo dramatic changes in the shape and number of granulosa cells accompanied by gradually enlarged immature oocyte. Here we show a thorough and high-resolution view of DNA methylation maps in oocyte free of somatic cells present at each distinct follicular development stages. We found that global DNA establishment occurs in Type5b follicles, the final stage of pre-antral follicles, and that the acquisition of DNA methylation at different trans-regulatory elements couples with different chromatin modifiers. Besides, we showed that Dnmt1 as well as Uhrf1 also play critical roles in requiring and retaining of de novo methylation statue, typically at LINE and LTR elements, in these immature oocytes, which successfully escape DNA replication. Our study thus refined the current knowledge on the establishment of unique DNA methylation profile in mammalian oocytes, and provide a valuable resource for further studies on female gametogenesis.
2021-06-30 | GSE111684 | GEO
Project description:Folliculogenesis in mammals is a cyclic and hierarchical process that the ovarian follicles undergo dramatic changes in the shape and number of granulosa cells accompanied by gradually enlarged immature oocyte. Here we show a thorough and high-resolution view of DNA methylation maps in oocyte free of somatic cells present at each distinct follicular development stages. We found that global DNA establishment occurs in Type5b follicles, the final stage of pre-antral follicles, and that the acquisition of DNA methylation at different trans-regulatory elements couples with different chromatin modifiers. Besides, we showed that Dnmt1 as well as Uhrf1 also play critical roles in requiring and retaining of de novo methylation statue, typically at LINE and LTR elements, in these immature oocytes, which successfully escape DNA replication. Our study thus refined the current knowledge on the establishment of unique DNA methylation profile in mammalian oocytes, and provide a valuable resource for further studies on female gametogenesis.
2020-12-25 | GSE111686 | GEO
Project description:In fully grown oocytes, the genome is considered to be globally transcriptionally silenced. However, this conclusion is primarily derived from the results obtained through immunofluorescence staining or inferred from the highly condensed state of chromosomes, lacking more direct evidence. Here, by using a kethoxal-assisted single-stranded DNA sequencing (KAS-seq) approach, we investigated the landscape of single-strand DNA (ssDNA) throughout the genome and provided a readout of the activity and dynamics of transcription during oocyte meiotic maturation. In non-surrounded nucleolus (NSN) oocytes, we observed a robust KAS-seq signal, indicating the high transcriptional activity. In surrounded nucleolus (SN) oocytes, the presence of ssDNA still persists although the KAS-seq signal was relatively weak, suggesting the presence of transcription. Accompanying with the meiotic resumption, the transcriptional activity gradually decreased, and global repression was detected in matured oocytes. Moreover, we preformed the integrative genomics analysis to dissect the transcriptional dynamics during mouse oocyte maturation. In sum, the present study delineates the detailed transcriptional activity during mammalian oocyte maturation.
2024-06-07 | GSE252350 | GEO
Project description:Reproductive aging is a major cause of fertility decline, attributed to decreased oocyte quantity and competence. Follicular somatic cells play crucial roles in the growth and development of the oocyte by providing nutrients and regulatory factors. Here we investigated how oocyte quality is affected by its somatic cell environment by creating chimeric follicles, whereby an oocyte from one follicle was transplanted into and cultured within another follicle whose native oocyte was removed. Somatic cells within the chimeric follicle re-establish connections with the oocyte and support oocyte growth and maturation in a three-dimensional (3D) culture system. We show that young oocytes transplanted into aged follicles exhibited reduced meiotic maturation and developmental potential, whereas the young follicular environment significantly improved the rates of maturation, blastocyst formation and live birth of aged oocytes. Aged oocytes cultured within young follicles exhibited enhanced interaction with somatic cells, more youth-like transcriptome, remodelled metabolome, improved mitochondrial function, and enhanced fidelity of meiotic chromosome segregation. These findings provide the basis for a future follicular somatic cell-based therapy to treat age-associated female infertility.
2024-07-22 | GSE270016 | GEO
Project description:KAS-seq profiling captures transcription dynamics during oocyte maturation
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Project description:The use of in vitro reproduction techniques is increasing worldwide in human and domestic species. However, the oocyte to embryo turnover in vitro remains marginal leading to the conclusion that the response could be in the in vivo events. Extracellular vesicles naturally present in follicular fluid (ffEVS) play a role in cell-to-cell communication and can participate in follicular development and oocyte maturation. However, there is limited understanding regarding the impact of the isolation methods on ffEVs contents and their use as a supplement during in vitro maturation (IVM). Here, we provide evidence that ffEVs isolated by ultracentrifugation (ffEVs-UC) and size exclusion chromatography (ffEVs-SEC) were different in terms of proteins, microRNAs (miRNAs), transcripts, and lipids contents. Proteins such as NPR2, and EGFR were detected in ffEVS-SEC at higher levels in ffEVS-UC. The bioinformatics analysis of miRNA and proteins indicates that these ffEVs contents play a role in modulating pathways associated with the regulation of transzonal projections (TZPs), such as the axon guidance. To evaluate the effects of ffEVS supplementation during oocyte IVM, ffEVs isolated by ffEVs-UC or ffEVs-SEC were added or not (Control group) in bovine cumulus-oocyte-complex (COCs) during IVM. COCs supplemented with ffEVs-SEC had lower number of TZPs, and an increased maturation rate than the Control group (P < 0.05). The analysis of transcriptional variants in cumulus cells supplemented for 9 h during IVM revealed that PDE5A-203 was upregulated in ffEVs-SEC group compared to the Control and ffEVs-UC group. PDE5A can decrease the levels of cGMP in cumulus cells in addition to increased levels of EGFR transferred by ffEVs-SEC contributing to meiosis progression and consequently TZP numbers reduction during maturation. Together, these findings suggest that EVs’ isolation method can recover EVs with different contents that, upon supplementation, can possibly transfer molecules (such as protein, lipids, miRNAs) and induce changes in transcripts as well as intracellular pathways involved in meiosis progression and TZPs-mediated communication in COCs during IVM.
2025-04-11 | PXD062865 | JPOST Repository