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Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

ABSTRACT: Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

PROVIDER: PRJNA987517 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25022200_1.fastq.gz	Fastqsanger.gz
	SRR25022200_2.fastq.gz	Fastqsanger.gz
	SRR25022201_1.fastq.gz	Fastqsanger.gz
	SRR25022201_2.fastq.gz	Fastqsanger.gz
	SRR25022202_1.fastq.gz	Fastqsanger.gz

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Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

Project description:The molecular mechanisms controlling the transition from meiotic arrest (germinal vesicle stage) to meiotic resumption (germinal vesicle breakdown stage) in mammalian oocytes have not been fully elucidated. Single-cell omics technology provides a new opportunity to decipher the early molecular events of oocyte maturation in mammals. Here we focused on analyzing oocytes that are collected from antral follicles of porcine puberty ovary. We used single-cell M&T-seq technology to analyze the nuclear DNA methylome and cytoplasmic transcriptome in parallel for 62 oocytes. We developed a package of pipelines for single-cell methylomics analysis, namely methyConcerto, to specifically and comprehensively characterize the methylation state and allele-specific methylation events for a single cell. We also performed 10X Genomics single-cell transcriptomic analyses to explore the bi-directional cell-cell communications within antral follicles. We characterized the gene expression and DNA methylation programs of individual oocytes in porcine antral follicle, thereby enabled defining two distinct types of oocytes, one of which is significantly more poised for maturation. Significantly differentially expressed or allele-specifically methylated genes were enriched in “RNA metabolism”, “oocyte meiosis” important signaling pathways, e.g., HIF-1/Ras/mTOR/Phospholipase D/ErbB signaling pathways etc. These results are in concert with the cellular communication results. We further confirmed Insulin Receptor Substrate-1 (IRS-1) in insulin signaling pathway is a key regulator of germinal vesicle stage oocyte maturation by in vitro maturation experiments. Our study provides new insights into the regulatory mechanisms between meiotic arrest and meiotic resumption in mammalian oocytes. We also provide a new analytical package for future single-cell methylomics study.

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Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

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Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

Project description:Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

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Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

Project description:Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

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Transcriptome analysis of rhesus monkey germinal vesicle and failed-to-mature oocytes

Project description:Oocyte maturation defects are one contributing factor in unexplained female infertility. Failure of some oocytes to undergo germinal vesicle breakdown or progress to second meiotic metaphase in response to an ovulatory stimulus can limit the number of high quality oocytes available for assisted reproduction. Understanding the molecular mechanisms that underlie oocyte maturation failure may lead to novel methods for increasing the number of high quality oocytes available for assisted reproduction, as well as providing new insight into the basic biology of oocyte maturation. Using RNA sequencing, we compared the transcriptome of rhesus monkey oocytes that failed to mature (FTM) in response to an ovulatory stimulus in vivo to normal germinal vesicle and metaphase II stage oocytes.

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Transcription profiling of mouse, bovine and xenopus germinal vesicle stage oocytes reveals a high degree of conservation among species

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Transcriptome analysis of rhesus monkey germinal vesicle, failed-to-mature oocytes and MII oocytes

Project description:Transcriptome analysis of rhesus monkey germinal vesicle, failed-to-mature oocytes and MII oocytes

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Project description:We aimed to reveal gene expression profiles of human oocytes at each maturation stage by single cell RNA-seq analyses. We investigated transcriptomes of immature oocytes at the germinal vesicle (GV) stage, maturating oocytes at the metaphase I (MI) stage and in vitro matured oocytes at the metaphase II (MII) stage.

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Project description:There is massive destruction of transcripts during maturation of mouse oocytes. The objective of this project was to identify and characterize the transcripts that are degraded versus those that are stable during the transcriptionally silent germinal vesicle (GV)-stage to metaphase II (MII)-stage transition using the microarray approach. A system for oocyte transcript amplification using both internal and 3'-poly(A) priming was utilized to minimize the impact of complex variations in transcript polyadenylation prevalent during this transition. Transcripts were identified and quantified using Affymetrix Mouse Genome 430 v2.0 GeneChip. The significantly changed and stable transcripts were analyzed using Ingenuity Pathways Analysis and GenMAPP/MAPPFinder to characterize the biological themes underlying global changes in oocyte transcripts during maturation. It was concluded that the destruction of transcripts during the GV to MII transition is a selective rather than promiscuous process in mouse oocytes. In general, transcripts involved in processes that are associated with meiotic arrest at the GV-stage and the progression of oocyte maturation, such as oxidative phosphorylation, energy production, and protein synthesis and metabolism, were dramatically degraded. In contrast, transcripts encoding participants in signaling pathways essential for maintaining the unique characteristics of the MII-arrested oocyte, such as those involved in protein kinase pathways, were the most prominent among those stables. Experiment Overall Design: Comparison immature GV-stage oocyte (3 biological replicates) with mature MII-stage oocytes (3 biological replicates)

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Transcriptome analysis of rhesus monkey germinal vesicle and failed-to-mature oocytes

Project description:Transcriptome analysis of rhesus monkey germinal vesicle and failed-to-mature oocytes

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