Epigenomic landscape of human cumulus cells in premature ovarian insufficiency using single-base resolution methylome and hydroxymethylome. [ACE-seq]
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ABSTRACT:
PROVIDER: PRJNA1112315 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29050141_1.fastq.gz | Fastqsanger.gz | |||
| SRR29050141_2.fastq.gz | Fastqsanger.gz | |||
| SRR29050142_1.fastq.gz | Fastqsanger.gz | |||
| SRR29050142_2.fastq.gz | Fastqsanger.gz | |||
| SRR29050143_1.fastq.gz | Fastqsanger.gz |
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Project description:Premature ovarian insufficiency (POI) has recently been reported to be linked with epigenetic changes. Previous studies have focused on the regulation of individual genes associated with ovarian function through single-gene epigenetic variations, however, there is a deficiency in the comprehensive comprehension of the epigenetic profile for POI. Therefore, we conducted a multi-omics study integrating methylation, hydroxymethylation, and transcriptome sequencing analyses in cumulus cells from women with POI and their matched controls. Our results showed significantly higher global methylation and hydroxymethylation levels in POI women compared to controls. The number of hyper-methylated/hyper-hydroxymethylated regions exceeded hypo-methylated/hypo-hydroxymethylated regions in differentially methylated and hydroxymethylated regions across chromosomes and genetic elements. Methylation within genebodies remained high and exhibited a slight negative correlation with gene expression. Variation in methylation levels was notable among promoter regions, with gene expression decreasing as methylation levels increased (displaying a pronounced negative correlation). Hydroxymethylation levels in both the genebody and promoter regions remained consistently low and showed no overall association with gene expression. Furthermore, we found that changes in methylation were linked to the epigenetic age clock rather than being specifically associated with POI causative genes or ovarian function genes. Our study sheds light on critical features of POI, characterized by widespread DNA hyper-methylation and hyper-hydroxymethylation across the genome. The observed relationship between hyper/hypo-methylation and gene expression regulation may provide valuable insights for identifying potential epigenetic biomarkers and treatment targets for POI.
2024-12-27 | GSE267640 | GEO
Project description:Epigenomic landscape of human cumulus cells in premature ovarian insufficiency using single-base resolution methylome and hydroxymethylome. [scWGBS_seq]
| PRJNA1112317 | ENA
Project description:Epigenomic landscape of human cumulus cells in premature ovarian insufficiency using single-base resolution methylome and hydroxymethylome. [RNA-Seq]
| PRJNA1112316 | ENA
Project description:Premature ovarian insufficiency (POI) has recently been reported to be linked with epigenetic changes. Previous studies have focused on the regulation of individual genes associated with ovarian function through single-gene epigenetic variations, however, there is a deficiency in the comprehensive comprehension of the epigenetic profile for POI. Therefore, we conducted a multi-omics study integrating methylation, hydroxymethylation, and transcriptome sequencing analyses in cumulus cells from women with POI and their matched controls. Our results showed significantly higher global methylation and hydroxymethylation levels in POI women compared to controls. The number of hyper-methylated/hyper-hydroxymethylated regions exceeded hypo-methylated/hypo-hydroxymethylated regions in differentially methylated and hydroxymethylated regions across chromosomes and genetic elements. Methylation within genebodies remained high and exhibited a slight negative correlation with gene expression. Variation in methylation levels was notable among promoter regions, with gene expression decreasing as methylation levels increased (displaying a pronounced negative correlation). Hydroxymethylation levels in both the genebody and promoter regions remained consistently low and showed no overall association with gene expression. Furthermore, we found that changes in methylation were linked to the epigenetic age clock rather than being specifically associated with POI causative genes or ovarian function genes. Our study sheds light on critical features of POI, characterized by widespread DNA hyper-methylation and hyper-hydroxymethylation across the genome. The observed relationship between hyper/hypo-methylation and gene expression regulation may provide valuable insights for identifying potential epigenetic biomarkers and treatment targets for POI.
2024-12-27 | GSE267643 | GEO
Project description:Premature ovarian insufficiency (POI) has recently been reported to be linked with epigenetic changes. Previous studies have focused on the regulation of individual genes associated with ovarian function through single-gene epigenetic variations, however, there is a deficiency in the comprehensive comprehension of the epigenetic profile for POI. Therefore, we conducted a multi-omics study integrating methylation, hydroxymethylation, and transcriptome sequencing analyses in cumulus cells from women with POI and their matched controls. Our results showed significantly higher global methylation and hydroxymethylation levels in POI women compared to controls. The number of hyper-methylated/hyper-hydroxymethylated regions exceeded hypo-methylated/hypo-hydroxymethylated regions in differentially methylated and hydroxymethylated regions across chromosomes and genetic elements. Methylation within genebodies remained high and exhibited a slight negative correlation with gene expression. Variation in methylation levels was notable among promoter regions, with gene expression decreasing as methylation levels increased (displaying a pronounced negative correlation). Hydroxymethylation levels in both the genebody and promoter regions remained consistently low and showed no overall association with gene expression. Furthermore, we found that changes in methylation were linked to the epigenetic age clock rather than being specifically associated with POI causative genes or ovarian function genes. Our study sheds light on critical features of POI, characterized by widespread DNA hyper-methylation and hyper-hydroxymethylation across the genome. The observed relationship between hyper/hypo-methylation and gene expression regulation may provide valuable insights for identifying potential epigenetic biomarkers and treatment targets for POI.
2024-12-27 | GSE267641 | GEO
Project description:Premature ovarian insufficiency (POI) has recently been reported to be linked with epigenetic changes. Previous studies have focused on the regulation of individual genes associated with ovarian function through single-gene epigenetic variations; however, there is a deficiency in the comprehensive comprehension of the epigenetic profile for POI. Therefore, we conducted a multi-omics study integrating methylation, hydroxymethylation and transcriptome sequencing analyses in cumulus cells from women with POI and their matched controls. Our data revealed significant global increases in methylation and hydroxymethylation levels in POI patients. We observed a predominance of hypermethylated and hyperhydroxymethylated regions across the genome, with methylation in gene bodies negatively correlating with gene expression, especially in promoter regions. Subsequent experimental validation was performed to confirm the involvement of candidate genes (EGR1, EGR2 and DLX5) in ovarian steroid hormone synthesis. Interestingly, our findings indicate that these epigenetic modifications are associated with genes implicated in POI, ovarian function and the epigenetic age clock. This comprehensive epigenetic profile underscores the potential for identifying novel biomarkers and therapeutic targets for POI by unravelling the complex interplay between DNA epigenetics and ovarian function.
| S-EPMC11661916 | biostudies-literature
Project description:Premature ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 (secondary amenorrhea) with hypergonadotropism and hypoestrogenism. Premature ovarian insufficiency has few known genetic causes but in familial cases a genetic link is often suspected. A large consanguineous family with three female affected with POI was investigated. All samples including 3 affected and 5 unaffecd underwent whole genome SNP genotyping using Affymetric Axiom_GW_Hu_SNP array. Linkage analysis was carried out using HomozygosityMapper and Allegro softwares.Linkage analysis mapped the disease phenotype to long arm of chromosome 20. Sequence data analysis of potential candidate genes failed to detect any pathogenic variant.
2014-03-20 | GSE56043 | GEO
Project description:Premature ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 (secondary amenorrhea) with hypergonadotropism and hypoestrogenism. Premature ovarian insufficiency has few known genetic causes but in familial cases a genetic link is often suspected. A large consanguineous family with three female affected with POI was investigated. All samples including 3 affected and 5 unaffecd underwent whole genome SNP genotyping using Affymetric Axiom_GW_Hu_SNP array. Linkage analysis was carried out using HomozygosityMapper and Allegro softwares.Linkage analysis mapped the disease phenotype to long arm of chromosome 20. Sequence data analysis of potential candidate genes failed to detect any pathogenic variant. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples. DNA of eight individuals including three affected subjects was used for homozygosity mapping. Genotyping was performed using the Affymetrix Axiom_GW_Hu_SNP array. Briefly, 250 ng genomic DNA was digested with Digestion Master Mix containing 2 µl NE buffer 2 (10X), 0.5 µl BSA (100X; 10 mg/ml) and 1 µl Nsp1. Digested DNA sample was ligated to Nsp1 adaptor using T4 DNA ligase and amplified by 2 µl of TITANIUM Taq DNA polymerase (50X) and 100 µM PCR primer. PCR products were purified on a Clean-Up plate (Clontech Lab, Madison, USA) and eluted by RB buffer. Purified PCR products were fragmented using Fragmentation Reagent (0.05U/µl DNase 1) for 35 minutes at 37°C followed by labeling of fragmented samples with Labeling Master Mix (30 mM GeneChip DNA Labeling Reagent, 30 U/µl Terminal Deoxynucleotidyl Transferase) for 4 hours at 37°C. Labeled samples were hybridized to Axiom_GW_Hu_SNP array by mixing the sample with Hybridization Master Mix, denatured on thermoblock and loaded on to Array. Array was then placed in a hybridization oven (GeneChip Hybridization Oven 640, USA) for 16-18 hours. After hybridization, array was washed and stained on an automated Fluidic Station 450 followed by scanning on GeneChip Scanner 3000 7G using GeneChip Operating Software (GCOS).
2014-03-20 | E-GEOD-56043 | biostudies-arrayexpress
Project description:Quantitative Real-time PCR (qrt-PCR) is used to detect the differential expression of Circular RNA in patients of Premature Ovarian Insufficiency, in order to explore the biomarkers of POI that can be detected from blood as soon as possible. Quantitative Real-time PCR (qrt-PCR) is used to detect the differential expression of Circular RNA in patients of Premature Ovarian Insufficiency, in order to explore the biomarkers of POI that can be detected from blood as soon as possible.
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Project description:This study is to identify urinary exosome microRNAs (miRNAs) that are unique to premature ovarian insufficiency (POI) with and without Turner syndrome and to use them as diagnostic markers for POI patients. We examined the miRNAexpression profile in urine exosomes from POI patients with and without Turner syndrome.
2022-09-28 | GSE205700 | GEO