Epigenomic landscape of human cumulus cells in premature ovarian insufficiency using single-base resolution methylome and hydroxymethylome. [ACE-seq]

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. We conducted WGBS-seq, ACE-seq, and RNA-seq analyses on six samples obtained from cumulus cells of three women with POI and three age- and BMI-matched control women.