DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3'-end GC density.

Bo Yu,Bruce H Howard,Silvia Gravina,James C Mullikin,James H Segars,Valya R Russanova,Alice Ignezweski,Alan H Decherney,Stephen Hartley,James Graham

doi:10.18632/oncotarget.2875

Abstract

Diminished ovarian function occurs early and is a primary cause for age-related decline in female fertility; however, its underlying mechanism remains unclear. This study investigated the roles that genome and epigenome structure play in age-related changes in gene expression and ovarian function, using human ovarian granulosa cells as an experimental system. DNA methylomes were compared between two groups of women with distinct age-related differences in ovarian functions, using both Methylated DNA Capture followed by Next Generation Sequencing (MethylCap-seq) and Reduced Representation Bisulfite Sequencing (RRBS); their transcriptomes were investigated using mRNA-seq. Significant, non-random changes in transcriptome and DNA methylome features are observed in human ovarian granulosa cells as women age and their ovarian functions deteriorate. The strongest correlations between methylation and the age-related changes in gene expression are not confined to the promoter region; rather, high densities of hypomethylated CpG-rich regions spanning the gene body are preferentially associated with gene down-regulation. This association is further enhanced where CpG regions are localized near the 3'-end of the gene. Such features characterize several genes crucial in age-related decline in ovarian function, most notably the AMH (Anti-Müllerian Hormone) gene. The genome-wide correlation between the density of hypomethylated intragenic and 3'-end regions and gene expression suggests previously unexplored mechanisms linking epigenome structure to age-related physiology and pathology.

Highlights

Since the first assisted conception in 1978, assisted reproductive technologies (ART) have enabled infertile couples to give birth to 4 million children
DNA methylomes were compared between two groups of women with distinct age-related differences in ovarian functions, using both Methylated DNA Capture followed by Generation Sequencing (MethylCap-seq) and Reduced Representation Bisulfite Sequencing (RRBS); their transcriptomes were investigated using mRNA-seq
Gene transcription as well as genomic DNA methylation patterns in ovarian granulosa cells were compared between two groups of women: (i) oocyte donors (n = 20) who were young and had robust response to ovarian stimulation during assisted reproductive technology (ART); versus (ii) poor responders (n = 20) who were older and responded poorly to ovarian stimulation during ART

Summary

Introduction

Since the first assisted conception in 1978, assisted reproductive technologies (ART) have enabled infertile couples to give birth to 4 million children. Even with ART, only 12.2% of women between age and 42, or 4.2% of women older than achieve live births with their own oocytes, compared to 40.1% live birth rate in women younger than 35 seeking ART [1]. Due to this low success with ART in older women and the increased delay in childbearing during the last 40 years, age-related decline in female fertility has become the largest and most difficult problem to be solved in the field of human reproduction. Menopause occurs at an average age of 51 and is associated with dramatic increase in many age-related diseases

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Conclusion