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

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 3ʹ-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 3ʹ-end regions and gene expression suggests previously unexplored mechanisms linking epigenome structure to age-related physiology and pathology.

Ovarian regeneration: The potential for stem cell contribution in the postnatal ovary to sustained endocrine function

“…Increases in mitochondrial DNA (mtDNA) deletion mutations have also been documented in women >38 years of age as compared to women <34 (Seifer et al, 2002), and upregulation of the mitochondrial gene Glutathione S-transferase theta 1 ( GSTT1 ) in granulosa cells with age has been shown (Ito et al, 2008). More recently, global alterations in gene transcription and methylation with age have also been revealed (Yu et al, 2015). Although the mechanisms underlying poor oocyte quality with age have yet to be fully elucidated, evidence suggests that aging granulosa cells may fail to properly support oocyte function.…”

The Regulatory Mechanisms of Intragenic DNA Methylation

“…Other types of cancer cells also appear to use gene repression mediated by hypomethylation of intragenic regions. Young ovarian granulosa cells showed significant differences in methylation levels of 3′-end CpG-rich regions and their hypomethylation correlated with downregulated gene expression, which is crucial for age-related declines in ovarian function [18]. Chronic lymphocytic leukemia cells also show widespread hypomethylation of intragenic DNA, and 65% of hypomethylated genes were repressed [19].…”

LPS-induced expression of CD14 in the TRIF pathway is epigenetically regulated by sulforaphane in porcine pulmonary alveolar macrophages

“…39 The high densities of hypo-methylated CpG-rich regions crossing the gene body are preferentially associated with gene down-regulation. 46 Although several recent studies investigated the role of gene body DNA methylation in gene expression, its function is poorly understood. To identify potential epigenetic changes that mediate the effect of SFN on CD14 gene expression, we assessed the methylation status of CpG islands embedded in the CD14 promotor and the whole CDS (gene body) region.…”