Gene-specific alterations in DNA methylation in primary ovarian endometriosis stromal cells (OESC) compared to control endometrial stromal cells (CESC), chromatin state enrichment analysis of DM genes in endometriosis, and bi-seq validation for DAPK1.

Iveta Yotova (451965), Emily Hsu (224819), Catherine Do (139725), Aulona Gaba (3710608), Matthias Sczabolcs (3710614), Sabine Dekan (3710611), Lukas Kenner (46891), Rene Wenzl (3506993), Benjamin Tycko (237065)
2017 · doi:10.1371/journal.pone.0170859.g001 · W6961288703
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This study investigated gene-specific DNA methylation alterations in primary ovarian endometriosis stromal cells compared to control endometrial stromal cells using 450K methylation BeadChip data. The analysis revealed that differentially methylated CpG sites were significantly enriched in enhancer regions while being depleted in promoter areas, highlighting distinct epigenetic landscapes between diseased and healthy tissue. Researchers validated these findings by mapping hypomethylation in the DAPK1 promoter region, which overlaps with an active promoter flanked by a strong enhancer, confirming specific chromatin state changes associated with the disease. This paper is centrally about endometriosis — specifically focusing on the epigenetic mechanisms involving DNA methylation in ovarian endometriosis stromal cells.

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Abstract

A) Heat maps of gene-specific methylation changes in endometriotic stroma cells vs. controls. Supervised hierarchical clustering of the 450K methylation BeadChip data analyzed at the CpG level (FDR q-values .15) and at the element-level (q-values .15 for multiple CpG segment and>0.1 for single CpG segment) are shown. Biological samples are on the x-axis and differentially methylated loci are on the y-axis, with relative hypermethylation and hypomethylation indicated by the color scale. The fractional methylation values for each CpG are centered and standardized to have mean 0 and standard deviation 1. The red color represents a methylation level above the mean methylation of the CpG across all samples, the white color represents mean methylation and the blue color represents methylation lower than the mean. B) DM CpGs are enriched in enhancers but depleted in promoter regions. For each chromatin state, enrichment and under-representation are symmetrically visualized using log2(OR). C) Validation and mapping of the DMR in DAPK1 using bis-seq. A map of the DAPK1 gene showing hypomethylation in the promoter region is given on the top. The DMR overlaps an active promoter region (color coded in red) flanked by a strong enhancer (yellow). Bis-seq amplicons for validation and mapping of the DMR are indicated by the numbered rectangles. The bis-seq data (bottom panel) is visualized by the circles representing consecutive CpGs with black circles indicating methylated CpGs and white circles unmethylated CpGs, with each line being a unique DNA clone.
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Epigenetic Alterations Affecting Transcription Factors and Signaling Pathways in Stromal Cells of Endometriosis Fig 1 Gene-specific alterations in DNA methylation in primary ovarian endometriosis stromal cells (OESC) compared to control endometrial stromal cells (CESC), chromatin state enrichment analysis of DM genes in endometriosis, and bi-seq validation for DAPK1. A) Heat maps of gene-specific methylation changes in endometriotic stroma cells vs. controls. Supervised hierarchical clustering of the 450K methylation BeadChip data analyzed at the CpG level (FDR q-values .15) and at the element-level (q-values .15 for multiple CpG segment and>0.1 for single CpG segment) are shown. Biological samples are on the x-axis and differentially methylated loci are on the y-axis, with relative hypermethylation and hypomethylation indicated by the color scale. The fractional methylation values for each CpG are centered and standardized to have mean 0 and standard deviation 1. The red color represents a methylation level above the mean methylation of the CpG across all samples, the white color represents mean methylation and the blue color represents methylation lower than the mean. B) DM CpGs are enriched in enhancers but depleted in promoter regions. For each chromatin state, enrichment and under-representation are symmetrically visualized using log2(OR). C) Validation and mapping of the DMR in DAPK1 using bis-seq. A map of the DAPK1 gene showing hypomethylation in the promoter region is given on the top. The DMR overlaps an active promoter region (color coded in red) flanked by a strong enhancer (yellow). Bis-seq amplicons for validation and mapping of the DMR are indicated by the numbered rectangles. The bis-seq data (bottom panel) is visualized by the circles representing consecutive CpGs with black circles indicating methylated CpGs and white circles unmethylated CpGs, with each line being a unique DNA clone.

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