Fig. 3
From: DPPA3 facilitates genome-wide DNA demethylation in mouse primordial germ cells
Hypermethylated regions are enriched for H3K9me3. (A) Increase in CG methylation (%) (KO– control) and histone mark profiles of a portion of mouse chromosome 1 in E13.5 wild-type female PGCs. Published ChIP-seq data [34] were retrieved and reprocessed. RefSeq genes are indicated at the bottom. (B) Violin plots showing the enrichment of histone marks in the hypermethylated (10-kb windows, n = 14,395) and other regions (n = 249,787) regions in E13.5 wild-type female PGCs. Horizontal bars indicate the median values. (C) Scatterplots comparing CG methylation levels of regions with specific histone marks (10-kb windows) in control and KO E13.5 female PGCs. Top 5% genomic regions with enrichment for specific histone marks were analyzed. The actual numbers of used windows are indicated for individual graphs. (D) Heatmap showing regional increase in CG methylation (%) in E11.5–16.5 PGCs and FGOs. H3K9me3 enrichment is from wild-type E13.5 female PGCs. (E) Violin plots showing the H3K9me3 enrichment in E13.5 wild-type female PGCs for regions hypermethylated only in E13.5/E16.5, persistent in FGO and only in FGO (identified in Additional file 1: Fig. S3F). Horizontal bars indicate the median values. (F) Violin plots showing the regional CG methylation levels in control and KO FGOs for regions hypermethylated only in E13.5/E16.5, persistent in FGO and only in FGO. Horizontal bars indicate the median values