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Fig. 8 | Genome Biology

Fig. 8

From: RNF40 regulates gene expression in an epigenetic context-dependent manner

Fig. 8

The upregulation of a subset of RNF40-suppressed genes is associated with the activation of FOXL2-bound enhancers. a Venn diagram displaying the overlap between enhancers activated following RNF40 loss (“RNF40-supp. enhancer”), H3K27me3-enriched genes (H3K27me3+), and genes upregulated following Rnf40 deletion (up). RNF40-suppressed enhancers were obtained by DiffBind analysis (see Additional file 1: Figure S8D) and selected based on increased H3K27ac at intergenic regions (fourfold increased H3K27ac occupancy in Rnf40 –/– MEF, FDR < 0.05). RNF40-suppressed enhancer associated genes were identified by performing GREAT analysis of the significantly increased enhancers. b Plot displaying the Fisher and Z Scores of motif analysis performed using the 254 gene-associated enhancers shown in A. The Fisher Score >5 & Z Score > 10 indicates significantly enriched motifs (shown in red). c Venn diagrams showing the numbers shared by upregulated genes and FOXL2-enriched enhancer associated genes. FOXL2-enriched enhancer-associated genes were obtained by GREAT analysis of FOXL2-enriched enhancers (from Additional file 1: Figure S8G). d, e Aggregate profiles show FOXL2 average signal surrounding the center (±3 kb) of FOXL2-bound peaks displaying increased H3K27ac signals in Rnf40 +/+ or Rnf40 –/– MEFs (the 166 gene-associated enhancers from C). The p value (e) was calculated by unpaired Wilcoxon-Mann-Whitney test. f qRT-PCR analysis of Foxl2, Esr2, and Efna5 genes in Rnf40 +/+, Rnf40 –/–, and EZH2i-treated Rnf40 +/+ MEFs transfected with non-targeting siRNA (siNT) and Foxl2 specific targeting siRNA treatment. g The ChIP-seq profiles for H2Bub1, H3K4me3, H3K27me3, H3K27ac, FOXL2, and H3K4me1 on the Efna5 gene. h Model describing the role of increased Foxl2 expression in enhancer and gene activation following RNF40 loss

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