Figure 7
From: MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy
MBD3 DNA binding in control and amygdala-stimulated rats.
(A) Venn diagram showing numbers of DNA regions occupied by MBD3 in sham-operated (magenta) and stimulated (dark blue) rats. Regions with increases and decreases in MBD3 occupancy in stimulated animals are indicated in red and green, respectively. (B) Functional annotation of genes associated with sites that were differentially occupied by MBD3 in control and stimulated animals. (C) Heatmap of DNA regions that were differentially occupied by MBD3 in control and stimulated animals (FDR < 0.1). Each column represents an individual animal and each row represents the genome region. Colors on the heatmap represent the Z-score, with relatively high (dark green) and relatively low (light green) levels of MBD3 binding to DNA. (D) Distribution of sites differentially (cut-off P < 0.01) occupied by MBD3 in stimulated animals in defined genomic features (TSS, TES, gene body, exon, intron, UTR, downstream, enhancer, promoter, CpG and non-genic). Notice that a single peak can overlap with more than one type of feature in this analysis. (E) Frequency of observed MBD3 binding changes (cut-off P < 0.01) in stimulated animals compared with sites with no changes in MBD3 binding, with upper and lower 95% confidence intervals for defined genomic features. Increased binding of MBD3 relative to controls is coded with red bars and decreased binding of MBD3 relative to controls is coded with green bars. O/E, observed/expected ratio. *P < 0.05, **P < 0.01, ***P < 0.001 (Fisher’s Exact test). (F) qPCR validation of MBD3 binding at nine selected target loci in sham-operated rats. Average Ct values for individual ChIP and IgG controls are expressed as a percentage of input ± SD.
