Fig. 7: MeCP2 differentially regulates gene expression depending on H3K27me3 and H3K9ac pattern.
From: MeCP2 regulates gene expression through recognition of H3K27me3
a Gene clusters classified by co-modification of MeCP2, H3K27me3, and H3K9ac within 1 kb up- and 5 kb downstream of the TSS. Genes sorted by descending order of mean signal intensity (numbers of genes in each cluster indicated on the left). Average profile of MeCP2 (bottom left), H3K27me3 (bottom center), and H3K9ac (bottom right). The shaded areas are up to ±S.D. from the average profile. Mouse OE is the tissue source for all subsequent analyses in this figure. b The expression levels of genes from cluster1 (purple, n = 4,159), cluster2 (gray, n = 628), and cluster3 (green, n = 1747). N = 3 (WT) from biologically independent animals. p = 7.70 × 10−73 (cluster1 vs cluster2); p = 2.25 × 10−218 (cluster1 vs group3); p = 2.93 × 10−5 (cluster2 vs cluster3). (two-tailed Mann–Whitney testing with Bonferroni corrections, ***p < 0.0001). Box-and-whisker plots show median, 10–90 percentile, and min and max values. Mean is marked by “+.” c–e Differential gene expression between WT and Mecp2 KO was shown by enrichment scores, determined by GSEA, within each cluster1 (c), cluster2 (d) and cluster3 (e). N = 3 (per genotype, WT vs Mecp2 KO) from biologically independent animals. f–h Comparison of gene expression between WT and Mecp2 KO using amplification-free NanoString technology. N = 2 (per genotype, WT vs Mecp2 KO) from biologically independent animals. Purple dots indicate up-regulated genes, and green dots represent down-regulated genes in cluster1 (f), cluster2 (g) and cluster3 (h). i The percentage of differentially expressed genes in each cluster in the NanoString nCounter gene expression assay.
