Supplementary Figure 4: Cell-type-specific neuronal and non-neuronal MeCP2-dependent gene misregulation in male Mecp2^–/y mice.

While MeCP2 is most highly expressed in neurons, it is expressed in nearly all cell types and in the brain its mutation may contribute to dysfunction in glia and microglia as well^51–54. (a) Venn diagram depicting the significantly up- and down-regulated genes that are expressed across all four cell types (FDR < 0.1, normalized expression > 0.1 in each cell type, 1230 cells sampled per cell type. Note that the corresponding supplementary tables have a greater number of significantly regulated genes in each cell type than the Venn diagrams because the tables do not require a minimum expression threshold across all cell types). We did sequence 112 WT and 154 KO astrocytes in these experiments, but differential expression analysis was underpowered compared to the other cell types. (b) Heatmap illustrating the relative mean expression level of significantly misregulated genes (columns) from (a) across each cell type (rows). (c) Preferential up-regulation of longer genes in certain mutant Mecp2 non-neuronal cell types such as oligodendrocytes and to a lesser degree vascular cells. Longer genes are more likely to be up-regulated in the absence of MeCP2 because they, on average, have more methylated cytosines within their gene bodies. Analysis of DNA methylation patterns in non-neuronal cell types will help interpret which genes are more likely to be direct targets of MeCP2. Graphs show mean fold-change in gene expression of Mecp2^-/y cells of the indicated cell type versus WT cells of the same cell type (KO v WT) or two groups of cells randomly sampled irrespective of genotype (Random) binned according to gene length. The lines represent mean fold-change in expression for all expressed genes in 1000 gene bins with 100 gene steps; the ribbon is s.e.m. of each bin.