Figure 4: Depletion of CHD8 in hNSCs significantly affects CHD8 target genes.

(a) Top, Schematic depicting functional domains within CHD8. Sites in CHD8 that are targeted by knockdown shRNA constructs C and G are indicated by vertical grey bars. Bottom, Representative western blot of hNSC protein lysates demonstrating depletion of CHD8 protein levels due to transfection of each shRNA construct compared with a non-targeting transfection control (shCTL). QPCR and western blots were performed for each knockdown experiment. (b) Conserved CHD8 targets are disproportionately affected by CHD8 depletion. For each subset of CHD8 target genes shown, the P value from a Wilcoxon rank test comparing the distribution of differential expression P values in that subset versus active genes not bound by CHD8 in hNSC is plotted on the y axis, and the number of genes in the subset is plotted on the x axis (Supplementary Information). The red curve shows the smoothed (quadratic) spline fit to the data. (c) Residual values for the indicated subsets of CHD8 targets calculated from the fit lines in b. The set of CHD8 targets conserved in mouse holds the greatest fraction of genes showing differential expression by each CHD8 knockdown.