MBD3/NuRD modulates gene expression patterns during mammalian neurogenesis. (A) Expression of genes found in clusters 35 and 39 are plotted individually for wild-type (left) and Mbd3 cKO (right) samples. (B) Relative expression of indicated genes in WT and mutant progenitors at E12.5, E14.5 and E16.5. In all cases, expression values are plotted relative to WT expression at E12.5. N = 3 to 4. For wild-type vs. mutant samples at E14.5 for Nhlh2 *P = 0.0066, df = 2. For wild-type vs. mutant samples at E16.5 *P = 0.0032, df = 2 (Nhlh1); P = 0.0002, df = 2 (NeuroD1); P = 0.0403, df = 2 (Nhlh2); P = 0.0001, df = 2 (NeuroD2). (C) Chromatin immunoprecipitation (ChIP) was performed using an anti-Mbd3 antibody or rabbit IgG control in wild-type (WT) and conditional knockout (KO) cortices at E14.5 and E16.5. Immunoprecipitates were probed with primer pairs (listed in Table 3) located across the indicated genes and plotted as percentage of input (y-axis; error bars represent st. dev.). Numbers across the x-axis indicate distance relative to the transcription start site for indicated genes. Gene structure is shown below the graphs: white boxes represent non-coding regions, blue boxes represent coding regions, and green boxes indicate the presence of putative enhancer regions based upon histone ChIP data available on mm9 from the UCSC genome browser. (D) Expression of genes found in clusters 28 and 29 are plotted individually for wild-type (left) and cKO (right) samples. (E) Relative expression of indicated genes in wild-type and mutant brain samples from E16.5. N = 3; *P = 0.0004 (NeuroD4), P = 0.0026 (S100β), P = 0.0001 (Gfap), df = 2; error bars represent st. dev. (F) Representative immunostaining of E18.5 coronal brain sections for S100β (red). White arrow indicates a rare, positively stained cell in the Mbd3 cKO sample Scale bar = 100 μm at 200× magnification and 50 μm at 630× magnification.