FIGURE 1.

Cortical layers are malformed in the absence of BAF complex, and attributable to loss of cell adhesion and glial fiber scaffolds. (A) Volcano plot showing genes downregulated and upregulated in the E17.5 dcKO_hGFAP-Cre cortex. Examples of top altered genes are indicated. (B) Graph showing downregulation of selected gene categories or pathways mainly related to cell adhesion and polarity formation in the E17.5 dcKO_hGFAP-Cre cortex. (C) Sections of E17.5 control and dcKO_hGFAP-Cre cortex immunostained for the glial fiber protein Nestin and the cell adhesion protein α-Catenin. Specifically quantified cortical areas are shown with rectangles with dashed or stippled lines. (D,E) Simple (D) and grouped (E) bar charts showing quantification of Nestin and α-Catenin, respectively, in the E17.5 control and dcKO_hGFAP-Cre cortex. (F) Micrographs showing immunostaining with antibodies against Ctip2 and Cux1 to mark neurons that make the lower (deep) and upper (superficial) cortical layers, respectively, in the E17.5 control and dcKO_hGFAP-Cre cortex. White dashed lines are used to delineate the deep (Ctip2+) and superficial (Cux1+) cortical layers. Bins (1–6) for neuronal distribution analysis are indicated. (G,H) Bar charts showing quantitative distributions of Ctip2+ deep layer neurons and Cux1+ superficial layer neurons in the E17.5 control and dcKO_hGFAP-Cre cortical wall. Quantified cortical area = (420 μm × 170 μm). (I) Micrographs showing the P0 control and dcKO_hGFAP-Cre cortex with Ctip2 and Tbr1 immunostaining. Where shown, sections are counterstained with DAPI (blue). Unpaired Student’s t-test was used to test for statistical significance: *p < 0.01, **p < 0.001, ***p < 0.0001; ns, not significant; n = 6. Scale bars: = 100 μm and 50 μm in overview and zoomed images, respectively. Results are presented as mean ± SEM. IC, intracortical; AS, apical surface; VZ, ventricular zone; SVZ, subventricular zone; IZ, intermediate zone; CP, cortical plate; MZ, marginal zone.