Fig. 6: EED depletion reduces apoptosis and brain dysplasia of the Snip1^Nes-KO brain.

a Schematic of the genetic cross depleting both SNIP1 and EED for downstream assays. b, c IF analysis of CC3 overlayed with DAPI of the E13.5 brain. Bar, 50 μm. Each data point represents one image. Eight control embryos, 7 Snip1^Nes-KO embryos, and 5 Snip1^Nes-Eed^Nes-dKO embryos were analyzed. For lateral ventricle, n = 38 images (control), n = 34 (Snip1^Nes-KO), and n = 23 (Snip1^Nes-Eed^Nes-dKO). For third ventricle, n = 38 (control), n = 36 (Snip1^Nes-KO), and n = 26 (Snip1^Nes-Eed^Nes-dKO). d–i IF of NPC marker SOX2, and intermediate progenitor markers TBR2 and INSM1 overlayed with DAPI of the E13.5 brain. Bar, 50 μm. The populations of (e) SOX2-positive, (g) TBR2-positive, or (i) INSM1-positive cells in the neuroepithelial lining of lateral and/or third ventricles were quantified. Each data point represents one image. In (g), n = 43 images (control), n = 30 (Snip1^Nes-KO), and n = 29 (Snip1^Nes-Eed^Nes-dKO). In (i), n = 27 (control), n = 17 (Snip1^Nes-KO), and n = 16 (Snip1^Nes-Eed^Nes-dKO). For Panels c, e, g, and i, data are presented as mean ± SEM, and two-way ANOVA was used for statistical analysis. j Unsupervised clustering of RNA-seq data from control (n = 3), Snip1^Nes-KO (n = 3), and Snip1^Nes-Eed^Nes-dKO (n = 6) brains at E13.5. RNAs from forebrain and midbrain regions were sequenced and merged for downstream analyses. Blue indicates a negative correlation and red indicates a positive correlation. k, m Venn diagrams displaying the numbers of differentially expressed genes with FDR < 0.05. The lists of downregulated genes in Snip1^Nes-KO vs. control and upregulated genes in Snip1^Nes-Eed^Nes-dKO vs. Snip1^Nes-KO are compared in (k). The lists of upregulated genes in Snip1^Nes-KO vs. control and downregulated genes in Snip1^Nes-Eed^Nes-dKO vs. Snip1^Nes-KO are compared in (m). l, n Gene ontology of the rescued genes corresponding to Fig. 6k, m. Genes were searched against Molecular Signatures Database (MSigDB) Hallmark 2020 using Enrichr⁵⁶. Source data are provided in a Source Data file (c, e, g, i, l, n).