Figure 3
From: p39-associated Cdk5 activity regulates dendritic morphogenesis
Transcriptome analysis of p39+/+ and p39−/− cortical neurons. (a) Heatmap showing the relative expression of differentially expressed genes between p39−/− and p39+/+ cortical neurons. There were 278 upregulated and 361 downregulated genes. The total RNA from p39+/+ and p39−/− cortical neurons was extracted at 10 days in vitro (DIV) for whole-transcriptome analysis. (b) Ingenuity pathway analysis (IPA) of the biofunctions of differentially expressed genes between p39−/− and p39+/+ cortical neurons. The activation of biofunctions according to differential gene expression in p39−/− and p39+/+ cortical neurons was determined by the z-score algorithm with a criterion of p < 0.05 (i.e., − log10 ≥ 1.3; black dots) using Fisher’s exact test. (c) Heatmap showing the differential gene expression of the “shape change of the neurite” group between p39+/+ and p39−/− cortical neurons. (d) Volcano plot showing the log2 fold change and − log10(p value) of each gene comparing p39−/− and p39+/+ cortical neurons. Differentially expressed genes with fold change > 1.5 and < −1.5 are highlighted in red and blue, respectively. The dashed line indicates p < 0.05 and a fold change > 1.5 or < −1.5. (e) Wdfy1 transcript levels in p39+/+ and p39−/− neurons determined by RNA sequencing analysis. (f) Real-time PCR analysis of Wdfy1 transcript levels in p39+/+ and p39−/− neurons. (g) WDFY1 protein expression at different developmental stages—embryonic day (E) 17, E17; postnatal day (P) 7, P7, and 1 month old—in C57/BL6 mouse brains. (h, i) Elevated WDFY1 protein expression in p39−/− mouse brains. Western blot analysis (h) and quantification (i) of WDFY1 protein in p39-knockout mouse forebrains at P7; n = 3 brains; *p < 0.05, **p < 0.01, unpaired Student’s t-test.
