Fig. 2: Hippocampal cells lacking KAT3 fail to express neuronal-specific genes. | Nature Communications

Fig. 2: Hippocampal cells lacking KAT3 fail to express neuronal-specific genes.

From: KAT3-dependent acetylation of cell type-specific genes maintains neuronal identity in the adult mouse brain

Fig. 2

a Cumulative graph showing the log2 fold-change value of DEGs in dKAT3-ifKOs (mRNA-seq, 1 month after TMX, n = 3 per genotype). Upregulated genes are presented in red and downregulated genes in blue (p.adj < 0.05 and |log2FC| ≥ 1). The bottom bar graph compares the area in each set. b Volcano plots of RNA-seq analysis. From left to right, we present all genes (left) and the subset of housekeeping genes listed in ref. 76 (right). Gray: genes that are not significantly deregulated; red: upregulated genes; blue: downregulated genes; purple: housekeeping genes. c The 10 most enriched categories identified by Gene Ontology (GO) analysis on up- (red) and downregulated (blue) genes with a p.adj < 0.05 and |log2FC| ≥ 1. The upregulated gene set only retrieved three categories. d RNA-seq profiles for three representative neuronal-specific genes: Rbfox3 (NeuN), Hpca, and Camk4. Scale: 2 kb. e Immunohistochemistry against the neuronal protein encoded by Camk4, Rbfox3 (NeuN), and Hpca. Dashed line labels the position of the stratum pyramidale based on DAPI images (n = 3). Scale: 60 μm. f Loss of NeuN immunoreactivity in DG neurons infected with a cre recombinase-expressing AAV (GFP+). The experiment was performed 3 times with different sets of mice. The virus was injected unilaterally into the DG of adult Crebbpf/f::Ep300f/f mice and the mice were perfused 1 month later (Supplementary Fig. 3e). See Supplementary Fig. 3f for immunostaining against CBP in the same brain slide. Scale: 200 μm. g Scheme representing the strategy to eliminate both KAT3 proteins in hippocampal PNCs from E17 dKAT3f/f embryos. h Representative images showing morphological changes in Crebbpf/f::Ep300f/f hippocampal neurons infected with LV-CRE compared with LV-GFP control (n = 6 in both groups). i RT-PCR demonstrates decreased levels of Neurod2 (ND2), Hpca (hippocalcin), and Rbfox3 (NeuN) transcripts in dKAT3-KO PNCs. In contrast, several housekeeping genes (Ppl1, Pgk1, Rpl23) are unaffected (n = 5–6 in both groups). Data are presented as mean values ± SEM. Two-tailed t-test: ****p < 0.0001, ***p < 0.001, **p < 0.01. Source data for graphs in panel (i) are provided as a Source data file.

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