Fig. 5: H3K27ac is strongly decreased in neuro-specific locations and correlates with gene downregulation.

a Immunostaining against H3K27ac in the CA1 subfield of single and dKAT3 ifKOs (IF signal control: 21.62 ± 2.24, dKAT3-ifKOs: 4.94 ± 1.03, p < 0.0001, unpaired t-test); the single ifKOs show non-significant difference compared to controls. The experiment was repeated 3 times. Scale: 10 μm. b Genome-wide analysis of H3K27ac changes in dKAT3-ifKOs. Volcano plots show the fold change and significance values for all peaks (Global) and for the subsets of neuron-specific (Neuro) and pancellular peaks. c Classification of regulatory regions categorized by genomic features. d Metaplots of ATAC-seq, KAT3, and H3K27ac ChIP-seq signals in neuronal and pancellular enhancers in controls and dKAT3-ifKOs. Plots are centered in the peak center and expanded ±1 kb. e Correlation between length of the enhancer and expression level of the proximal gene. f Number of downregulated genes that contain enhancers or super-enhancers in control mice and percentage that lose acetylation in dKAT3-ifKOs. g Barplot showing the top 10 enriched categories from the Phenotype analysis for genes harboring neuronal enhancers. h TFBS analysis of neuronal (green), non-neuronal (red), and pancellular (orange) KAT3 peaks. Each motif family name is a user-curated approximation to the results provided by the MEME-suite algorithm. The most enriched de novo-identified binding motif in neuronal KAT3 (upper right motif) is very similar to the NeuroD2 motif (bottom right). Log E-values obtained with the expectation maximization algorithm (MEME-ChIP suite): Neuro: bHLH = 1130, GLI = 258, SOX = 257; Pancell: FOX = 130, ETS = 67, SP = 57; NoNeuro: ETV = 157, FOX = 105, SOX = 49. i TFBS analysis of neuronal regions with a reduced ATAC-seq signal in dKAT3-ifKOs. j RNA-seq profiles for Neurod2 and NeuroD6. Scale: 1 kb. k Digital footprinting of NeuroD2 at neuronal and pancellular KAT3-bound regions. Values correspond to normalized Tn5 insertions. l Representative snapshots of KAT3, ATAC, and H3K27ac depletion with bHLH footprint and NeuroD2 overlaps, at two genes that are strongly downregulated in dKAT3-ifKOs. Source data for graphs in panels (e) and (h) are provided as a Source data file.