Fig. 2: Kat6b overexpression reverses gene expression changes present in Kat6a–/– E9.5 embryos.
a–i RNA-sequencing data of Kat6a+/+Kat6b+/+, Kat6a–/–Kat6b+/+, Kat6a+/+Tg(Kat6b) and Kat6a–/–Tg(Kat6b) E9.5 embryos. N = 4 embryos per genotype. Data were analysed as described in the ‘methods’ section. A false discovery (FDR) < 0.05 was used as the cut off for significance. a Multidimensional scaling plot of the leading gene expression differences between samples in pair-wise comparisons showing Kat6a+/+Kat6b+/+, Kat6a–/–Kat6b+/+, Kat6a+/+Tg(Kat6b) and Kat6a–/–Tg(Kat6b) E9.5 embryo RNA samples. b M (log ratio) and A (mean average) plot showing Kat6a–/–Kat6b+/+ vs. Kat6a+/+Kat6b+/+ and Kat6a–/–Tg(Kat6b) vs. Kat6a+/+Kat6b+/+ embryos. The total numbers of upregulated and downregulated genes at FDR < 0.05 are indicated in each comparison. Upregulated genes are represented in red, downregulated in blue and unchanged genes in grey. c Heatmap showing genes differentially expressed in the contrast of Kat6a–/–Kat6b+/+ vs. Kat6a+/+Kat6b+/+ embryos but displayed for all genotypes. d Venn diagram showing the intersection of genes downregulated (DR) in Kat6a–/– Kat6b+/+ vs. Kat6a+/+Kat6b+/+ embryos with those downregulated in Kat6a–/–Tg(Kat6b) samples vs. Kat6a+/+Kat6b+/+ embryos compared to those upregulated in Kat6a–/–Tg(Kat6b) samples vs. Kat6a+/+Kat6b+/+ embryos. e Top 20 gene ontology (GO) (BP) terms downregulated in Kat6a–/–Kat6b+/+ vs. Kat6a+/+Kat6b+/+ embryos and rescued in Kat6a–/–Tg(Kat6b) when compared to Kat6a+/+Kat6b+/+ embryos. GO terms enriched with p < 10–6 are shown. f Top 20 gene ontology (GO) (BP) terms upregulated in Kat6a–/–Kat6b+/+ vs. Kat6a+/+Kat6b+/+ embryos and rescued in Kat6a–/–Tg(Kat6b) when compared to Kat6a+/+Kat6b+/+ embryos. GO terms enriched with p < 10–6 are shown. g–i Specific gene families previously reported to be affected by loss of KAT6A17,18,44 were examined. Correction for multiple testing was conducted within gene family. FDRs for each comparison are shown above each bar. g–i Log2 fold-change in levels of HOX gene mRNA (g), DLX gene mRNA (h) and TBX gene mRNA (i) across pairwise comparisons Kat6a–/–Kat6b+/+ vs. Kat6a+/+Kat6b+/+ embryos, Kat6a–/–Tg(Kat6b) vs. Kat6a+/+Kat6b+/+ embryos and Kat6a–/–Tg(Kat6b) vs. Kat6a–/–Kat6b+/+ embryos. FDRs are displayed above or below the bars.
