β-actin affects neuron-related transcriptome during direct reprograming in a dosage-dependent manner.

(A) Principal component analysis of the transcriptomes of MEFs (WTM, HETM and KOM) and CiNeurons (WTN, HETN and KON). Color spheres represent individual samples. PC1 and PC2 account for 52% and 9% of the total variance, respectively. (B) Summary of the number of genes significantly up-regulated and down-regulated by at least 2 fold in each paired comparison. (C-E) Genes up-regulated in CiNeuron of each β-actin genetic background are subject to GO enrichment analysis respectively. The significantly enriched, neuron-related GO terms (gene counts of the GO term ≥ 30, fold of enrichment ≥ 1.5 and p value of enrichment (C), Cellular Components (D) and Molecular Functions (E) are shown. (F) Genes that are associated with ion channel activity and are significantly up-regulated by at least 2 fold in WTN vs WTM are selected. Heatmap shows the relative expression level of those genes in all MEFs and CiNeurons. Cluster I represents genes that failed to be up-regulated in CiNeuron of KO background (KON). Cluster II represents genes that are up-regulated in KON but the expression level is lower in comparison to WTN. Scale bar: log2 CPM. (G) Genes up-regulated in WTN vs WTM comparison and associated with each GO term were selected. The distribution of the relative expression level (Log2 CPM) of those genes in all MEFs and CiNeurons are displayed in bean plots. Horizontal line is the mean of each sample. Statistics: One-way ANOVA with Tukey’s multiple comparison as post hoc test: * pPp<0.001.