Fig. 3

The incorporation of H3mm7 enhances activated gene expression by increasing chromatin accessibility. a Trans-differentiation model by MyoD infection using H3mm7/H3.3-GFP-expressing NIH3T3 cells. This model was utilized to confirm each dependency for exerting the function of H3mm7 on the inherent cell lineage (skeletal muscle potential), transcription factor (MyoD), and differentiation stimuli (serum starvation). b The six types of gene expression patterns in time-series RNA-seq data of NIH3T3 cells. The plot was created as in Fig. 2b. The error bars indicate ±1 SD of the genes (n: the number of genes in the clusters) c Marked enhancement of gene expression occurred in activated genes during differentiation (cluster UA). The scatter plot of log2-transformed fold change of gene expression (H3mm7+ vs. WT cells, through time) and chromatin accessibility changes (H3mm7+ vs. H3.3+ cells, through time) are shown. The colors correspond to the clusters in b. The sizes of the points are proportional to −log10 (adjusted p-values of chromatin accessibility change). Enhanced: upregulated genes in control NIH3T3 cells over time with higher expression levels and higher accessibility in H3mm7+ cells compared with H3.3+ cells. Enhanced (negative): downregulated genes in control NIH3T3 cells over time with lower expression levels and lower accessibility in H3mm7+ cells compared with H3.3+ cells. d The expression levels of genes that showed marked enhancement. The expression levels are calculated as transcripts per million (TPM). e IGV snapshot of ATAC-seq shows increased chromatin accessibility at an H3mm7 incorporated promoter