Fig. 3
H3.1 K27M/I mutations modify H3K27me3 and H3K27ac marks and alter gene expression in leukemic cells. a Western blot analysis of H3K27me3 levels from total histone protein from TEX cells transduced with HIST1H3H WT/K27M, HIST1H3F WT/K27I, Luc2 control, or untransduced (UT) cells. b Volcano plot depicting genes showing differential expression in HIST1H3H K27M relative to WT. H3K27me3 change of K27M/WT is overlaid as a heatmap, with red and blue representing loss and gain, respectively. Dashed gates indicate genes called as being significantly down- or upregulated, using threshold of |z-score| >1.5, p-value <0.05. c Volcano plot depicting genes showing differential expression in HIST1H3F K27I relative to WT, as in b. d Venn diagram showing overlap of significantly upregulated genes observed in K27M and K27I expressing TEX cells. e Box-whisker plot showing change of promoter-specific H3K27me3 in the TEX cells, comparing all annotated promoters and the subset that showed up-regulation in both K27M and K27I. The lower and upper whisker represents the minimum and maximum, respectively, after removing outliers where the upper whisker = min(max(x), Q3+1.5 × IQR) and lower whisker = max(min(x), Q1−1.5 × IQR), where IQR = Q3-Q1. The two ‘hinges’ are versions of the first and third quartile. The notches extend to ± 1.58 IQR/sqrt(n) representing a confidence interval. IQR stands for interquartile range. Center line indicates median. f, g two-dimensional scatterplot depicting the change of H3K27me3 and H3K27ac at all annotated promoters in f K27M and g K27I overexpressing TEX cells. Corresponding K27M/WT RNA-seq z-score is overlaid as a heatmap, with red and blue representing up- and down-regulation, respectively. h, i Genome browser snapshot of the h GATA1 locus and i LIF locus with RNA-seq and Rx-normalized H3K27me3 and H3K27ac data
