Independent regulation of gene expression level and noise by histone modifications
Fig 2
Separate association with burst frequency and size among histone modifications.
A, The burst-like gene expression model. B, Similar to Fig 1B, expression level and noise of each gene in the human genome were plotted, where each dot represents one gene. Burst-size-dominant genes are above the major axis, while burst-frequency-dominant genes are below the major axis. C, Left panel: Correlations between the intensity of each histone modification and burst frequency and burst size (rBF and rBS, respectively) were shown, as well as rBF and rBS for the status of TATA box and nucleosome occupancy. Right panel: Correlations between the intensity of H3K4me3/H3K79me2 and burst size/frequency, respectively, as an illustration of the correlation calculation. Genes were divided into 200 equal-sized bins (bins with equal number of genes) based on their H3K4me3 or H3K79me3 intensity. In each bin of genes, the mean and standard error of H3K4me3 (or H3K79me2) intensity and burst size/frequency were calculated. In the last several bins, the variation of H3K4me3 (or H3K79me2) intensity is relatively larger, so the error bars are broader. Correlation coefficients were calculated with the raw data (N = 3350). D, The difference of the absolute values of rBF and rBS. Permutation test was used to determine the significance of difference between rBF and rBS. N = 3350. ***, P < 0.001; **, P < 0.01; *, P < 0.05. E, Average distributions of 8 histone modifications in human embryonic cells, aligned by TSS. Promoter-localized and gene-body-localized histone modifications are marked in cyan and coral, respectively.