Evidence for Gene-Specific Rather Than Transcription Rate–Dependent Histone H3 Exchange in Yeast Coding Regions
Figure 4
H3K79 trimethylation in coding regions is tightly linked to relative exchange.
(A) A histogram showing the correlation between each histone H3 modification (x-axis; Text S3) and two histone exchange measures: relative exchange (black) or total exchange (gray) in coding regions. y-Axis: −log P-value of Spearman correlation (see Methods). Positive/negative correlations appear above/below the x-axis. Among all histone marks, H3K79me3 has the strongest association with relative exchange. (B) Plot of the relationship among H3K79me3 enrichment against relative exchange in coding regions. The plot was generated using a moving average (window = 100, step = 1). H3K79me3 enrichment is the log2 ratio of H3K79me3 ChIP vs. anti-H3 ChIP [17]. (C) A heat map illustrating the functional relationship between transcription rate (x-axis, [8]), total exchange in coding regions (y-axis, [8]), and H3K79me3 enrichment in coding regions (color-coded). The heat map is depicted as in Figure 1A, except that the color-coding is different (see Methods). High/low H3k79me3 enrichment is indicated in red/green. The heat map demonstrates that H3K79me3 is linked to relative exchange but not to total exchange. (D) Composite profiles of probe's relative exchange along the coding region. Coding regions were divided into five groups according to their average H3K79me3 enrichment (shown in shades of blue). The plot is depicted as in Figure 2C, except that the partition into groups is different. We observe that the link between H3K79me3 enrichment and relative exchange holds along the entire coding region.