Figure 3

H3K9ac and H4K8ac profiles in RE1 promoters. The profiles of these acetylations were generated and plotted for four groups of genes with different colors (black, blue, red, and cyan), defined by the presences of cRE1, ncRE1, and REST in their promoters. The 'REST On & Exp Up' (red lines) refers to the group of genes with cRE1 and REST but an expression score >300. The profiles of modifications for these RE1 genes are shown with solid lines. For each of the four groups, a control was constructed by randomly selecting (5×) genes with the same expression levels but with neither RE1 nor REST in their promoters (see Materials and methods). The profiles of these controls are shown with dashed lines and colors matching to their targeted group. For the convenience of visual comparison, the zoom-in profiles for the four RE1 groups and their controls are re-drawn in the bottom panels. The color scheme and line style in the bottom panels apply to Figures 5-7. The x-axis shows the distance to transcription start sites with a unit representing 200 bp, and the y-axis shows the normalized counts of ChIP-Seq tags.