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Figure 5 | Genome Biology

Figure 5

From: Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells

Figure 5

High TFIIB/NC2 ratios select for TATA and combinations of TATA with other core promoter elements. (a) Correlation of TFIIB/NC2 ratio to gene expression. Genes were grouped into percentiles of expression levels (x-axis). For each group, the mean value of TFIIB or NC2 occupancy on all promoters within this group was determined. From these values the ratio was calculated and is plotted as a blue curve in the graph. (b) Nucleotide frequency plots [28] of the top 100 TFIIB-dominated genes (upper panel) or the top 100 NC2-dominated genes (lower panel). Core promoter sequences from position -50 to +50 were extracted and aligned at the TSS (broken arrow). Letter heights reflect relative base frequencies at the given position. Shaded boxes on top of each panel indicate matches to the consensus sequences of core promoter elements shown above. (c) Pie charts depicting the percentage of promoters of either TFIIB-dominated genes or NC2-dominated genes that contain zero, one, two, or three motifs in their core region. (d) Matrix showing absolute frequencies of the indicated core promoter motifs or motif combinations in TFIIB-dominated genes (left) or NC2-dominated genes (right). (e) Synergistic motif combinations in core promoters of TFIIB-dominated genes. The bar graph depicts how often one of the specified reference motifs is found in combination with a second motif in the same promoter. Co-occurrence of two motifs is expressed as fractional percentage, with the reference motif alone set to 100%.

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