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Figure 1 | Genome Biology

Figure 1

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

Figure 1

Genome-wide promoter occupancy of TFIIB. (a) TFIIB enrichment on human promoter arrays in two biological ChIP-chip replicates. Each spot represents the median of hybridization intensities obtained on 15 probes per individual promoter region (log2 scale). Pearson's correlation is denoted by r. (b) Signal tracks of the two TFIIB replicates for the HIST1 histone gene cluster and an adjacent BTN butyrophilin gene cluster on chromosome 6. Signals are bar-plotted as ChIP over non-enriched input DNA (ChIP/total) in log2 scale. (c) Resolution of ChIP-chip signals at a single gene promoter. The left panel shows the fragment length distribution of sheared ChIP DNA in the two replicates as determined by ethidium bromide staining of 250 ng (lanes 2 and 4) or 500 ng (lanes 3 and 5) of purified DNA loaded on a 1.4% agarose gel. Lane 1 is a DNA size marker with fragment lengths indicated on the left. The right panel shows magnified signal plots of the two TFIIB replicates at the RNPS1 promoter region. Scale is indicated at the top. The approximate width of the peak area is outlined in red, with the vertical hatched line denoting the peak center. The broken arrow marks the location and direction of the TSS. (d) Average binding profiles of the top 5% probesets for TFIIB replicate 1 (black line) and replicate 2 (grey line) relative to aligned TSSs at 10-bp resolution.

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