Figure 2

The effects of promoter architecture features on the TFBS distribution. (A) Strong negative correlation between the TFBS frequency and the genome-wide average of nucleosome occupancy in the ~200 bp region upstream of the TSS. The intergenic regions were aligned with reference to TSS. (B) The yeast genes were clustered into four groups by k-means clustering based on a 1201 bp region surrounding the TSS. (C) The frequency distributions of TFBSs relative to the TSS in four clusters of genes with diverse nucleosome occupancy patterns. The figure is presented in the same way as Figure 1A. (D) The TFBS distribution differs between TATA box-containing and TATA box-less genes. The TATA box-containing genes have more broadly distributed TFBSs and higher TFBS frequency in the promoter region. (E) The distributions of TFBSs relative to the TSS in three categories of 5'UTR length: short, medium and long. The long 5'UTR genes have more broadly distributed TFBSs and a higher TFBS frequency in the promoter region.