Figure 6

GR half sites predominate at GBRs near non-selective, activated genes. (A) More 17mers containing half sites (green circle) than full sites (red circle) are expected because the information-containing region of the motif is shorter; similarly, most full sites contain a good half site because the constraints (that is, the sequence motifs) are similar and there are two positions available in a full site for a good half site due to the palindromic nature of dimer. Nonetheless, not all full sites contain half sites, as the half site motif is more strongly constrained than the full site motif; the additional specificity may be due to the lack of cooperative binding at these sites. (B) Individual information (measured in bits) of the best full site (x-axis) and half site (y-axis) found at GBRs (circles) located within 20 kb of the transcriptional start sites of a set of genes; contour lines encompass same number of GBRs, and thus localize regions of high GBR density. Genes that lost activation with A477T (B, red) generally had peaks with good full sites (>10 bits) and good half sites (>9 bits). Genes that gained activation with A477T (B, green) generally had GBRs with poor full sites (<5 bits) and good half-sites (>10 bits). Genes that were non-selectively^c activated (B, blue) also generally had GBRs with poor full sites and good half sites.