Figure 4

Binding of Myc to all possible 8-mers and comparison with genomic occupancy. (A) Fluorescent signal generated by Myc in vitro binding with an array containing all possible 8-mers was normalized. Twelve core 6-mer sequences with the highest in vitro occupancy are shown. The relative affinity of all 8-mers for each 6-mer is shown (10 points if the 6-mer is a palindrome or 16 if it is not). The inset shows the sorted in vitro binding signal for all possible 8-mers. (B) Genome browser view of a region on chromosome 19 comparing Myc, Max, and Pol II occupancy with the distribution of the top 12 6-mers (from A). The height of each 6-mer peak is equal to its relative in vitro occupancy (shown as percent). (C, D) Zoomed in views of two regions shown in (B) that demonstrate the lack of correlation of Myc and Max occupancy with the intrinsic affinity for the underlying DNA determined in vitro.