Figure 2

The GR and AP-1 motifs are calculated to be well-bound by nucleosomes. (A) Distribution of the INOS for 32,896 GR-like 8-mers (N-NNN---NNN-N). The INOS for each split 8-mer is calculated from 1,000 simulated 150-bp DNA sequences with the GR-like 8-mer in the center. The GR motifs are calculated to bind nucleosome better than the average GR-like 8-mer. The two GR motifs (G-ACA---^T/_CGT-C) are highlighted. Average INOS for all split 8-mers is shown as a dashed vertical red line. Distribution of INOS (0.141±0.015) for 32,896 random control set following Gaussian distribution is shown in purple. (B) Distribution of the INOS for all continuous 8-mers (NNNNNNNN). (C) Average INOS for 8,235 Hoxa2 ChIP-seq peaks [23]. (D) Average INOS near (±750-bps) canonical Pbx motifs (TGATTGAT); 638 bound as observed in the Hoxa2 ChIP-seq peaks and 59,164 unbound Pbx motifs are shown. (E) The blue histogram shows the distribution of INOS for all 59,802 Pbx motifs and the red histogram shows the percent bound by Hoxa2.