Figure 2

Average sequence preferences for nucleosomes, aligned with respect to the center of the experimentally determined nucleosomes at SDN-enriched promoters (A) and SDN-less promoters (B). For each DNA sub-sequence with the length of the nucleosome, Segal et al. have predicted its sequence preferences for nucleosomes based on dinucleotide probability distributions [15]. These values were normalized, such that their values are between 0 and 1. The x axis corresponds to the distance between the midpoint of the sub-sequence and the center of the experimentally determined nucleosome [7]. Considering that nucleosomes were measured by DNA microarray with 4-bp resolution [7], the evident peak in the middle region of (A) indicates the sequence-dependent nucleosome positioning at SDN-enriched promoters, while the evident valley in the middle region of (B) indicates the less sequence-dependent nucleosome positioning at SDN-less promoters. Error bars were calculated by bootstrapping.