Figure 5.

The effects of phasing of nucleosomal sequences in Saccharomyces cerevisiae. For this analysis, A and T were set to 1, and C and G to 0. (A) Phasing of sequences is evident in the Fourier space at period 10.5 bp. Nucleosomes were ranked according to the strength of 10.5-bp periodicity and divided into five quintiles (the five circular rings separated by black circles). The phases (with respect to the dyad) of their discrete Fourier transform at period 10.5 bp were then binned into 20 equal intervals (the 20 bins within each ring). Colors indicate the fraction of nucleosomes lying in each bin divided by the expectation under a uniform null distribution (Supplementary Methods section 1.4). (B) Circular-linear correlation between the phase and strength of 10.5-bp periodicity (Supplementary Methods section 1.4). (C) Circular–circular correlation between the phase of nucleotide Fourier transform and the phase of nucleosome location Fourier transform at period 10.5 bp (black curve, Supplementary Methods section 1.4). Consensus nucleosomes were first ranked according to the strength of their 10.5-bp nucleotide periodicity and then divided into 10 groups of equal size. The x-axis represents the group index, with group 1 having the smallest strength of 10.5-bp periodicity. Blue curve shows the median correlation coefficient among all fundamental frequencies excluding 1/10.5, with whiskers showing the range from the 5th percentile to the 95th percentile.