Fig. 4.

Nucleosome-free control experiments yield sequences with nucleosome-like dinucleotide distributions. (A) Rank-order plots of energies of 2 bp words: the energy of each word is ranked using a position-independent model of order N = 2 trained on either in vitro nucleosome-positioning sequences or fragments of mononucleosomal size obtained from sonication and MNase digestion assays of nucleosome-free yeast DNA. Each curve shows the number of words whose ranks are separated by a given distance or less in the sonication and MNase digestion vs. nucleosomal fits. ρ is the Spearman rank correlation coefficient. (B) Same as Fig. 2A except the dinucleotide frequencies are from mononucleosome-size DNA sequences (defined by > 5 sequence reads) from yeast genomic DNA digested by MNase in the absence of nucleosomes.