MNase digestion leads to systematic measurement bias.

<p>(<b>A</b>–<b>C</b>) Density plot comparison between the normalized coverage per base pair in the MNase generated map on naked DNA (<i>x</i> axis) and (<b>A</b>) the <i>in vitro</i> reconstituted, (<b>B</b>) the <i>in vivo</i> (YPD) and (<b>C</b>) the predicted nucleosome map (<i>y</i> axis). The color of each point represents the density of base pairs mapping to it, where the density-color relationship is shown at the right of each plot. The Pearson correlation coefficients <i>r</i> between the data sets are indicated. (<b>D</b>) The GC-content profile in percent (3 base pair moving average) around the start coordinate of the reads. The gray filled curve corresponds to the profile obtained by digesting naked DNA with MNase and the blue and green curve represent the profile for the <i>in vitro</i> and <i>in vivo</i> (YPD) data, respectively. The dashed horizontal line indicates the average GC content in the yeast genome (38.3%) and the box indicates the selected fragment (0–149 base pairs).