Figure 3.

Isw2 and Ino80 affect nucleosome positioning in the rDNA IGS. (A) Micrococcal nuclease digestion followed by deep-sequencing (MNase-seq) profiles in the IGS, with Isw2 ChIP-seq data overlaid. From each paired end sequencing read, the nucleosome dyad was inferred and plotted. (B) Ribbon plots, generated as described in Figure 2A, focused on two pairs of nucleosomes, indicated with boxes in (A). Different subspecies of nucleosome positions are indicated with colored arrows and letters. (C) Cartoon diagram depicting five nucleosomes flanking the rARS, illustrating possible arrangements of nucleosomes reflecting different predominant subspecies of positions for each nucleosome in WT vs. isw2∆ nhp10∆ cells. (D) MNase-seq comparing WT and isw2∆ nhp10∆ cells across three different strengths of MNase digestion.