Supplementary Figure 2: Verification and characterization of remodeler depletion and effects on nucleosome occupancy and stability.

a, Fluorescence microscopy of cells bearing FRB-GFP fusions of Sth1, Snf2, Isw2 and Chd1; cells were treated with rapamycin for indicated times, fixed and stained with DAPI. b, Western blotting (anti-myc antibodies) of cell lysates from an untagged strain and strains bearing Ino80-AID*-myc and Isw1-AID*-myc fusions treated with auxin for indicated amount of time. c, Growth assays (serial dilution “spot assays”, as in Supplementary Fig. 1a) of the indicated anchor-away or AID depletion strains on YPAD medium. “WT” indicates the parental anchor-away and/or AID strains background. d, Pearson correlations for all pairwise comparisons of genome-wide nucleosome occupancy change over 100 bp windows for the indicated CR depletion strains in the absence of depletion (mock-treated). e, Screenshots of sample regions in which nucleosomes become stabilized (marked with a red rectangle) upon depletion of RSC (top) or SWI-SNF (bottom). f, Average plots of nucleosome occupancy for all nucleosomes becoming stabilized upon depletion of RSC (top) or SWI-SNF (bottom). g, Screenshots of sample regions in which nucleosomes become destabilized (marked with a red rectangle) upon depletion of ISW2 (top) or INO80 (bottom). h, Average plots of nucleosome occupancy for all nucleosomes destabilized upon depletion of ISW2 (top) or INO80 (bottom). i,j, Average plots of nucleosome occupancy with (red) or without (blue) depletion of ISW1 (i) or CHD1 (j), plotted separately for genes with the lowest (top) or highest (bottom) binding by the relevant CR (average binding profiles shown in green).