Figure 3.

Nucleosome remodeling by Isw1. (a) Percentage of nucleosomes with at least two-fold reduced occupancy upon deletion of ISW1, as a function of their normalized location with respect to the start and stop codons. Shaded area shows the strongest enrichment. (b) Percentage of nucleosomes with shifts (>15 bp) upon deletion of the three chromatin regulators, as a function of their normalized location with respect to the gene start and stop codons. (c) Heatmap of nucleosome shifts across approximately 5,000 S. cerevisiae genes, sorted by transcription rates [54] (top, lowly transcribed; bottom, highly transcribed). See Figure S2 in Additional file 1 for similar heatmaps of the other mutant strains and for heatmaps of changes in nucleosome occupancy. (d) Increased nucleosome fuzziness at the coding region of HOL1 in Δisw1 cells. Shown are HOL1 nucleosome scores for all strains, and the percentage of reads that map to within 20 bp of estimated nucleosome center positions is indicated for each strain. (e) Number of genes with increased fuzziness for each strain of S. cerevisiae (black) and S. paradoxus (grey). Genes were defined to have increased fuzziness in a particular strain if the percentage of reads that map to within 20 bp of the estimated nucleosome center positions was lower by at least 5% than that of all other strains, while the number of predicted nucleosomes is unchanged. WT, wild type.