Figure 4

Patterns of Isw1-dependent shifts. (a) Percentage of Isw1-shifts that are upstream (green; nucleosomes are moved towards the 5' end in Δisw1) and those that are downstream (blue; nucleosomes are moved towards the 3' end in Δisw1) as a function of the relative position within genes (with respect to the start and stop codons). (b) Asymmetric effects at nucleosomes adjacent to those with shifts. For each gene with Isw1-shifts above 15 bp, we examined the extent of upstream shifts at the maximally shifted nucleosome and at its upstream and downstream adjacent nucleosomes, and the average shift sizes are shown. (c) Distribution of estimated distances between nucleosome centers of mid-coding nucleosomes (that are shifted upstream in Δisw1) and their flanking upstream nucleosomes, for wild-type (WT) and Δisw1 strains. (d) Average sizes of Isw1 upstream shifts at the +5 nucleosome for 10 subsets of genes ordered by various histone modifications, gene length, or mRNA expression levels. H3K79me2/3 and H2Bub were taken from Schulze et al. [55] and all other modifications from Pokholok et al. [56]. (e) Average levels of the histone modifications in (d), normalized to mean of zero and standard deviation one, throughout promoters and coding regions. (f) Average patterns of modifications for genes with Isw1 upstream shift of the +5 nucleosomes of at least 20 bp (red) and those without upstream shifts (green), shown for H3K14 acetylation (top) and H3K79 trimethylation (bottom).