Isw1 effects on gene expression and cryptic initiation. (a) Nucleosome scores for TMA10 show stabilization of the -2 nucleosome in Δisw1, which covers multiple binding sites . (b) Log2 expression ratios (mutant divided by wild type (WT)) for TMA10 in the three deletion strains. (c) Expression differences are not correlated with Isw1-dependent changes in nucleosome positioning for both comparison of wild-type with Δisw1 cells (left) and comparison of the two species (right). Left: scatterplots of log2 expression changes in Δisw1 versus changes in nucleosome positioning in Δisw1. Right: scatterplots of log2 expression ratios of the two species versus difference in the effects of ISW1 deletion on nucleosomes in the two species. Top: shift size at the +5 nucleosome; in the right panel, minus and plus reflect upstream and downstream shifts, respectively, and in the left panel they reflect larger Isw1 shifts in S. cerevisiae and S. paradoxus, respectively. Middle: differences in promoter occupancy. In the right panel, log2-ratio of the number of reads that map to within 250 bp upstream of the TSS in Δisw1 versus wild type. In the left panel, differences in that log2-ratio between the two species. Bottom: differences in coding-region occupancy. Same as in the middle panel but for reads that map to the first 500 bp of each coding region. In all cases, red lines represent the linear least square fit, and no significant correlation was observed (P > 0.05). (d) Average sizes of Isw1-dependent upstream shifts at nucleosomes +1 through +7 for genes with detected cryptic initiation in three mutant strains (for Spt6, Spt16 and Set2) and for genes without cryptic initiation in any of the three mutants. The three datasets of cryptic initiation include 960, 1,130 and 429 genes, respectively, and are all strongly associated with long genes (median length of 2,063, 2,090, and 2,453, compared to 857 for genes without cryptic initiation). Long genes are also enriched with Isw1-dependent shifts (Figure 4d; Figure S6 in Additional file 1).