The extent of shifts in nucleosome positioning is comparable between Isw1 and PolII. (a) Average shift size for nucleosomes +1 through +7 upon deletion of ISW1 (red, upstream shifts) or inactivation of PolII (green, downstream shifts). Opposite shifts (downstream for ISW1 or upstream for PolII) were given negative values. (b) White bars display the distribution of observed shift sizes (positive and negative values reflect upstream and downstream shifts, respectively) for Isw1 (top) and PolII (bottom). Nucleosomes +5 and +4 were chosen in this analysis for Isw1 and PolII, respectively, as these had the most extensive effects. Assuming that Isw1 only shifts nucleosomes upstream, and that the same amount of genes display upstream and downstream shifts due to errors in estimation of nucleosome positioning, we can decompose the observed shifts into those due to errors (black) and those reflecting the activity of Isw1 (red). This analysis predicts that ISW1 deletion shifts the +5 nucleosome for 50% of the genes. Similarly, we assumed that PolII only shifts nucleosomes downstream and decomposed the observed shifts into errors (black) and PolII activity (green), with the latter predicted to occur for 33% of the genes. Note that even if we relax these assumptions and simply count the number of observed Isw1 (upstream) shifts and PolII (downstream) shifts, then we obtain a similar fraction of genes (for example, approximately 40% of the genes are shifted by at least 15 bp for both Isw1 and PolII; not shown).
Tirosh et al. Genome Biology 2010 11:R49 doi:10.1186/gb-2010-11-5-r49