Fig. 6

Effects of slow and fast Pol II mutants on nucleosome positioning. a Average nucleosome midpoints per promoter from MNAse-seq for WT, rpb1 H1085Y, and rpb1 E1103G were mapped for Taf1-enriched promoters anchored on experimentally determined + 1 nucleosome positions at + 1 (− 200 to + 800 positions shown). Both rpb1 H1085Y and rpb1 E1103G shift genic nucleosomes downstream relative to WT. WT average nucleosome positions determined by autocorrelation analysis of WT nucleosome midpoints. Data are from two (WT), seven (rpb1 H1085Y), or eight (rpb1 E1103G) independent biological replicates. Yellow dashed lines allow comparison of WT nucleosome positions with rpb1 mutants. b Nucleosome repeat lengths determined by autocorrelation analysis on the independent replicates noted in a. Both rpb1 H1085Y and rpb1 E1103G nucleosome repeat lengths are significantly different from WT (Wilcoxon matched-pairs signed rank test, two tailed, p < 0.0001). c + 1 nucleosome positioning in rpb1 H1085Y is subtly altered from WT for Taf1-enriched promoters. Top violin plot shows the distribution of individual + 1 nucleosomes for rpb1 H1085Y biological replicates (n = 7) relative to the position determined from the WT average (n = 2) for Taf1-enriched promoters (n = 4161). + 1 nucleosome position median is significantly different from zero (Wilcoxon signed rank test, p < 0.0001). Middle violin plot as in top but for Taf1-enriched promoters in the top expression decile (n = 321). + 1 nucleosome position median is significantly different from zero (Wilcoxon signed rank test, p = 0.0005 (approximate)). Bottom violin plot as in middle but for Taf1-enriched promoters in the lowest expression decile (n = 376). + 1 nucleosome position median is not significantly different from zero (p = 0.2274 (approximate) test as above). d + 1 nucleosome positioning in rpb1 E1103G is subtly altered from WT for Taf1-enriched promoters. Violin plot shows the distribution of individual + 1 nucleosomes for rpb1 E1103G biological replicates (n = 8) relative to the position determined from the WT average (n = 2) for Taf1-enriched promoters (n = 4161). + 1 nucleosome position median is significantly different from zero (Wilcoxon signed rank test, p < 0.0001)