A genome-wide comprehensive analysis of nucleosome positioning in yeast
Fig 6
Remodeler deletions have varying effects on the interdependence with other genomic properties.
The orange bars in panels A, C, and E show the ratio of correct predictions, and blue bars are wrong guesses. As we distinguish between two clusters, the dashed black line at 0.5 indicates random guessing. The dashed grey line with black edging in panels B, D, and F display the linear boundary for the Pearson clusters. Panels A and B: WT conditions are seemingly correlated with the sequence composition. However, the results are different for the B replicate, and therefore non-conclusive. All possible correlations are surprisingly low. Panels C and D: chd1Δ mutants increase particularly their dependence on Pol II and other transcription-coupled properties, such as Mediator presence. Surprisingly, the mutant showed also an increased interdependence on NDR length. Panels E and F: despite the Rsc8-mediated gene limits, there is no correlation with coordinated nucleosome phasing and the size of transcribed regions or NDR length. Although Sth1 indicates a slightly increased interdependence, this cannot be confirmed when plotting the groups with respect to the Pearson clusters. This is in line with our hypothesis that positioning in different regions interfere, and therefore, nucleosome localisation become increasingly independent from region-specific factors.