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A genome-wide comprehensive analysis of nucleosome positioning in yeast

Fig 4

The fPCs, their gene specific scores, and the discriminating boundary explain changing collective phasing in double mutants.

The figure shows the cluster distribution with respect to , the impact of the determined fPCs, and the location-specific impact of the separating boundary for all double mutants, in particular isw2Δchd1Δ (i.e. panels A-C), rsc8chd1Δ (i.e. panels D-F), and isw1Δisw2Δ (i.e. panels G-I). The linear separation of the cluster distribution with respect to factors indicate a notable gene-specific change for the three mutants in panels A, D, and G. The two clusters are given in orange and blue, and the SVM boundary is depicted by the black dashed line. Whilst isw2Δchd1Δ and isw1Δisw2Δ require both fPCs to linearly separate the Pearson clusters, rsc8chd1Δ is almost exclusively dependent on the second fPC, which means this mutant decreased the slope tilt. This can be better understood when analysing the two fPCs and their effect on the mean ((B) for isw2Δchd1Δ, (E) for rsc8chd1Δ, and (H) for isw1Δisw1Δ). The solid lines in magenta and green in these plots indicate a positive contribution of the fPC and a negative contribution, respectively, whereas the black dashed line depicts the mean. Grey arrows along the gene suggest general trends. Grey vertical bars suggest positions that remain largely unperturbed by the fPC. Grey arrows pointing to a single peak suggest remarkable properties. Interestingly, whilst the first fPC of the isw2Δchd1Δ and isw1Δisw2Δ strains shows a similar transformation of the mean, the second fPC indicates a different behaviour, particularly with respect to the +2 nucleosome. As suggested by the fact that clusters in the rsc8chd1Δ mutant are exclusively dependent on the second fPC, the first fPC explains only the average profile amplitude and does not contain any information about collective phasing. The location-specific effect of the linear separator for each mutant is given in (C), (F), and (I). The grey areas indicate the importance of each position to determine the clusters, whose median profile is shown as a blue and orange dashed line. The mean is depicted in black. Although the impact on the grouping of the +1 and +2 position in isw2Δchd1Δ conditions is similar to the isw1Δisw2Δ strain, the latter is seemingly particularly dependent on the +3 and +4 nucleosome. Positions thereafter become less important, which keep having a strong impact on clustering in isw2Δchd1Δ. As expected rsc8chd1Δ is exclusively dependent on the second fPC. Interestingly, the entire profile seems to be influential for classifying genes, with the largest impact allocated to the first two nucleosomes. All axes are scaled to the same size for each strain; shapes and amplitudes are therefore comparable (see Methods for more details).

doi: https://doi.org/10.1371/journal.pcbi.1011799.g004