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A genome-wide comprehensive analysis of nucleosome positioning in yeast

Fig 3

The fPCs, their gene specific scores, and the discriminating boundary explain collective phasing and how this changes in chd1Δ with respect to WT conditions.

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 WT (i.e. panels A-C) and chd1Δ conditions (i.e. panels D-F). Panels A and D show the fPC scores of WT and chd1Δ strains, respectively. For the latter, the boundary slope changed notably (black dashed line). As indicated by the fCPs in panels B and E for WT and chd1Δ, respectively, the functional description of the data changes. Indeed, the second fPC of chd1Δ abates quickly after the +1, with a strong effect on the effect of the +2 (grey arrows). The dashed black line as well as the solid lines in magenta and green indicate the mean, a positive contribution of the fPC, and a negative contribution, respectively. When exact positions were seemingly not affected by the fPC, we marked the positions with a grey vertical bar. General trends are given in grey arrows along the gene. The location-specific impact of the separating boundary is given in panel C for WT and panel F for chd1Δ strains. Interestingly, despite the median distributions of the clusters (blue and orange) are clearly different with respect to the +1 and +2 in WT conditions, later positions are much more important for allocating a profile to a particular group (grey areas, mean in black). Whilst this is also true for chd1Δ, the importance of later nucleosomes is even more accentuated, whereas the influence of the +1 and +2 positions are further decreased. 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.g003