A genome-wide comprehensive analysis of nucleosome positioning in yeast
Fig 2
Nucleosome phasing is strictly limited to the gene body, which is maintained by Rsc8 but antagonised by Chd1.
The cluster distribution plots in panels A-C show the distribution of both gene groups with respect to the small-gene fPCs of WT, rsc8-depleted cells, and chd1Δ strains. Orange and blue indicate the two clusters, and the black dashed line shows the separating boundary determined by a linear SVM. The histograms present the cluster distribution with respect to each axis. Panels D-F display the transformation of the average small-gene nucleosome profile by the two major fPCs for WT, rsc8 depletion, and chd1Δ, respectively. The dashed black line as well as the solid lines in magenta and green display the mean, a positive contribution of the fPC, and a negative contribution. Turquoise arrows indicate the effect on the +1, dark blue arrows on the +4, and orange arrows on the +6 position. (A) When plotting the cluster distribution with respect to small-gene fCPs in WT, the linear separability is lost. (B) The fPCs of the rsc8-depleted strain maintain the linear separability, despite the fact that the groups were established for all genes. As we interpret the Pearson clusters as similarity in positioning between genes of 1000 bp mediated by chromatin remodelers, it possibly suggests that positioning outside coding regions influences nucleosomes inside and vice versa. (C) Whilst most mutants that were rsc8 depleted could discriminate between the all-gene clusters using small-gene fPCs, this separability is lost again in rsc8-depleted chd1Δ, revealing partly antagonistic roles to maintain gene-specific phasing for Rsc8 and Chd1. (D) The effect of two fPCs sheds light on why the Pearson groups are not linearly separable in WT using small-gene fPCs. The distribution of the second fPC changes its regular wave-like form to much broader peaks and valleys after the +2 nucleosome, which corresponds to approximately the size of the smallest genes in budding yeast. (E) Nucleosome positioning in rsc8-depleted conditions is clearly visible along the entire considered region, despite the included genes being smaller. This suggests that gene-specific nucleosome arrangement cannot be maintained. It is of note that the phasing also changes for the +1 nucleosome, and the NDR can be seemingly not conserved. (F) On the other hand, rsc8-depleted chd1Δ loses the regular wave-like shape of its second fPC after the +2 nucleosome to form broader peaks, indicating the presence of gene-specific nucleosome profiles as in WT conditions. All axes are scaled to the same size for each strain; shapes and amplitudes are therefore comparable (see Methods for more details).