Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
Figure 5
Testing the universality of nucleosome positioning signals across eukaryotes.
Our nucleosome model trained from yeast predicts nucleosome locations across several eukaryotes. For various nucleosome collections, including five new ones in fly and human that we isolated here, shown are scores assigned by our full model (“1”; score(S) from Equation 1 of the Methods section), by only the (position-independent) individual 5-mer component of the nucleosome-disfavoring component (“2”; Pl from Equation 1 above), by the entire nucleosome-disfavoring component of our model (“3”; PL from Equation 1 above), and by the (position-dependent) periodic component of our model (column “4”; PN from Equation 1 above). The sequences in each collection were mapped to their respective genome, and the score shown in each column at x-axis position i is the average score across all sequences in the collection, of the 147 bp (5 bp for column “2”) sequence whose center is i basepairs away from the center of the mapped sequence. For the full model (“1”) and nucleosome-disfavoring component (“3”), scores are shown in a window that extends up to 73 bp (half a nucleosome) around the center of the mapped nucleosome. Successful predictions assign their highest (“1”) or lowest (“3”) score at x-axis position zero. The p-value represents a student t-test that tests whether the distribution of scores in the 40 bp region centered on the mapped nucleosome is significantly higher (“1”) or lower (“3”) than that in the outer 40 bp (20 bp on each end of the mapped nucleosome). For the periodic component (“4”) scores are shown in a 10 bp window around the center of the mapped nucleosome, such that successful predictions assign the highest score at x-axis position zero; the P-value tests whether the distribution of scores in the 5 bp centered on the mapped nucleosome is significantly higher than that in the outer 6 bp (3 bp on each side, i.e., bp −5,−4,−3 and bp +3,+4,+5 from the center of the mapped nucleosome). Note that in several collections (e.g., worm), the 5-mer component itself (“2”) precisely demarcates the nucleosome positions, by assigning higher scores at the linker regions (more than 73 bp away from the center) compared to the nucleosomal regions (central 147 bp). For all four columns, the y-axis is scaled between the minimum and maximum score of the entire 293 bp region centered around the mapped nucleosome.