(A) Schematic of annotation scheme for nucleosomes based on their position relative to transcribed units. Intergenic nucleosomes were assigned to the following categories: promoter region (anything upstream of a coding region), nucleosome immediately upstream to the TSS (“distal”), and the nucleosome immediately downstream of the TSS (“proximal”). Transcribed regions were separated into 5′, middle, and 3′ CDSs. Finally, to capture features of chromatin not associated with PolII genes, we independently classified nucleosomes associated with ARS sequences, tRNA genes, and Null (any other intergenic region).
(B) Hierarchical clustering of 2,288 nucleosomes. Left panel: each row corresponds to a single nucleosome, and each column to a particular modification. Red (green) denotes hyper-acetylation (hypo-acetylation) in the first nine columns and relative level of methylation in the last three columns. Rows are sorted according to the dendogram built during clustering. PolII shows the PolII occupancy of the gene associated with the nucleosome in question. Right panel: each row corresponds to a nucleosome (matching the left panel), and each column corresponds to an annotation of the nucleosome according to the scheme of (A). A blue cell denotes a positive annotation of the nucleosome with the appropriate column label. Numbers indicate examples of clusters, as follows: (1) nucleosomes enriched for H3K9Ac, H3K14Ac, and H3K4Me3 that are mostly upstream of transcribed regions; (2) strongly hypo-acetylated nucleosomes, mostly at upstream regions or 3′ of coding regions; (3) nucleosomes acetylated at H4K8 and K16, and H2B K16 that are almost exclusively at the middle and 3′-ends of coding regions; and (4) hyper-acetylated and methylated nucleosomes that are mostly found at the 5′-end of coding regions.
(C) The Pearson correlations of the 12 modification levels between different probes show that there are two tightly correlated groups of acetylations at specific residues. The first group consists of H2A K7; H3K9, K14, and K18; and H4K5 and K12. The second group consists of H2B K16; and H4K8 and K16. Mono- and di-methylation of H3K4 are correlated with the second group, while tri-methylation of H3K4 is correlated with the first group.
(D) The percent of variance captured by using different number of components. The x-axis denotes the number of components, and the y-axis denotes the percent of the variance in the data explained by each components (blue bars) as well as the cumulative percentage explained (red bars).
(E) Representation of all nucleosomes in two-dimensional modification space. In the left panel, each point represents a nucleosome plotted according to the relative level of the first principal component (x-axis) and second principal component (y-axis) for the modification pattern. The right panel is a three-dimensional plot showing density of points along the plane.