Supplementary Figure 1

(A) A 4kb region on chromosome 5 showing signal intensity across the URA3 deletion in

strain BY4741. Green graph represents signal intensity at each individual probe position.

Red boxes are annotated coding regions, those above the x-axis are transcribed left-to-

right (Watson strand) and annotations below the X-axis are on the opposite strand.

(B) A 4 kb region on chromosome 3 showing raw signal intensity across the LEU2

deletion in strain BY4741.

(C) An 8 kb region on chromosome 12 showing the high raw signal intensity for the

highly repetitive RDN1 region, as compared to nonrepetitive segments.

Supplementary Figure 2

K-means clustergrams for promoter nucleosome signatures. Each of these clustergrams is

identical to Figure 4b except with a different value of k. (a) k=3 (b) k=5 (c) k=6

Supplementary Figure 3

(A) K-means clustergram for the set of ~3600 verified transcripts with known

annotations. Blue represents areas depleted for nucleosomes, yellow areas are more

occupied.

(B) Kernel density plot showing distribution of expression levels for transcripts in each

cluster.

(C) Table listing the GO Slim biological process term that is most overrepresented by

genes in each cluster and the hypergeometric p-value for each term.

(D) Kernel density plot showing the distribution of expression levels for transcription

segments in cluster 2. The green plot is identical to the plot in panel C. The magenta plot

shows the distribution for the genes in cluster 2 minus all RPL/RPS ribosomal protein

genes.