The Cyc8–Tup1 complex regulates TATA-containing genes via nucleosome organization. (A) Frequency of TATA-containing genes plotted as a function of Cyc8 or Tup1 binding intensity. We ranked the genes by Cyc8 or Tup1 binding intensity from highest to lowest, and use 1000-gene sliding windows in 10-gene increments down each rank to produce overlapping groups. Then the percentage of TATA-containing genes in each group was calculated. (B) Frequency of TATA-containing genes plotted as function of fold expression change in the cyc8Δ or the tup1Δ strain relative to the wild-type strain. Genes were ranked based on the expression fold change and grouped into 100-gene bins with no overlap between any two bins. The fraction of the TATA-containing genes in each bin was plotted against the corresponding average gene expression fold change. Correlation coefficients were calculated based on the Spearman method. Up-regulated genes (top panels) and down-regulated genes (bottom panels) were analyzed separately. (C) Nucleosome occupancy change plotted as function of distance to transcription start sites of either all yeast genes or Cyc8–Tup1 target genes, as defined by Cyc8–Tup1 binding and expression change upon loss of these factors. Nucleosome occupancy increases (left panels) and occupancy decreases (right panels) were analyzed separately.
