Fig. 2

Transcription downregulation in scc1-73 cells is associated with chromatin changes. a Volcano plot of altered genes in scc1-73 cells relative to wild-type cells (1014 out of 6692 genes; ~ 15%). Changes in gene expression (log₂) are plotted against q-values (–log₁₀). Genes with a q-value < 0.01 are shown in green for downregulated (445) and in red for upregulated (569). b Overlap between downregulated genes, and genes with promoters that contain nucleosomes with higher occupancy (up-nucleosomes), in scc1-73 cells as compared to wild-type cells. The number of genes in each case is indicated in parentheses. The probability of producing the given overlap based on random distributions was generated using a hypergeometric test. The rate between the observed and expected frequencies of common genes is also shown. c Nucleosome occupancy profiles of the scc1-73 up- and downregulated genes, aligned relative to their TSS. Non-affected genes from chromosomes VII and XII were used as control groups. The number of genes of each group is indicated in parentheses. Statistically significant differences in occupancy at the peak of nucleosomes − 2 to + 5 between the wild-type cells and the scc1-73 mutants are shown (paired two-tailed Student’s t test, whereby one, two and three asterisks indicate p values of < 0.05, < 0.01 and < 0.001, respectively)