Set3C recruitment predicts induction and depletion predicts repression.

<p>(A) Microscopic images of cells undergoing yeast-to-hypha differentiation. The cells at each time point do not correspond to the cells at the other time points. Scale bar corresponds to 5 µm. (B) Transcript landscape of hyphal cells 30 minutes after induction. The fold change in RNA expression between hyphal and yeast cultures at each gene is plotted against the expression level of the gene in wild type yeast cells measured by RNA-Seq. Each dot represents one gene. Set3C binding targets were defined by Set3C ChIP-Seq experiments (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003118#s4" target="_blank">Materials and Methods</a>). The Set3C target genes are divided into yeast-specific, hypha-specific and constitutively bound subgroups. The distribution of RNA fold changes of the genes belonging to each category is shown on the right panel. Statistical significance was determined by the Mann-Whitney U-test relative to the “all targets” set. *P<0.05, **P<0.01, ***P<0.001, ns: not significant. (C) Correlation of RNA fold change and differential ChIP enrichment signals. Each dot corresponds to one gene, and only the genes defined as Set3C binding targets in at least one phase are shown. “<i>r</i>” denotes a Pearson's correlation coefficient. (D) qPCR verification of the correlation on (C). Histone H4 has two loci in <i>C. albicans</i> (<i>HHF1</i> and <i>HHF22</i>), and the primers used in the qPCR bind alleles of both. Data are shown as mean+SD of three independent experiments. Statistical significance was determined by two-tailed t-test. *P<0.05, **P<0.01, ***P<0.001. (E) Comparison of the gene induction profiles of wild type and <i>set3</i>Δ/Δ cells undergoing hyphal differentiation. Fold change between the hyphal and yeast phases for the two genotypes are plotted on the two axes. Each dot corresponds to one gene. The categories of Set3C binding targets are defined as on (B). “<i>r</i>” denotes a Pearson's correlation coefficient, and “m” denotes the slope of the linear regression.