Fig. 6.

Excess Yox1 represses genes that are critical for cell fitness during replication stress. a Overview of the RNA-seq experiment. WT cells containing pBY011 (empty vector) or pBY011-YOX1 (GAL1-10pr-YOX1) vectors were cultivated in synthetic media containing raffinose. Overexpression of YOX1 was induced by adding galactose and replication stress was induced by HU treatment. RNA was extracted at the indicated time points. b Heatmap of expression ratios generated by hierarchical clustering, showing genes that were differentially expressed upon YOX1 overexpression. Two different ratios are represented: +HU:−HU compares expression values in the control strain (empty vector) between the HU condition and the untreated condition, and GAL1-10pr-YOX1:empty vector compares expression values between the YOX1-overexpressing strain and the control strain at each time point. Light blue bars indicate genes that were downregulated after 2 h and/or 4 h in HU in lsm1∆ compared to WT (as in Fig. 1). Purple bars denote genes that are described as Yox1 targets in the Yeastract database. c The number of genes with decreased mRNA abundance upon YOX1 overexpression, with the overlap of genes that also have decreased mRNA abundance in lsm1∆ is plotted as a stacked bar graph. The indicated P-values were calculated using a hypergeometric test. d Identification of potential Yox1 targets during replication stress at the intersection of three datasets. Heatmaps are as presented in b. e Fitness data in HU for the single mutants identified in d. Each data point represents a single replicate (n = 5). Horizontal bars represent the average of the replicates. P-values are from a Student’s t-test. f Condition-dependent negative genetic network of interactions between the 8 targets in d. Red edge thickness is proportional to the difference between the double mutant fitness in absence and presence of 25 mM HU