Fig. 4.

Opi1 is important to modulate gene expression during MMS-induced genotoxic stress. a) Schematic representation of RNA-seq performed in wild-type and opi1Δ cells cultured in minimal medium (SC + INO) with or without 0.1% MMS treatment for 60 min. Created with BioRender.com. b) Volcano plot illustrating the differential gene expression between opi1Δ and wild-type cells (top panel) and between opi1Δ + MMS and wild-type + MMS cells (bottom panel). c) Volcano plot displaying the differential gene expression between wild-type + MMS and wild-type cells. For b) and c), genes with significant differential expression are plotted based on a threshold of ±0.8 log₂ fold change and an adjusted P-value of 0.05. The red line (x-axis) and dotted line (y-axis) represent the significant cutoff. Known genes regulated by Opi1 are labeled in both plots. d) Bar plot illustrating the top enriched biological processes identified in the gene set that are repressed during MMS treatment in an Opi1-dependent manner (Supplementary Table 6). Each bar represents a specific biological process, and the height of the bar corresponds to the fold enrichment with a P-adjusted value of 0.05. GO analysis was conducted in PANTHER using the overrepresentation test with S. cerevisiae serving as the reference list, which includes all genes in the database. The test type used was FISHER, and the FDR correction was applied. e) GO term enrichment network depicting the relationships between genes grouped in clusters that are repressed during MMS treatment in an Opi1-dependent manner (Supplementary Table 6). The enrichment analysis was performed using the STRING database, which integrates various sources of functional information with a confidence score of >0.4 (medium confidence). Nodes in the network represent genes, while edges indicate the connections between them. The color of the nodes represents a biological process, and the thickness of the edges represents the increased confidence of the interaction between nodes.