Figure S1. Gene expression and methylation changes upon 2-HG accumulation.

(A) DLD3 gene expression (in TPM) in the BY4741 and FY4 strains highlighting the effective gene deletion. (B) Intracellular concentration of 2-HG is increased upon deletion of DLD3, as shown here for the FY4 strain. (C) Gene expression changes upon deletion of DLD3 for the BY4741 and FY strains are different. Correlation plot comparing the fold changes between two strains with the fold changes (log₂) of the FY4 strain on the y-axis and the BY4741 strain on the x-axis. The R value represents the Pearson correlation. Each dot represents a gene with the red dots being the commonly differentially expressed genes. (D) Principal component analysis of the gene expression for the strains FY4 and BY4741 (WT and dld3Δ). Each dot represents a replicate and with red are highlighted the BY4741 samples, and with blue, the FY4 samples. The differences depending on the genetic background (PC1 94% of the variance) are higher than the changes induced by accumulation of 2-HG (PC2 2% variance). (E, F, G, H) Correlation of gene expression with either H3K4me3 or H3K36me3 levels in (E, F) BY47441 WT and (G, H) dld3Δ strains. CPM values (log₁₀) are on the y-axis and TPM values (log₁₀) on the x-axis. Each dot represents a gene, and the R value represents the Pearson correlation.