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Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness

Fig 4

Rescue of SBF-activated gene expression by chimeric SBF TFs.

Gene expression profile of SBF-activated regulon at two time points (0 and 30 mins) after release from alpha-factor block. We plot the regularized-logarithm transformed data of each gene (row) for each strain (wild-type or DBD chimeras, columns) for visualization. All RNA-seq experiments were done in triplicate. The RNA-seq expression of each gene (heatmap) is plotted as a Z-score relative to the mean and standard deviation of all values on the same row. Statistical analysis with DESeq2 was performed on the raw data. Genes that had no statistical difference between RNA-seq expression at 0 and 30 mins between wild-type and chimeras were grouped together within the same contiguous box. Genes (rows) outside the box indicate that expression was significantly different from wild-type and not rescued by DBD chimeras of the corresponding species (column). Genes were organized top-down starting with the genes from SBF-activated regulon that were only rescued by ScerSwi4BD (Scer-specific SBF regulon). We then list genes from SBF-activated regulon that were also rescued by KlMbp1 (Klac Mbp1DBD-rescued regulon). Genes rescued by KlMbp1DBD were usually rescued by CaMbp1BD with occasional rescue by NcResBD and SpRes2BD. Last, we show those genes not rescued by KlMbp1BD, but which were rescued by CaMbp1BD with occasional rescue by NcResBD. Each module was organized using hierarchical clustering of RNA-seq profiles.

Fig 4