Dal80 recruitment to promoters correlates with nitrogen- and Dal80-sensitive gene expression.

(A) Scatter plot of densities (tag/nt, log2 scale) for genes in wild-type (WT) cells grown in proline- or glutamine-containing medium. For each condition, total RNA was extracted from exponentially growing biological replicates of 25T0b (WT). After rRNA depletion, strand-specific RNA-Seq libraries were constructed and then sequenced. Tag densities were computed using uniquely mapped reads. NCR- and revNCR-sensitive genes were identified on the basis of a proline/glutamine ratio ≥2 or ≤0.5, respectively, with a P-value ≤0.01 upon differential expression analysis using DESeq [93]. Unaffected (4116), NCR-sensitive (754) and revNCR-sensitive (928) genes are shown as grey, orange and green dots, respectively. (B) Scatter plot of densities (tag/nt, log2 scale) for genes in 25T0b (WT) and FV080 (dal80Δ) cells grown in proline-containing medium. RNA extraction and construction of RNA-Seq libraries were as described above. Dal80-regulated genes were identified using a mutant/WT ratio ≥2 (Dal80-repressed) or ≤0.5 (Dal80-activated), with a P-value ≤0.01 upon differential expression analysis using DESeq [93]. Unaffected (n = 5252), Dal80-repressed (n = 232) and Dal80-activated (n = 314) genes are shown as grey, red and blue dots, respectively. (C) Proportion of Dal80-activated (blue bars) and Dal80-repressed (red bars) genes among revNCR-sensitive, NCR-sensitive and unchanged (ie neither revNCR nor NCR) genes. The numbers of genes among each group are presented in S2B Fig. P S2C Fig for the numbers of genes among each group. P S2D Fig for the numbers of genes among each group. P UGA3. RNA-Seq signals are visualized as a heatmap. The upper and lower panels show the signals for the + and—strands, respectively. The color turns from yellow to dark blue as the signal increases (scale on the right). The UGA3 mRNA is highlighted using the red box. The neighboring genes (YDL173W, GLT1 and YDL169C) are also indicated. The snapshot was produced using the VING software [94].