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Fig. 3 | Genome Biology

Fig. 3

From: High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

Fig. 3

Increased upstream alternative TSS usage has varying effects on expression from the main TSS. a Main and upstream alternative TSS expression changes at the NDC80 locus during T1, T2, and T3. Negative controls representing mock-treated samples for T1 and T2 (no induction of transition (No T) for main TSS and upstream alternative TSS (UA)) were included. The y-axis represents TPM values of the main and alternative TSSs. b Schematic of main and upstream alternative (UA) TSS pairs relative to their associated ORF (left). A subset of genes in which the alternative TSS was strictly upstream of the main TSS was used for the analysis. Increased expression from upstream alternative TSSs was linked to different outcomes on expression of the downstream main TSS (Right). Violin and overlaid boxplots showing increased expression from upstream alternative TSSs was linked to different outcomes on expression of the downstream main TSS. The dataset was drawn from upstream alternative TSSs paired with a downstream main TSS of the same gene. Observations were only included if the upstream alternative TSS was upregulated by twofold or more (FDR < 0.05), and the log2 fold change of the downstream main TSS was plotted on the y-axis. “T1” refers to transition 1 and represents the following comparisons: 3 h, 4 h, 5 h, or 6 h vs 2 h SPO. “T2” refers to transition 2 and represents the following comparisons: 7 h, 8 h, or 9 h vs 6 h SPO. “T3” refers to transition 3 and represents the following comparisons: 15 min, 60 min, or 120 min YPD vs 6 h SPO. The horizontal dashed lines mark log2 fold changes of 1 or − 1. The data represents TSS pairs from 546, 565, and 460 genes from T1, T2, and T3 respectively, and is an average of 3 biological repeats. c Violin plots representing log2 fold changes of main TSSs at the same time when a “TSS switching” event occurred. A switching event was counted when upstream alternative TSS expression increased by twofold or more (transition time point vs prior transition, FDR < 0.05). In addition, the TPM of an upstream alternative TSS had to be greater or equal to that of the downstream main TSS (TPM) at the same time point. The log2 fold change of the downstream main TSS was plotted on the y-axis. “T1” refers to transition 1 and represents the following comparisons: 3 h, 4 h, 5 h, or 6 h vs 2 h SPO. “T2” refers to transition 2 and represents the following comparisons: 7 h, 8 h, or 9 h vs 6 h SPO. “T3” refers to transition 3 and represents the following comparisons: 15 min, 60 min, or 120 min YPD vs 6 h SPO. The horizontal dashed lines mark log2 fold changes of 1 or − 1. The data represents TSS pairs from 109, 93, and 86 genes from T1, T2, and T3 respectively and is an average of 3 biological repeats. d The number of TSS switching events in a set of 380 genes were selected from Cheng et al. [19]. The number of genes with a single TSS is displayed. In addition, the number of genes with multiple TSSs with TSS switching events are shown. e Main and alternative TSS expression changes for example loci. Depicted are TSS switching events for SWI4, ORC1, POP1, RAD16, RAD2, and PCL1. f Similar as e, except that co-regulation events are displayed for MCM2, SPO75, and SUM1

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