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Fig. 6 | Genome Biology

Fig. 6

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

Fig. 6

Chromatin factors mediate repression exercised by upstream alternative TSSs. a Schematic for determining how chromatin factors (Set2, Set3, and FACT) contribute to repression of the main TSS through transcription from alternative upstream TSSs. In short, cells harboring deletions (set2Δ (FW5767), set3Δ (FW5770), and set2Δ set3Δ (FW2912)) or depleted for Spt16 deletion (FVW6083) were compared to the control (FW2795) at the end of transition 1 (SPO 6 h). All these cells also had the pCUP-IME1 and GAL4.ER pGAL-NDT80 alleles. The Spt16 depletion allele (SPT16-AID, FVW6083) harbored pCUP-TIR1, while its matching control (FW6109) did not. Genes with upstream alternative TSSs were considered for this analysis. b Numbers of genes that displayed increased relative expression of the main TSS (black) or showed de-repression of the main TSS (white) (deletion or depletion mutants versus control). Genes within the de-repression category were selected for having increased relative expression of their main TSS in the different mutants and the main TSS was downregulated in the presence of expression of an upstream alternative TSS in control cells. The de-repression category is a subset of the “increased relative expression” category. Statistically significant changes in TSS usage were determined using the Cochran–Mantel–Haenszel (CMH) test on three independent repeats. c Venn diagram showing the number of genes de-repressed after Spt16 depletion and overlapped with genes de-repressed in the set2Δ, set3Δ, or set2Δ set3Δ deletion mutants. d Box and whisker plots of main TSS usage of genes under the de-repression category. The main TSS usage was calculated by dividing the main TSS value (TPM) over the sum of all TSSs values associated with the same gene for the same time point (0 h or 6 h in SPO). *** p < 0.0001. The number of data points corresponds to 87, 60, 90, and 102 genes for set2Δ, set3Δ, set2Δset3Δ, and Spt16 depletion, respectively. e Meta-profiles of MNase-seq signals for set2Δ, set3Δ, and set2set3Δ cells or Spt16 depleted cells (green) and control cells (red) at the end of T1 (6h SPO). The signals were centered on the main TSS. The top panels show the profiles for de-repressed genes and the bottom panels for the same number of randomly selected genes (87, 60, 90, and 102 genes for set2Δ, set3Δ, set2set3Δ, and Spt16 depletion, respectively)

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