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. 2021 Oct 15;10:e71013. doi: 10.7554/eLife.71013

Figure 5. Distinct alterations to transcription start site (TSS) distribution in ssl2 mutants.

(A) Schematic illustrating TSS ‘spread’ reflecting the distance encompassing 80% of TSSs in a promoter window and the measurement of mutant changes in TSS spread. (B) TSS spreads in ssl2 and Pol II mutants at Taf1-enriched or -depleted promoters. All mutants show a statistical difference in medians from wild type (WT) at p < 0.05 (Kruskal-Wallis test with Dunn’s multiple comparisons test). Asterisks indicate differences in means from WT (*p < 0.05, **p < 0.01, ***p < 0.005, ****p < 0.001). (C) Heatmap showing TSS spread changes for ssl2 or rpb1 mutants by promoter class (hierarchical clustering by mutant on the x-axis and promoter on the y-axis). (D) ssl2 upstream and downstream shifting mutants narrow and widen TSS distributions at promoters as measured in (A). The median TSS spread changes of all the ssl2 and Pol II mutants are statistically distinguished from zero at p < 0.0001 (Wilcoxon signed rank test).

Figure 5—source data 1. Figure 5B Taf1-enriched graph data.
Figure 5—source data 2. Figure 5B Taf1-depleted graph data.
Figure 5—source data 3. Figure 5CD Taf1-enriched heatmap and graph data.
Figure 5—source data 4. Figure 5CD Taf1-depleted heatmap and graph data.

Figure 5.

Figure 5—figure supplement 1. Analysis of transcription start site (TSS) spread in ssl2 and polymerase II (Pol II) mutants.

Figure 5—figure supplement 1.

(A) Heatmap and hierarchical clustering of TSS spread change for ssl2 or rpb1 mutant in individual replicate. As described in Figure 5C. SSL2WT_2,3,4 are technical replicates as are SSL2WT_5,6,7. All other libraries represent biological replicates. (B) Principal component analysis (PCA) for change of TSS spread in ssl2 and Pol II individual TSS sequencing (TSS-seq) libraries. TSS-seq libraries are separated into five major classes (ssl2 upstream and downstream mutants, wild type [WT], Pol II upstream and downstream mutants).
Figure 5—figure supplement 1—source data 1. Figure 5—figure supplement 1A Heatmap data.
Figure 5—figure supplement 2. Number of promoters affected by ssl2 or polymerase II (Pol II) mutants.

Figure 5—figure supplement 2.

(A) Bar plot showing number of promoters that shift median transcription start sites (TSS) position either upstream or downstream in each mutant for any degree of shift. (B) Bar plot indicating number of promoters that shift median TSS position significantly upstream or downstream in each mutant, as determined by Kruskal-Wallis test with Dunn’s correction for multiple comparisons (p ≤ 0.05). The test was performed individually on each promoter and all mutants were taken into account. (C) Bar plot showing number of promoters that shift median TSS position significantly upstream or downstream in each mutant as in (B) but determined by Mann-Whitney U test (p ≤ 0.05). (D–F) As tested in A–C but examined for change of TSS spread instead of median TSS shift. (D) Bar plot showing number of promoters that have narrower or wider TSS spread in each mutant. TSS spread was determined as described in Figure 5A. (E) Bar plot indicating number of promoters that have significantly increased or decreased TSS spread in each mutant as determined by Kruskal-Wallis test with Dunn’s correction for multiple comparisons (p ≤ 0.05). The test was also performed individually on each promoter and all the mutants were taken into account. (F) Bar plot showing number of promoters that have significantly increased or decreased TSS spread in each mutant as in E but determined by Mann-Whitney U test (p ≤ 0.05).
Figure 5—figure supplement 2—source data 1. Figure 5—figure supplement 2A Graph data.
Figure 5—figure supplement 2—source data 2. Figure 5—figure supplement 2B Data table.
Figure 5—figure supplement 2—source data 3. Figure 5—figure supplement 2B Graph data.
Figure 5—figure supplement 2—source data 4. Figure 5—figure supplement 2C Data table.
Figure 5—figure supplement 2—source data 5. Figure 5—figure supplement 2C Graph data.
Figure 5—figure supplement 2—source data 6. Figure 5—figure supplement 2D Graph data.
Figure 5—figure supplement 2—source data 7. Figure 5—figure supplement 2E Data table.
Figure 5—figure supplement 2—source data 8. Figure 5—figure supplement 2E Graph data.
Figure 5—figure supplement 2—source data 9. Figure 5—figure supplement 2F Data table.
Figure 5—figure supplement 2—source data 10. Figure 5—figure supplement 2F Graph data.