Skip to main content
. 2019 Jan 25;8:e43654. doi: 10.7554/eLife.43654

Figure 7. Taf1 depletion selectively affects TFIID-dependent genes.

(A) Mean Pol II occupancy averaged over 453 well-transcribed ‘SAGA’ or ‘TFIID’ genes in parental or Taf1-depleted strains. (B) Pol II (C) TBP, TFIIB, and TFIIA, and (D) Taf1 occupancies at ‘SAGA’ (PMA1 and CCW12) or ‘TFIID’ (ACT1, TEF1, RPL28, RPS14B) coding regions in the Taf1-depletion strain treated or untreated with rapamycin. (E) TBP:TAF1 occupancy ratios in the Taf1-depletion strain treated or untreated with rapamycin. (F) Log2 change in Pol II occupancy (measured at +200–400 from the TSS) for the indicated gene classes upon Taf1 depletion. ‘Active’ genes are the top 10% of transcribed genes, broken up into ‘SAGA’ and ‘TFIID’-dependent categories. Ribosomes include only the ribosomal genes from the TFIID-dependent category. ‘TFIID active, no ribosomes’ are the remainder of the top 10% transcribed genes in the TFIID-dependent category after ribosomal genes have been removed. ‘All’ genes are the entire set of ~5000 s. cerevisiae genes, broken up into ‘SAGA’ and ‘TFIID’-dependent categories.

Figure 7.

Figure 7—figure supplement 1. Taf1 depletion selectively affects TFIID-dependent genes.

Figure 7—figure supplement 1.

(A) TFIIB:Taf1, TFIIA:Taf1, TFIIB:TBP, and TFIIA:TBP occupancy ratios in the Taf1-depletion strain treated or untreated with rapamycin. (B) Log2 change in Pol II occupancy (measured at 0 to +100 bp from the TSS) for the indicated gene classes upon Taf1 depletion. ‘Active’ genes are the top 10% of transcribed genes, broken up into ‘SAGA’ and ‘TFIID’-dependent categories. Ribosomes include only the ribosomal genes from the TFIID-dependent category. ‘TFIID active, no ribosomes’ are the remainder of the top 10% transcribed genes in the TFIID-dependent category after ribosomal genes have been removed. ‘All’ genes are the entire set of ~5000 s. cerevisiae genes, broken up into ‘TATA’ and ‘TFIID’-dependent categories.
Figure 7—figure supplement 2. Analysis of Taf11 and Taf13 depletion in SC medium using published data (Warfield et al., 2017) shows selective effects at TFIID-dependent genes.

Figure 7—figure supplement 2.

(A) Mean Pol II occupancy averaged over 453 well-transcribed ‘SAGA’ or ‘TFIID’ genes in parental or Taf1-depleted anchor-away strains (black; present study) as well as Taf11- and Taf13-depleted auxin-degron strains (red) treated with DMSO or with 3IAA (Warfield et al., 2017). (B) Log2 change in Pol II occupancy (measured at +200–400 from the TSS) for the indicated gene classes upon Taf13 and Taf11 depletion. ‘Active’ genes are the top 10% of transcribed genes, broken up into ‘SAGA’ and ‘TFIID’-dependent categories. Ribosomes include only the ribosomal genes from the TFIID-dependent category. ‘TFIID active, no ribosomes’ are the remainder of the top 10% transcribed genes in the TFIID-dependent category after ribosomal genes have been removed. ‘All’ genes are the entire set of ~5000 s. cerevisiae genes, broken up into ‘SAGA’ and ‘TFIID’-dependent categories. (C and D) Screenshots in the Integrated Genome Browser of Pol II levels at the indicated TFIID-dependent and SAGA-dependent genes before and after anchor-away depletion of Taf1 or before and after auxin-degron depletion of Taf11 and Taf13.