Requirements for RNA polymerase II preinitiation complex formation in vivo
- Harvard Medical School, United States
- University of Macau, China
Figures
Figure 1 with 1 supplement
Conditional depletion of GTFs causes severe growth and transcriptional defects.
(A) Growth of the indicated anchor-away cells (5-fold serial dilutions) in the presence or absence of rapamycin. (B) Occupancy of the indicated FRB-tagged GTFs at the PMA1 and CCW12 promoters in the …
Figure 1—figure supplement 1
Conditional depletion of GTFs causes severe growth and transcriptional defects.
Pol II occupancy at the PMA1 and RPL28 coding regions in the indicated strains grown in the presence or absence of rapamycin.
Figure 2
All GTFs are generally required for ongoing Pol II transcription.
(A) Mean Pol II occupancy averaged over 453 well-transcribed genes (metagene analysis) in strains depleted (+rap) for the indicated factor and in the parental (WT) strain (±rap). Partial reduction …
Figure 3 with 1 supplement
All GTFs are required for transcriptional induction upon heat shock.
(A) Mean Pol II occupancy at the HSP12 coding region (ORF) and promoter in strains depleted (or not) for the indicated factor and then induced for 15 min by shifting to 39°C. (B) FRB-tagged GTF:Pol …
Figure 3—figure supplement 1
All GTFs are required for transcriptional induction upon heat shock.
(A) Pol II occupancy at the coding region (ORF) and promoter of the indicated genes in strains depleted (or not) for the indicated factor and then induced for 15 min by shifting to 39°C. (B) …
Figure 4 with 1 supplement
All GTFs are required for TBP occupancy, and hence PIC stability/formation.
(A) TBP occupancy at the CCW12 and TEF1 promoters in strains depleted (+rap) or not (-rap) for the indicated factor. (B) TBP occupancy at the HSP12 and HSP82 promoters in strains depleted (+rap) or …
Figure 4—figure supplement 1
All GTFs are required for TBP occupancy, and hence PIC stability/formation.
(A) TBP occupancy at the PMA1 and ACT1 promoters in strains depleted (+rap) or not (-rap) for the indicated factor. (B) TBP occupancy at the SSA4 and SED1 promoters in strains depleted (+rap) or not …
Figure 5 with 1 supplement
A general loss of PICs in cells depleted for uracil.
(A) Pol II (ORF and promoter) and TBP occupancies at promoters (PMA1 and RPL28) of genes inhibited by metabolic stress in cells depleted for uracil or leucine for various times (color scale). (B) …
Figure 5—figure supplement 1
A general loss of PICs in cells depleted for uracil.
(A) TBP occupancy at Pol III (tRNA) promoters, as well as growth curves for cultures depleted of uracil or leucine. (B) Pol II (ORF and promoter) and TBP occupancies at promoters of genes inhibited …
Figure 6
Depletion of Spt16 subunit of FACT reduces transcription and PIC formation.
Mean Pol II occupancy and TFIIB occupancy averaged over 453 well-transcribed genes and promoters before and after Spt16 depletion.
Figure 7 with 2 supplements
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’ (PM…
Figure 7—figure supplement 1
Taf1 depletion selectively affects TFIID-dependent genes.
(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 …
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.
(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 …
Additional files
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Supplementary file 1
List of strains.
- https://doi.org/10.7554/eLife.43654.015
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Transparent reporting form
- https://doi.org/10.7554/eLife.43654.016
