Comparison of transcriptional initiation by RNA polymerase II across eukaryotic species
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, United States
Figures
Figure 1 with 1 supplement
Association of general transcription factors (GTFs) at mRNA promoters and distal regulatory regions.
(A) Mean occupancies (metagene analyses) of the indicated proteins at the 600 most active yeast mRNA promoters with respect to the transcription start site (TSS) in cells depleted (+rap) or not …
Figure 1—figure supplement 1
Association of general transcription factors (GTFs) at promoters in human cells.
(A) Mean occupancies of the indicated proteins at the 10,000 most active mRNA promoters (by TATA-binding protein [TBP] occupancy) in the indicated cell lines with respect to the transcription start …
Figure 2
Mediator association and distance between factors at promoters and enhancers.
(A) Medan occupancy values at and surrounding the preinitiation complex (PIC) peak center defined by general transcription factor (GTF occupancy) of the top 10,000 promoters and enhancers as well as …
Figure 3 with 1 supplement
Relationship of Mediator, TATA-binding protein (TBP), and Pol II levels at promoters.
(A) Pairwise correlations of Med1, TBP, and Pol II occupancies at the 10,000 most active (by TBP occupancy) mRNA promoters (dots) in the indicated human cell lines; red dots indicate promoters with …
Figure 3—figure supplement 1
Pairwise correlations of Cdk7 (TFIIH) and Pol II occupancies at the 10,000 most active mRNA promoters (dots) in MM1S cells.
Figure 4 with 1 supplement
Association of Mediator, TATA-binding protein (TBP), Pol II, and GAGA transcription factor in Drosophila cell lines.
(A) Mean occupancies of the TBP, Pol II, Mediator (Med1 and Med30 subunits), and GAGA at the 1000 most active (by TBP occupancy) promoters in the indicated Drosophila cell lines with respect to the …
Figure 4—figure supplement 1
Screenshots of Med1 and Med30 occupancy levels at several fly genes in ML-DmBG3 cells.
Figure 5 with 1 supplement
Relationship of TATA-binding protein (TBP) occupancy with various forms of Pol II.
(A) Relative occupancy levels of TBP and total Pol II in the vicinity of individual promoters (10,000 most active by TBP occupancy) in the indicated human cell lines. (B) Relative occupancy levels …
Figure 5—figure supplement 1
Correlations of Pol II occupancies in biological replicates and datasets from different laboratories.
Figure 6 with 2 supplements
Relative occupancy of TBP-associated factors (Tafs) and TATA-binding protein (TBP) at promoters.
(A) Relative occupancy levels of TBP, Pol II, and the indicated Tafs at the 1000 most active Drosophila and 10,000 most active human mRNA promoters with respect to the transcription start site …
Figure 6—figure supplement 1
Relative occupancy of TBP-associated factors (Tafs) and TATA-binding protein (TBP) at promoters in Drosophila.
(A) Heat map of occupancies of the indicated factors at the most active mRNA promoters in the indicated cells lines with the histone cluster genes indicated. (B) Correlation of TBP and Taf2 …
Figure 6—figure supplement 2
Relative occupancy of TBP-associated factors (Tafs) and TATA-binding protein (TBP) at promoters in human cell lines.
(A) Relative levels of TBP and TFIIB (top) or TBP and Taf1 (bottom) at individual promoters (dots) in the indicated cell lines. Promoters with low (orange) or high (green) Taf1:TBP ratios indicated. …
Figure 7 with 3 supplements
Location and relative occupancy of Taf7, Taf1, and TATA-binding protein (TBP).
(A, B) Relative occupancy levels of TBP and Taf7 at individual mRNA and non-coding RNA promoters in Schizosaccharomyces pombe. Genes with relatively high Taf7:TBP ratios (red dots) are indicated …
Figure 7—figure supplement 1
Relative occupancy of Taf7, Taf1, and TATA-binding protein (TBP) in human cells.
(A) Relative occupancy levels of TBP and Taf7 at the 10,000 most active mRNA promoters in the indicated cell lines. (B) Comparison of Taf1 and TBP occupancy ratios at individual promoters in …
Figure 7—figure supplement 2
Comparison of mRNA promoters in which Taf7 is located downstream or at the transcription start site (TSS) in K562 (A, B) and human embryonic stem cell (hESC) (C, D) lines.
(A, B) are biological replicates to the datasets in Figure 6E and F. Mean Pol II occupancies of Pol II, TATA-binding protein (TBP), Taf1, and Taf7 at promoters in which Taf7 is located near (A, C) …
Figure 7—figure supplement 3
Relationship of Taf7 location with Pol II location and occupancy.
Distance (in bp) between the TATA-binding protein (TBP) and Pol II-binding summit, obtained using MACS, in promoters having the indicated distance between Taf7 and TBP in K562 cells.
Figure 8 with 2 supplements
Relationship between Taf7 and Med26 occupancy in the vicinity of promoters.
(A) Mean occupancies of the indicated proteins in the indicated mouse and human cell lines at the 10,000 most active mRNA promoters (by TATA-binding protein [TBP] occupancy). (B) Mean occupancies of …
Figure 8—figure supplement 1
Relationship between Taf7 and Med26 occupancy in the vicinity of promoters.
(A) Enriched gene categories for promoters having Med26 downstream or at the transcription start site (TSS) with FDR-corrected p-values indicated. (B) Binding profiles of the indicated proteins …
Figure 8—figure supplement 2
Relationship of Taf7 (left) or Taf1 (right) and Med26 occupancies at individual promoters in the indicated human cell lines.
Additional files
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Supplementary file 1
Table of datasets used.
- https://cdn.elifesciences.org/articles/67964/elife-67964-supp1-v2.xlsx
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Supplementary file 2
Table of Taf7 and Med26 downstream and at transcription start site (TSS).
- https://cdn.elifesciences.org/articles/67964/elife-67964-supp2-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/67964/elife-67964-transrepform1-v2.docx
