1. Chromosomes and Gene Expression
  2. Genetics and Genomics
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Comparison of transcriptional initiation by RNA polymerase II across eukaryotic species

  1. Natalia Petrenko
  2. Kevin Struhl  Is a corresponding author
  1. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, United States
Research Article
Cite this article as: eLife 2021;10:e67964 doi: 10.7554/eLife.67964
8 figures and 3 additional files

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 depleted (-rap) for the Kin28 subunit of TFIIH. (B) Mean occupancies of the indicated proteins at the 10,000 most active mRNA promoters (by TATA-binding protein [TBP] occupancy) in the indicated human cell lines. (C) Mean occupancies of the indicated proteins at the 10,000 most active mRNA promoters in the indicated mouse cell lines. (D) Correlation of Med1 and Cdk8 occupancies at individual mRNA promoters (dots) in MM1S and HCT116 cells; red dots indicate promoters with relatively high Med1 levels with respect to Cdk8 levels.

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 site (TSS). (B) Correlation of Med1 and Cdk8 (left) or Med1 and Med12 (right) occupancies at individual mRNA promoters (dots) in the indicated cell lines. Red dots indicate promoters with relatively high Med1 levels along with the enriched gene categories.

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 all promoters and enhancers in MM1S cells. All enhancers include the ~60,000 genomic regions where any Mediator signal is detected, including the top 10,000. It does not include the ~100,000 enhancers where no Mediator signal is detected. (B) Absolute values of the distances in base pairs betwen the indicated factors (or replicates) at top 10,000 promoters and enhancers (Loven et al., 2013) in MM1S cells. The boxplot indicates the median value (also written as a number), as well as the 25th and 75th percentiles, represented as the edges of the box.

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 relatively high Mediator levels with respect to Pol II levels. Enriched gene categories for promoters with relatively high Mediator levels with respect to Pol II levels in the indicated cell lines are given in the Supplementary file 2. (B) Pairwise correlations of Med1, Cdk7 (TFIIH), and Pol II occupancies at ~8000 enhancers (Loven et al., 2013) in MM1S cells.

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 transcription start site (TSS). (B) Relative occupancy levels of Med30 and Med1 at individual promoters. Genes with relatively high Med30:Med1 ratios (blue dots) and relatively low Med30:Med1 ratios (green dots) indicated along with enriched gene categories.

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 of total Pol II and the form of Pol II phosphorylated at serine 5 in the C-terminal domain in the vicinity of individual promoters in K562 cells. (C) Relative occupancy levels of total Pol II and the form of Pol II phosphorylated at serine 2 in the C-terminal domain in the vicinity of individual promoters in K562 cells. (D) Relationship between TBP occupancy levels subdivided into deciles, in which high values indicate high occupancy with the Pol II pausing index (ratio of Pol II in the promoter-proximal peak relative to the coding region).

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 (TSS). (B) Number of Drosophila mRNA promoters having the indicated TBP:TBP replicate or Taf2:TBP ratios (among 900 most active promoters); median ratio set to 1.0. Promoters with low (orange) or high (green) Taf2:TBP ratios indicated along with enriched gene categories. (C) Number of human promoters having the indicated TFIIB:TBP or Taf1:TBP ratios (among 3500 most active promoters) in the indicated cell lines; median ratio set to 1.0. Promoters with low (orange) or high (green) Taf1:TBP ratios indicated along with enriched gene categories.

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 replicates (top) and relative levels of TBP and Taf2 (bottom) at the 900 most active mRNA promoters (dots) in Kc167 cells. Promoters with low (orange) or high (green) Taf2:TBP ratios indicated along with enriched gene categories.

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. (B) Enriched gene categories for promoters with high or low Taf1:TBP occupancy ratios with raw and FDR-corrected p-values.

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 along with enriched gene categories. (C) Relative Taf7:TBP and Taf1:TBP occupancy ratios at 10,000 most active promoters (by TBP occupancy) in the indicated human cell lines. Genes with relatively high Taf7:Taf1 ratios (red dots) are indicated along with enriched gene categories. (D) Relative occupancy levels of Taf7 and Taf1 at the 300 most expressed (by TBP occupancy) non-coding RNA promoters in the indicated cell lines. (E) Mean occupancies of the TBP, Taf1, Taf7, and Pol II with respect to the transcription start site (TSS) at promoters in the K562 cells with Taf7 at downstream locations. (F) Mean occupancies of the TBP, Taf1, Taf7, and Pol II with respect to the TSS at promoters in the K562 cells with Taf7 at the TSS. The genes in each category for E and F are presented in Supplementary file 2.

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 biological replicates, to complement Figure 6C. (C) Relative occupancy levels of Taf7 and Taf1 at the 10,000 most active mRNA promoters in the indicated cell lines. (D) Screenshot of TBP, Taf1, and Taf7 occupancy levels at two non-coding RNA promoters.

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) or downstream (B, D) of the TSS. (E) Enriched gene categories for promoters with Taf7 located near or downstream of the TSS with raw and FDR-corrected p-values.

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 Med1, Med26, and Taf7 in the indicated mouse and human cell lines for mRNA genes where Med26 is located downstream or at the transcription start site (TSS). (C) Venn diagram showing the intersection of promoters with Taf7 (K562 cells) and/or Med26 (HCT116 cells) at downstream locations. (D) Relative occupancies of Taf7 and Med26, versus Taf1 levels, at Taf1-enriched non-coding RNAs and relative occupancies of Taf1 and Med26 binding, versus Taf7 levels, at Taf7-enriched non-coding RNAs.

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 around the TSS at ribosomal protein promoters in the indicated human and mouse cell lines. (C) Binding profiles of the indicated proteins around the TSS at histone promoters in the indicated human and mouse cell lines.

Figure 8—figure supplement 2
Relationship of Taf7 (left) or Taf1 (right) and Med26 occupancies at individual promoters in the indicated human cell lines.

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