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. 2023 Apr 25;42(4):112387.
doi: 10.1016/j.celrep.2023.112387. Epub 2023 Apr 13.

Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity

Jeremy A Schofield  1 , Steven Hahn  2
Affiliations

Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity

Jeremy A Schofield et al. Cell Rep. .

Abstract

Three classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA, and Mediator (MED) Tail, but whether this dependence is determined by the core promoter, upstream activating sequences (UASs), or other gene features is unclear. Also unclear is whether UASs can broadly activate transcription from the different promoter classes. Here, we measure transcription and cofactor specificity for thousands of UAS-core promoter combinations and find that most UASs broadly activate promoters regardless of regulatory class, while few display strong promoter specificity. However, matching UASs and promoters from the same gene class is generally important for optimal expression. We find that sensitivity to rapid depletion of MED Tail or SAGA is dependent on the identity of both UAS and core promoter, while dependence on TFIID localizes to only the promoter. Finally, our results suggest the role of TATA and TATA-like promoter sequences in MED Tail function.

Keywords: CP: Molecular biology; SAGA; TFIID; core promoters; enhancers; large-scale reporter; mediator; transcriptional coactivators; upstream activating sequences (UASs).

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Figures

Figure 1.
Figure 1.. A large-scale transcriptional reporter assay to measure expression and coactivator sensitivity for tens of thousands of UAS-core promoter combinations
(A) Yeast genomic UASs (200 nt) and random genomic sequences are cloned upstream of four core promoters from varying coactivator classes (CR, coactivator redundant class; TFIID, TFIID class; TI, Mediator-Tail independent; TD, Mediator-Tail dependent). CR core promoters contain consensus TATA boxes at the preinitiation complex (PIC) location, while TFIID core promoters contain a GA element (GAE) at the PIC location. (B–E) Violin plots comparing log2 reporter expression of the KRS1 (CR/TI) (B), SIT1 (CR/TD) (C), NOP13 (TFIID) (D), and RPC10 (TFIID) (E) core promoters paired with all UASs compared with control regions from accessible chromatin (control acc.) or inaccessible chromatin (control inacc.). Data are average of 2 biological replicates. Wilcoxon statistic is shown, with significance levels defined as ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05, ns p > 0.05. See also Figure S1.
Figure 2.
Figure 2.. Yeast UAS activation across differing core promoter contexts
(A) Plot of log2-reporter expression vs. expression rank for the four tested core promoters paired with all UASs. Points indicate expression level of UAS paired with its endogenous core promoter. (B) Heatmap displaying log2 reporter expression for UASs activating the four tested core promoters. UASs fall into 3 clusters (K-means). (C) Boxplot of log2-expression of genes with corresponding UASs in each of the three clusters from (B). Wilcoxon statistic is shown, with significance levels defined as ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05, ns p > 0.05. (D) Log2 enrichment of UASs from CR or TFIID genes in each of the three clusters from (B). Data are average of 2 biological replicates. Chi-squared test statistic is shown, with significance levels defined as ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05, ns p > 0.05. See also Figure S2.
Figure 3.
Figure 3.. Yeast UASs more efficiently activate core promoters from their genomic coactivator class
(A) Density plot of UAS reporter activation bias for CR (KRS1 and SIT1) vs. TFIID (NOP13 and RPC10) core promoters, comparing UASs from CR and TFIID genes. Median activation biases for each UAS gene class are shown as dotted lines. Data are average of 2 biological replicates. Wilcoxon test p value is shown. (B) UAS variance across reporter core promoters compared with variance between experimental batches. Highly promoter-specific UASs are defined as those with a promoter variance:batch variance ratio 2 standard deviations above the median. Data are average of 2 biological replicates within each experimental batch, with 2 experimental batches performed. (C) Percentage of UASs displaying the strongest reporter activation at each core promoter, comparing UASs from CR and TFIID genes. Dashed lines represent genomic percentages of TFIID-class genes (87%) and CR-class genes (13%). Number of UASs displaying highest activation at each core promoter shown (n). Chi-squared test statistic is shown. Data are average of 2 biological replicates. (D) Percentage of highly promoter-specific UASs displaying the strongest reporter activation at each core promoter, comparing UASs from CR and TFIID genes. Data are average of 2 biological replicates. Chi-squared test statistic is shown. Significance levels defined as ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05, ns p > 0.05. See also Figure S3.
Figure 4.
Figure 4.. Coactivator sensitivity dependence on UAS and core promoter classes
(A–C) Log2-fold change in reporter transcription after Med15 depletion (A), Spt7 depletion (B), or Taf13 depletion (C) for the four test core promoters, comparing UASs from CR class genes (C) or TFIID class genes (T). Data are log2 ratio of average of 2 auxin-treated biological replicates vs. 2 untreated biological replicates. Wilcoxon statistic is shown, with significance levels defined as ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05, ns p > 0.05. See also Figure S4.
Figure 5.
Figure 5.. Mediator-Tail sensitivity is dependent on UAS localization and core promoter identity
(A) Log2 fold change in reporter transcription after Med15 depletion for the four test promoters, comparing UASs from Mediator-Tail-dependent vs. Mediator-Tail-independent genes. Tail dependence of CR cores is noted (TI, Tail independent; TD, Tail dependent). (B) Log2 fold change in reporter transcription after Med15 depletion for the four test promoters, comparing genes with endogenous Mediator ChEC-seq signal in the UAS region vs. genes without endogenous Mediator ChEC-seq signal. Data are log2 ratio of average of 2 auxin-treated biological replicates vs. 2 untreated biological replicates. Wilcoxon statistic is shown, with significance levels defined as ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05, ns p > 0.05.
Figure 6.
Figure 6.. TATA-like elements and Mediator UAS localization independently promote Mediator-Tail sensitivity
(A) Log2 fold change in genomic transcription after Med15 depletion (data from Warfield et al.), comparing CR-class vs. TFIID-class genes, additionally comparing genes containing a weak TATA element (TWTWWA, W = A/T), a canonical TATA box (TATAWAW), or no TATA element in the core promoter. (B) Log2 fold change in genomic transcription after Spt7 depletion (data from Donczew et al.), comparing CR-class genes containing a weak TATA element (TWTWWA), a canonical TATA box (TATAWAW), or no TATA element in the core promoter. Wilcoxon statistic is shown, with significance levels defined as ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05, ns p > 0.05.
Figure 7.
Figure 7.. Model
Mediator-Tail and SAGA sensitivity depend on a combination of UAS localization and flexible core promoter elements. TFIID sensitivity is dependent on the core promoter sequence and independent of UAS identity.
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References

    1. Larsson AJM, Johnsson P, Hagemann-Jensen M, Hartmanis L, Faridani OR, Reinius B, Segerstolpe Å, Rivera CM, Ren B, and Sandberg R (2019). Genomic encoding of transcriptional burst kinetics. Nature 565, 251–254. - PMC - PubMed
    1. Hornung G, Bar-Ziv R, Rosin D, Tokuriki N, Tawfik DS, Oren M, and Barkai N (2012). Noise–mean relationship in mutated promoters. Genome Res. 22, 2409–2417. - PMC - PubMed
    1. Zenklusen D, Larson DR, and Singer RH (2008). Single-RNA counting reveals alternative modes of gene expression in yeast. Nat. Struct. Mol. Biol 15, 1263–1271. - PMC - PubMed
    1. Chubb JR, Trcek T, Shenoy SM, and Singer RH (2006). Transcriptional pulsing of a developmental gene. Curr. Biol 16, 1018–1025. - PMC - PubMed
    1. Jeronimo C, Langelier MF, Bataille AR, Pascal JM, Pugh BF, and Robert F (2016). Tail and kinase modules differently regulate core mediator recruitment and function in vivo. Mol. Cell 64, 455–466. - PMC - PubMed

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