Jeremy A. Schofield, Steven Hahn
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.
Jeremy A. Schofield, Steven Hahn. Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity. 2023-04-25. https://doi.org/10.1016/j.celrep.2023.112387
The combinatorial episomal reporter library was assayed in the SHY1043 Taf13-degron strain after rapid auxin-mediated Taf13 depletion. This long-format table contains published log2(auxin/no-auxin) reporter fold changes for element–core-promoter pairs, together with their published baseline activity and genomic annotations.
An episomal, barcoded plasmid MPRA tested approximately 4,200 genomic yeast UASs and 222 genomic control sequences upstream of four representative yeast core promoters. This long-format table contains the published baseline reporter-expression summary for each element–core-promoter pair.
The combinatorial episomal reporter library was assayed in the SHY1055 Med15-degron strain after rapid auxin-mediated Med15 depletion. This long-format table contains published log2(auxin/no-auxin) reporter fold changes for element–core-promoter pairs, together with their published baseline activity and genomic annotations.
The combinatorial episomal reporter library was assayed in the SHY1045 Spt7-degron strain after rapid auxin-mediated Spt7 depletion. This long-format table contains published log2(auxin/no-auxin) reporter fold changes for element–core-promoter pairs, together with their published baseline activity and genomic annotations.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
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