Genomic environments scale the activities of diverse core promoters

Abstract

A classical model of gene regulation is that enhancers provide specificity whereas core promoters provide a modular site for the assembly of the basal transcriptional machinery. However, examples of core promoter specificity have led to an alternate hypothesis in which specificity is achieved by core promoters with different sequence motifs that respond differently to genomic environments containing different enhancers and chromatin landscapes. To distinguish between these models, we measured the activities of hundreds of diverse core promoters in four different genomic locations and, in a complementary experiment, six different core promoters at thousands of locations across the genome. Although genomic locations had large effects on expression, the intrinsic activities of different classes of promoters were preserved across genomic locations, suggesting that core promoters are modular regulatory elements whose activities are independently scaled up or down by different genomic locations. This scaling of promoter activities is nonlinear and depends on the genomic location and the strength of the core promoter. Our results support the classical model of regulation in which diverse core promoter motifs set the intrinsic strengths of core promoters, which are then amplified or dampened by the activities of their genomic environments.

Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers

“…A remarkable result, obtained independently by Bergman et al [12] and Hong et al [27], is that promoters and enhancers generally act multiplicatively on transcriptional input. We asked whether Enformer qualitatively captured the same rule.…”

“…To further probe the ability of Enformer to correctly account for distal sequence context in its predictions, we used TRIP (thousands of reporters integrated in parallel) sequencing data compiled by Hong et al [27]. In this experiment, six different short promoter fragments were integrated at thousands of locations across the genome and then their activity at each location was measured.…”

“…Trip-Seq (Hong et al) We collected the data and relevant construct sequences from the supplements of the Hong et al [27] manuscript. We followed the standard procedure to replicate this experiment.…”

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

“…Our assays were performed using a reporter plasmid library and it is known that the genomic environment affects the absolute level of transcription. Based on prior results, it is likely that the absolute but not relative expression level of UAS-core combinations is partially dependent on chromatin 40,49 , so use of the reporter likely does not affect conclusions on functional compatibility and coactivator…”

“…We next focused on the behavior of the most highly specific UASs. For the small subset of UASs that display highly biased expression at CR core promoters Prior work demonstrated that inducible metazoan core promoters tend to exhibit lower intrinsic activity than constitutive core promoters 40,41 . To test if this feature is conserved in yeast, we examined whether CR promoters display low intrinsic activity, given that CR genes, like metazoan inducible genes, tend to be stress responsive and are enriched for TATA-containing promoters.…”