Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures

Promoters process signals through recruitment of transcription factors and RNA polymerase, and dynamic changes in promoter activity constitute a major noise source in gene expression. However, it is barely understood how complex promoter architectures determine key features of promoter dynamics. Here, we employ prototypical promoters of yeast ribosomal protein genes as well as simplified versions thereof to analyze the relations among promoter design, complexity, and function. These promoters combine the action of a general regulatory factor with that of specific transcription factors, a common motif of many eukaryotic promoters. By comprehensively analyzing stationary and dynamic promoter properties, this model-based approach enables us to pinpoint the structural characteristics underlying the observed behavior. Functional tradeoffs impose constraints on the promoter architecture of ribosomal protein genes. We find that a stable scaffold in the natural design results in low transcriptional noise and strong co-regulation of target genes in the presence of gene silencing. This configuration also exhibits superior shut-off properties, and it can serve as a tunable switch in living cells. Model validation with independent experimental data suggests that the models are sufficiently realistic. When combined, our results offer a mechanistic explanation for why specific factors are associated with low protein noise in vivo. Many of these findings hold for a broad range of model parameters and likely apply to other eukaryotic promoters of similar structure.Author Summary: Combinatorial regulation of gene expression is an important mechanism for signal integration in prokaryotes and eukaryotes. Typically, this regulation is established by transcription factors that bind to DNA or to other regulatory proteins. Modifications of the DNA structure provide another layer of control, for instance, in gene silencing. However, it is barely understood how complex promoter architectures determine key features of promoter dynamics such as gene expression levels and noise. Here, we employ realistic mathematical models for prototypical promoters of yeast ribosomal protein genes as well as simplified versions thereof to analyze the relations among promoter design, complexity, and function. By comprehensively analyzing stationary and dynamic promoter properties, we find that functional tradeoffs impose constraints on the promoter architecture. More specifically, a stable configuration in the natural design results in low transcriptional noise and strong co-regulation of target genes in the presence of gene silencing. Combined, our results offer a mechanistic explanation for why specific factors are associated with low protein noise in vivo. We expect that many of these findings apply to other promoters of similar structure.