Comparative Study of Quantitative TSS Maps among Yeast Strains Demonstrates Key Genetic Sites Required for TSS Selection

Gene transcription is finely regulated to ensure proper cellular functions. Transcription initiation is a critical step of gene regulation as it integrates most regulatory signals, determines the location of transcription start sites (TSS), and establishes the transcript abundance. Recent studies have shown that transcription of most genes in eukaryotes can be initiated from multiple spatially located TSSs. Furthermore, different TSSs were used in various cell types as well as in response to environmental stress. How TSSs are selected during transcription, however, remains largely unknown. We aimed to infer important genetic variations associated with divergence of TSSs to better understand the role of genomic context in TSS selection. Specifically, we used no-amplification non-tagging cap analysis of gene expression (nAnT-iCAGE) sequencing to accurately determine TSSs on a genome-wide scale for three different populations of budding yeast (Saccharomyces cerevisiae). Comparative studies of these quantitative TSS maps and their genomic sequences showed that transversion substitutions at several positions, such as -8, -1, and +1 position relative to the TSS, coincided with divergence of the dominant TSS in many promoters. Additionally, a range of transversion substitutions upstream of the TSS at around the -150 position showed divergence of the dominant TSS in many promoters as well. However, many divergent TSSs did not have genetic variations nearby, suggesting that transcription factors likely played a major role in TSS selection. This study lays a solid foundation for further functional characterization of these genetic variations, contributing to a better understanding of the genetic mechanisms underlying the regulation of transcription initiation.