Factors controlling internal initiation of transcription at PRY3 in budding yeast

Transcription initiation from within the coding regions of genes has been observed in budding yeast as a natural phenomenon induced by environmental changes. However, such ‘internal initiation’ events have also been observed in mutant yeast strains with aberrant chromatin structure. Failure to suppress initiation from cryptic internal promoters is thought to result from either loss of appropriate nucleosome density or loss of appropriate histone modifications in the coding region. PRY3 is a gene previously shown to undergo internal initiation in response to mating pheromone. This project aimed to uncover which factors are involved in suppressing inappropriate transcription initiation from an internal TATA-box at PRY3 in the absence of mating pheromone. This work demonstrates that factors controlling nucleosome density (Spt6, Spn1 and Spt10) but not histone deacetylation (Eaf3) are required to suppress internal initiation at PRY3 in the absence of mating pheromone. In addition, TATA-box binding protein (TBP) is required for internal initiation at PRY3. Taken together, these results indicate that internal initiation at PRY3 is predominantly suppressed by a nucleosome reassembly mechanism rather than histone modifications, and suggest that the transcriptional output at PRY3 is controlled by competition between TBP and nucleosomes for binding an internal TATA-box.