Global repression driven by RNA polymerase II stalling in yeast

In multicellular eukaryotes, RNA polymerase (pol) II pauses transcription ~30-50 bp after initiation, and involves DSIF and other factors. While the budding yeast Saccharomyces has its transcription mechanisms mostly conserved with other eukaryotes, it appears to lack this fundamental promoter-proximal pausing. However, we now discover that acute stress (e.g., peroxide) causes most yeast genes, including constitutive and stress-induced genes, to manifest two distinct pausing or stall sites during the early elongation phase of Pol II transcription. The first stall occurs at the promoter, where Pol II melts the DNA and acquires all tested interactions normally. The second stall occurs 100-200 bp downstream. It too has most, but not all, of the tested interactions. This stall is phenocopied by depletion of DSIF. Our results suggest that similar to other eukaryotes, in yeast stalling globally down regulates nearly all Pol II transcription, but primarily in response to acute stimuli, whereas in other eukaryotes it represents the default state in all cells. ChIP-exo was used to study the stalling of RNA polymerase II following acute stress by hydrogen peroxide.