Antisense transcription‐dependent chromatin signature modulates sense transcript dynamics

Abstract

Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNA-FISH, we observed changes in sense transcript distributions in nuclei and cytoplasm as antisense transcript levels were altered. To determine the mechanistic differences underlying these distri-butions, we developed a mathematical framework describing tran-scription from initiation to transcript degradation. At GAL1, high levels of antisense transcription alter sense transcription dynam-ics, reducing rates of transcript production and processing, while increasing transcript stability. This relationship with transcript stability is also observed as a genome-wide association. Establish-ing the antisense transcription-associated chromatin signature through disruption of the Set3C histone deacetylase activity is suf-ficient to similarly change these rates even in the absence of anti-sense transcription. Thus, antisense transcription alters sense transcription dynamics in a chromatin-dependent manner.