The nucleosome DNA entry-exit site is important for transcription termination in Saccharomyces cerevisiae

Compared to other stages in the RNA polymerase II transcription cycle, the role of chromatin in transcription termination is poorly understood. Through a genetic screen, we identified histone mutant strains that exhibit transcriptional readthrough of terminators in vivo. Amino acid subtitutions map to the nucleosome DNA entry-exit site. On a genome-wide scale, the strongest H3 mutants revealed increased sense-strand transcription upstream and downstream of Pol II transcribed genes, increased antisense transcription overlapping gene bodies, and reduced nucleosome occupancy particularly at the 3 ends of genes. Replacement of the native sequence downstream of a gene with a sequence that increases nucleosome occupancy in vivo reduced readthrough transcription and suppressed the effect of a DNA entry-exit site substitution. Our results suggest that nucleosomes can facilitate termination by serving as a barrier to RNA polymerase II progression and highlight the importance of the DNA entry-exit site in maintaining the integrity of the transcriptome.