Transcription is ubiquitously terminated in thousands of bidirectional termination zones in yeast

Pervasive transcription of eukaryotic genomes requires intricate mechanisms to delineate boundaries for each transcriptional unit. How transcription is efficiently terminated before invading neighboring genes remains an open question. Here, after dissecting the cleavage and polyadenylation landscape using a hybrid approach, we observed thousands of bidirectional termination zones in the genome of Saccharomyces cerevisiae. These zones are [~]120 bp wide and terminate transcription from both sense and antisense strands in yeast. They are ubiquitously used as termination sites for both coding and non-coding genes. We suggest that the known transcription termination efficiency element, UAUAUA motifs, serves as the central elements in these zones. Notably, bidirectional termination zones are specifically nucleosome depleted, suggesting chromatin structure plays a key role in the formation of bidirectional termination zones in yeast. Finally, we provide evidence for transcriptional interference in these bidirectional termination zones, and expression level of each cleavage site is influenced by sequence contexts both upstream and downstream. We provide the first global fine-scale picture of transcription termination in a eukaryotic genome.