Base Composition Influences the Position and Precision of RNA Polymerase II Disassociation in Basal and Perturbed Conditions

RNA Polymerase II (Pol II) transcribes all protein-coding and many non-protein coding genes in the genome. Pol II transcription termination is crucial for mRNA maturation and, when disrupted, can lead to altered mRNA processing and mRNA export. Termination involves two intertwined processes: pre-mRNA cleavage and Pol II release from the DNA (disassociation). Despite its importance, the exact mechanisms underlying Pol II disassociation from the DNA remain poorly understood. Moreover, under certain cellular stress conditions, there is a partial failure of cleavage, leading to a shift of the position of disassociation further downstream, a phenomenon known as run-on transcription. We performed the first-ever systematic analysis of Pol II termination across cell types and species and provide novel insights into the mechanism of disassociation. Using a probabilistic mixture model to quantify Poll II dynamics across an entire gene body from nascent RNA sequencing data, we discovered that genes have two types of conserved regions near the disassociation site: one characterized by a T-rich region upstream of disassociation, and another characterized by a GC-rich region surrounding disassociation. Strikingly, the GC-rich disassociation regions have more accessible chromatin and higher levels of phospho-threonine 4 on the CTD of Pol II. Additionally, we find that upstream T-rich genes are preferentially affected by perturbations that alter disassociation, including heat-shock, viral infection, kinase inhibition, and arsenic treatment. Thus, our work has determined there are two types of Pol II disassociation regions, which are differentially affected by perturbation of cellular homeostasis.