Base composition reflects RNA polymerase II displacement

RNA Polymerase II (Pol II) transcribes all protein-coding and many nonprotein-coding genes in the genome. Pol II transcription termination is crucial for RNA maturation and, when disrupted, can lead to altered RNA processing and RNA export. Termination involves two intertwined processes: RNA cleavage and Pol II release from the DNA (displacement). Despite its importance, the exact mechanisms underlying Pol II displacement 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 displacement further downstream, a phenomenon known as readthrough transcription. We present a systematic analysis of Pol II termination across cell types and species and provide novel insights into the mechanism of displacement. Using a probabilistic mixture model to quantify Pol II dynamics across entire gene bodies from nascent RNA sequencing data, we find that genes fall into two classes defined by conserved base composition patterns near the displacement site. Both classes share a T-rich region upstream of displacement, and one class additionally carries a GC-rich region surrounding displacement. We find that GC-rich predisplacement regions have more accessible chromatin and higher levels of phospho-threonine 4 on the CTD of Pol II. Additionally, we find that displacement at genes with only the upstream T-rich pattern are more likely to be affected by perturbations that alter displacement, including heat shock, viral infection, kinase inhibition, and arsenic treatment. Thus, our work identifies two types of Pol II displacement regions, which are differentially affected by perturbations of cellular homeostasis.