Lee Davidson1,5, Jérôme O. Rouvière2,5, Rui Sousa-Luís3, Takayuki Nojima3,4, Nicholas J. Proudfoot3, Torben Heick Jensen2 and Steven West1 1The Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom; 2Department of Molecular Biology and Genetics, Aarhus University, 8000C Aarhus, Denmark; 3Sir William Dunn School of Pathology, Oxford OX1 3RE, United Kingdom; 4Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan Corresponding authors: s.westexeter.ac.uk, thjmbg.au.dk

↵5 These authors contributed equally to this work.

Abstract

The best-studied mechanism of eukaryotic RNA polymerase II (RNAPII) transcriptional termination involves polyadenylation site-directed cleavage of the nascent RNA. The RNAPII-associated cleavage product is then degraded by XRN2, dislodging RNAPII from the DNA template. In contrast, prokaryotic RNAP and eukaryotic RNAPIII often terminate directly at T-tracts in the coding DNA strand. Here, we demonstrate a similar and omnipresent capability for mammalian RNAPII. Importantly, this termination mechanism does not require upstream RNA cleavage. Accordingly, T-tract-dependent termination can take place when XRN2 cannot be engaged. We show that T-tracts can terminate snRNA transcription independently of RNA cleavage by the Integrator complex. Importantly, we found genome-wide termination at T-tracts in promoter-proximal regions but not within protein-coding gene bodies. XRN2-dependent termination dominates downstream from protein-coding genes, but the T-tract process is sometimes used. Overall, we demonstrate global DNA-directed attrition of RNAPII transcription, suggesting that RNAPs retain the potential to terminate over T-rich sequences throughout evolution.

Received June 1, 2024. Accepted October 2, 2024.