Start-TimeLapse-seq (STL-seq). We have developed a method to probe the kinetics of promoter-proximal pausing in metazoa. Start-TimeLapse-seq (STL-seq, “stall”-seq) combines existing methods Start-seq, developed in the Adelman lab, and TimeLapse chemistry, developed in our lab, to measure the dynamics of short, capped RNA associated with RNA polymerase II at the promoter-proximal pause site. STL-seq directly measures promoter-proximal pausing half-lives and quantifies changes in pausing kinetics upon perturbation. Treating cells with an inhibitor of pause release allows for deconstruction of total turnover into pause release and premature termination. This analysis revealed that premature termination is the major fate of paused Pol II.
(Figures adapted from Zimmer et al., Mol Cell. 2021)
Zimmer J.T., Rosa-Mercado N.A., Canzio D., Steitz J.A., and Simon M.D. (2021). STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. Mol Cell, 81(21), 4398-4412. doi: 10.1016/j.molcel.2021.08.01