Timing polymerase pausing with TV-PRO-seq: dissecting the interplay of pausing duration and location, and gene expression

Abstract

Transcription of many genes in metazoans is subject to polymerase pausing, which corresponds to the transient arrest of transcriptionally engaged polymerase. It occurs mainly at promoter proximal regions and is not well understood. In particular, a genomewide measurement of pausing times at high resolution has been lacking.We present here an extension of PRO-seq, time variant PRO-seq (TV-PRO-seq), that allowed us to estimate genome-wide pausing times at single base resolution. Its application to human cells reveals that promoter proximal pausing is surprisingly short compared to other regions and displays an intricate pattern. We also find precisely conserved pausing profiles at tRNA and rRNA genes and identified DNA motifs associated with pausing time. Finally, we show how chromatin states reflect differences in pausing times.

Bayesian inference of PolII dynamics over the exclusion process

“…The evidences of PolII transport are particularly clear in time-course experiments, where sequencing data are collected over time following a perturbation. As an example, time-variant PRO-seq has been suggested to estimate pausing times in key peak regions [16]. A classical way to perturb these molecular dynamics is inhibiting the initiation by treating the cells with triptolide (Trp) [17,18].…”