Fig. 6

Mathematical model of Pol II pausing dynamics. a Scheme of the mathematical model. The velocity of elongation (\(v\)) is assumed to be a function of the distance to the TSS (\(x\)), and the pause is modelled by a decrease of velocity at the pausing site (PS) near the PAS. Pol II occupancy between TSS and PS and that after the PS is then computed by solving two partial differential equations that link the Pol II occupancy to the velocity of elongation. b Comparison of model-predicted and actual Pol II occupancy profiles in Col-0. Curves indicate the average Pol II occupancy profiles for all genes with a specific exon number estimated from the pNET-seq data, and the shaded areas indicate model-predicted ranges of the Pol II occupancy based on parameters estimated by fitting the experimental data. c Comparison of model-predicted 3’ end pausing time across genes with different numbers of exons in Col-0. The pausing time was computed by the decrease in the total time for the entire process of transcription initiation, elongation, and termination to complete if there was no 3’ end pause. d Comparison of model-predicted 3’ end pausing time between Col-0 and the xrn3 mutant for genes with different numbers of exons. e Comparison of model-predicted 3’ end pausing time between the DMSO- and herboxidiene-treated groups for genes with different numbers of exons