Extended Data Fig. 7: P-TEFb activation shapes the transcriptional response to Mediator loss.

a, PRO-seq read-through upon 2 h MED14 degradation. Additionally inhibiting CDK9 with 500 nM NVP2 in the last 30 min reverses the read-through. Zoom-ins show 30 kb windows around the polyadenylation site. Arrows highlight transcription start site (TSS) regions shown in g. b, Aggregated PRO-seq coverages show read-through even for long genes, where newly initiated Pol II has not yet reached the termination site. Mean±bootstrapped confidence region. c, Aggregated TT-seq coverages show read-through transcription after MED14 degradation also in HCT-116 cells. d,e, Changes in PRO-seq pausing index of all n = 5,558 genes (d) and calculated pause duration at all n = 6,954 transcription units (e) after MED14/CDK9 perturbation. f, Changes in productive initiation rates for all n = 6,954 transcription units. Box plot elements: medians with interquartile range, 1.5x whiskers and confidence region notches. g, PRO-seq signal around transcription start sites (TSS) of two non-SE and one auto-regulatory TF gene. Paused polymerase does not re-accumulate at the MYB TSS upon combined MED14/CDK9 perturbation. h, TT-seq SE-gene set enrichment upon combined MED14/CDK9 perturbation. Less significant enrichment confirms that CDK9 activity aggravated the SE-selectivity of Mediator disruption.