Fig. 4: Acute KAP1 depletion leads to increased elongation kinetics at early serum stimulation.

a, b PRO-Seq metagene profile at 16-fold IEGs showing active Pol II density at the: a 5 min (with zoomed-in profile to show differences) and b 10 min serum stimulation time points. See legend for sample identification. c PRO-Seq quantitation of nascent transcription (GB density) for 4-fold IEGs (n = 69) and 16-fold IEGs (n = 16). Data represents the Log₂FC value for the respective sample (see X-axis) normalized to serum 0 min in DMSO-treated cells using PRO-Seq signal from 2 biological replicates. The n number represents the number of genes in each cluster plotted. The Tukey plots indicate the median (black center line), the first and third quartiles (edges of the box), and the 1.5× interquartile range below and above the box as whiskers. Dots are presented as genes with normalized signals beyond these defined ranges. Statistics were calculated between the indicated samples in the plot (dTAG vs. DMSO at both 5 and 10 min serum time points). Two-sided Wilcoxon signed-rank test. P-values are indicated. d Pol II ChIP-Seq, PRO-Seq, and HA ChIP-Seq browser track in multiple conditions at the FOSB locus. See legend for sample identification. e Rate of Change in Coverage (ROCC) calculation (Proxy Rate) for 4-fold IEGs (n = 69) and 16-fold IEGs (n = 16) computed through the serum stimulation time course. Data represents the absolute average ROCC values for the respective sample (see X-axis) using PRO-Seq data from 2 biological replicates. The n number represents the number of genes in each cluster plotted. The Tukey plots indicate the median (black center line), the first and third quartiles (edges of the box), and the 1.5× interquartile range below and above the box as whiskers. Dots are presented as genes with normalized signals beyond these defined ranges. Statistics were calculated between the indicated samples in the plot (dTAG vs. DMSO) with a two-sided Wilcoxon signed-rank test. P-values are indicated.