Fig. 7: NELF occupancy is correlated with Pol II pause release and causal to transcription induction in vivo.

a Example track that shows an activity-induced gene, Junb (Blue shaded at its promoter) and its nearby enhancer (Yellow shaded area). Transcript units determined by de novo transcript calls are shown on the top together with tracks for ChIP- (H3K27ac, NELF-E, and Pan Pol II), GRO-, and mRNA-seq. b, c The average GRO-seq profiles of four different gene groups based on the levels of NELF binding (NELF-high [216], -mid [133], -low [199], or -unbound [75]) (b) and two different enhancer groups (NELF-bound [144] or -unbound [108] (c). The profiles are shown for ±2 kb regions centered on the TSSs or the enhancer centers upon 0, 10, 30, and 60 min KCl stimulation. Orange lines denote the sense strand at promoters and the forward strand at enhancers. Green lines denote the anti-sense strand at promoters and the reverse strand at enhancers. d, e Pausing index (PI) profiles of four different gene groups based on their levels of NELF binding with all genes (d) and KCl-up/NELF-bound (144) or -unbound (108) enhancers (e). Each gene group is analyzed at four time points (0, 10, 30, and 60 min KCl). The PI is defined in Supplementary Fig. 11d. Statistical significance between cumulative probability graphs was determined by the Kolmogorov–Smirnov test. Source data for (b–e) are provided in a Source Data file.