Fig. 1: Pol II promoter–proximal pausing in resting BMDM is marked by NELF co-localization.

a Heat map of Pol II ChIP-seq signals around the TSS regions for BMDM-expressed highly paused (group 1), moderately paused (group 2), and non-paused (group 3) genes. Each row indicates one gene. In each group, the rows were sorted by the decreasing Pol II ChIP-seq signal in TSS region. b Average Pol II ChIP-seq signals around TSS regions of group 1 (brown), group 2 (red), and group 3 (gray) genes, as indicated. c Pie graph shows the percentage of BMDM-expressed genes in each group. d Heat map of PRO-seq signals (sense strand) around the TSS regions for three groups of genes classified based on PRO-seq defined PI. Each row indicates one gene. In each group, the rows were sorted as in (a). e Average PRO-seq signals (sense strand) around TSS regions of group 1–3 genes from (d). f, g Heat maps for CDK9 (f) and NELF-E (g) ChIP-seq signals around the TSS regions for three groups of genes. In each group, the rows were sorted as in (a). h The genomic distribution of NELF-E ChIP-seq peaks. TSS and gene body regions were defined as shown in Supplementary Fig. 1a. i Average NELF-E ChIP-seq signals around TSS of group 1–3 genes, as indicated. j NELF-E ChIP-seq reads quantified in −250 to +250 bp region (boxed in (i)) are shown as box-plots for group 1–3 genes, as indicated. Boxes outline the data from first quartile to third quartile, and bars indicate the boundary whose distribution does not exceed 1.5-fold of interquartile range extended from both first quartile and third quartile. p Values (group 1/group 2P < 2.2e⁻¹⁶, group 1/group 3P < 2.2e⁻¹⁶, group 2/group 3P < 2.2e⁻¹⁶) were calculated by two-sided Mann–Whitney U test. k The percentage of group 1–3 genes in NELF⁺ BMDM-expressed genes. l Tracks of Pol II ChIP-seq, PRO-seq (sense strand), and NELF-E ChIP-seq are shown for Tnf and Jun group 1 genes.