Fig. 2

DRB/POLR2A ChIP-Seq measures RNAPII elongation rates across genes. a Examples of DRB/POLR2A ChIP-seq signals at two representative genes (NUP210 and USO1) at different time points following the release from DRB-induced inhibition of transcriptional elongation. Arrows indicate the front of the transcription wave. b DRB/POLR2A ChIP-seq metagene profiles for the genes longer than 80 kb (N = 2217). Arrows indicate the front of the calculated transcription wave. c Schematic representation of the regions amplified in the ChIP-qPCR. The wave front represents the region where RNAPII transcribes only in the condition without 5-Ph-IAA treatment. The upstream region represents the common interval where RNAPII transcribes with or without 5-Ph-IAA treatment. The downstream region represents the interval where RNAPII does not transcribe with or without 5-Ph-IAA treatment. d POLR2A ChIP-qPCR showing the RNAPII enrichment in different areas of example long genes in mAID-RBM22 cells with 5-Ph-IAA or without 5-Ph-IAA treatment. Values are mean ± SD (n = 4). The p values are determined using the two-tailed unpaired t-test (*p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001; ****p < 0.00001; ns, not significant). e Calculation of the RNAPII average elongation rates based on metagene profiles using linear regression for all the genes longer than 80 kb with high POLR2A ChIP-seq signals in control (2.13 kb/min) or RBM22 knockdown (1.39 kb/min) HepG2 cells. f Boxplot analysis of the RNAPII elongation rates for individual 415 genes with robust signal at all time points. g–h Boxplot analysis of the RBM22 ChIP-seq signals (g) and the elongation rate changes upon RBM22 knockdown (h) for the genes with different elongation rates in control cells. The 598 genes with computable elongation rates were divided into three groups based on elongation rate in control cells: low (rate < 1.87 kb/min), medium (1.87 kb/min < rate < 2.36 kb/min), and high (rate > 2.36 kb/min). The p values are determined using the two-tailed unpaired t-test (*p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001; ****p < 0.00001)