RNAPII transcription elongation rates are variable among and within genes. (A) Histogram showing the distribution of RNAPII elongation rates for 3009 genes estimated in U2OS cells using DRB/TTchem-seq2. Only genes with linear regression adjusted R2 ≥0.95 are included. (B) Violin plots comparing the distributions of the RNAPII elongation rates between protein-coding and lncRNA genes. Gene samples were matched in number for fair comparison (n = 300 in each group). (C) Correlation between RNAPII elongation rates and gene lengths. Genes are colored based on their biotypes. Only genes with linear regression adjusted R2 ≥0.975 are shown. (D) Correlation between RNAPII elongation rates and GC content of genomic sequences. GC content was calculated as the ratio of the number of G and C nucleotides to the total number of nucleotides per gene, based on the union of all transcripts. (E) Correlation between RNAPII elongation rates and mean read coverage in log scale of the DRB/TTchem-seq2 data. (F) Violin plots showing distances traveled by RNAPII during different time intervals after release from promoter-proximal pausing sites. Data included 1339 genes (see Methods). Wilcoxon rank-sum tests were used between each pair of samples. (***) P-value <1×10−6. (G) Distribution of RNAPII elongation rates for 1185 single genes in wild-type (WT) and ELOF1 knockout (KO) HCT116 cells. Rates were calculated using the DRB/TTchem-seq2 computational pipeline. Raw data from Geijer et al. (2021). (H) Distribution of RNAPII elongation rates for 1026 individual genes in both control and heat shock (HS) conditions in MRC5-VA cells. Rates were calculated using the DRB/TTchem-seq2 computational pipeline for data from Cugusi et al. (2022).
