Fig. 3: Aberrant gene body Pol II accumulation is associated with more highly paused genes.

a For each RNAi condition, the PRO-seq (non-shrunken) log2 fold-changes within early gene bodies (300–1300 bp from the TSS) following FP are plotted (y-axes) against the DMSO PRO-seq signals either (left panels) within those same early gene body regions, or (right) within the pause regions (0–100 bp from TSS) immediately upstream. Filtered genes >1.6 kb are plotted (n = 1243). Linear regression lines (red) are shown with 95% confidence intervals. b For the same genes as panel a, 3-dimensional MA plot showing the relationship between pause region and gene body PRO-seq densities in DMSO conditions (x and y axes) and the log2 fold-change in NELF RNAi +FP vs. LacZ RNAi +FP (tile color). To avoid overplotting, genes are grouped into 2D bins (x and y axes) and tile colors show the mean shrunken log2 fold change for each group of genes. c Metagene profiles of gene body PRO-seq (bootstrapped mean + 50% confidence interval) divided into quartiles according to pause region (0–100 bp from TSS) PRO-seq signal. Genes from panels a-b were further subset to obtain a set of genes that represent a wide-range of pausing levels while having roughly similar Pol II densities within the early gene body region (n = 492, Supplementary Fig. 4c, d).