The pausing index changes during terminal maturation and is associated with transcriptional repression. (A) Pausing index in day 7 and day 10 cells, as determined by Ser5 Pol II ChIP-seq. Similar results were obtained with Ser5 and Ser2 cut and tag (supplemental Figure 11). ** P < 2.2e-16. (B) Percent of genes with pausing index >4 in day 7 and day 10 cells, determined by analyses of Ser5 Pol II ChIP-seq. (C) Pausing index at upregulated and downregulated genes at day 7 and day 10, determined by analyses of Ser5 Pol II ChIP-seq. (D) Pathway analyses of downregulated genes with pausing index >4. (E) Quadrant plots showing the change in Ser 2 Sol II and Ser 5 Pol II occupancy at the promoter and gene body as cells mature from day 7 to day 10. The plots show genes that have a pausing index >4 in day 7 cells, with Ser5 Pol II (i) and Ser2 Pol II (ii). (F) Changes in Ser2 Pol II and Ser5 Pol II occupancy at the RPS7 locus, which has a PI >4 at day 7, during erythroid maturation. Black arrow denotes the promoter. (G) Quadrant plots showing the change in Ser2 and Ser5 Pol II occupancy at the promoter and gene body for all genes during maturation, with the location of erythroid specific genes highlighted. (H) Changes in Ser2 Pol II and Ser 5 Pol II occupancy at the GYPA locus, which is a highly expressed gene during erythroid maturation, and maintains high levels of Ser2 Pol II and Ser5 Pol II. Black arrow denotes the promoter. **P < 0.2.2e-16.