GC skew defines distinct RNA polymerase pause sites in CpG island promoters

Predominant Pol II pausing class is conserved across cell types. (A) Heatmap representation of the GRO-seq sense tag density from MCF10A and IMR90 cells. CGI promoters are oriented to transcription and sorted within each class by the distance from the TSS to the downstream CGI edge using the same sort order as Figure 1C. (B) Pol II (S5 phosphorylated) ChIP-seq tag density from CD4+ T cells oriented and sorted as in Figure 1C. (C) Average tag densities of nascent transcripts (GRO-seq sense) and phospho-S5-Pol II for promoters in the three pausing classes shown in A and B. CGI-associated promoters were oriented to transcription and the distance from the TSS to the upstream and downstream CGI edge independently scaled and anchored to the TSS (arrow). The average tags per 20-bp bin for 800 bp to either side of the CGI (unscaled) are included.