Figure 5

RNA polymerase II is located at a subset of transcriptionally active, methylated LCG promoters. When we study the LCG and HCG promoters defined by RNAPII-Ser5 (P) from Figure 4, we find that while HCG promoters are relatively uniformly less methylated (greater HELP-tagging signal, panel (a), orange), the LCG promoters have what appears to be a bimodal distribution, with a substantial proportion showing higher DNA methylation (lower HELP-tagging signal, blue). By taking the group of promoters below the red dashed line (a) and comparing their expression (panel (b), blue) with the genome-wide pattern (gray), we see that the genes associated with these promoters are comparably active to those throughout the genome as a whole (density plot of FPKM values). LCG, low-CG dinucleotide observed/expected ratio; HCG, high-CG dinucleotide observed/expected ratio; RNAPII-Ser5 (P), serine 5-phosphorylated RNA polymerase II; FPKM, fragments per kilobase per million reads.