Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome (original) (raw)
Figure 3
Trimethylated H3K4 is the signature chromatin mark at CGIs and is grossly proportional to CpG density.
(A, B) Sequence read profiles for H3K4me3 in ES cells (green) and CAP-seq in sperm (blue) are depicted for human chr17: 7,054,500–7,203,500 (A) and mouse chr10: 80,726,000–80,874,000 (B). (C) Bar plot indicating the percentage (displayed within each bar) of H3K4me3 positive CGIs in human (pink) and mouse (black). Categories of CGI position relative to genes are represented as for Figure 2E. (D) Box plots of H3K4me3 reads per base (averaged across 500 bp with a 100 bp slide) spanning 5 kb surrounding all mouse CGIs at the following CpG densities (CpGs per 100 bp): <5, 5–6, 6–7, 7–8, 8–9 and >9, in ascending order from the top. Box plots represent the distribution of the central 50% of the data (filled box) and the median (black bisecting line). The numbers of islands in each category (n) is noted in parenthesis. Figure S3 shows equivalent data for human CGIs. (E) Summary plot relating the CpG density of each bin to the mean H3K4me3 read value for the central 2 kb of regions displayed in (D). Plots illustrate the relationship for all CGIs (green) and orphan CGIs (blue).