Figure 3.

H3K4me3 Restoration Is Complete within 6 hr with Fastest Kinetics in Highly Expressed Promoters

(A) Outline of H3K4me3 qChOR-seq time course analysis. Cell cycle progression was monitored by FACS analysis of DNA content.

(B) Comparison of H3K4me3 nascent and mature qChOR-seq profiles.

(C) Boxplot of H3K4me3 qChOR-seq signal in replicated parental peaks subsetted into 25 bp non-overlapping windows.

(D) Average profiles of H3K4me3 qChOR-seq signal across 4 kb centered on replicated TSSs.

In (B)–(D), signal is quantitated using reference-adjusted reads per million (RRPM).

(E) Left: scheme of strategy used to parse H3K4me3-enriched regions by restoration kinetics. Regions were defined as R0, R1, R6, or R12 based on the time point at which R12 H3K4me3 levels were reached. Right: bar chart of the proportion of H3K4me3-enriched regions in each restoration category. Regions are defined as 500 bp non-overlapping windows in replicated parental peaks.

(F) Boxplot of ENCODE H3K4me3 signal in R1 and R6 regions. Signal is quantitated using reads per kilobase per million (RPKM).

(G) Boxplot of RNA-seq signal over genes associated with R1 and R6 promoters. RNA-seq data are from Mortazavi et al. (2008). Signal is quantitated using fragments per kilobase per million (FPKM).

(H) Boxplot showing the CpG densities of CpG islands overlapping R1 and R6 regions. CpG content data are from Illingworth et al. (2010).

See also Figure S3.