Fig. 4.

Polycomb-regulated regions have unique methylation patterns in PMDs and HMDs. (A and B) DNA methylation within the polycomb-regulated DLX5/6 (A) and MSX1 (B) loci for six different tissues. The RNA-seq track is from the non-poly-A selected placental library with reads mapped to the entire genome using Bowtie. RING1B and EZH2 ChIP-seq data tracks are from Ku et al. (25). The hidden Markov model analysis showed entirely within a placental HMD (A) and entirely within a placental PMD (B). (C) Comparison of placenta methylation levels in nonpolycomb HMDs (NH), polycomb HMDs (PH), nonpolycomb PMDs (NP), and polycomb PMDs (PP). For each group, CpG islands were removed before assessing average percent methylation. For nonpolycomb regions, genomic DNA was divided into ≤100-kb subregions for better comparison with polycomb regions. (D) Comparison of non-CpG island methylation levels within polycomb regions between six different tissues. Placenta (red) is distinct from other tissues in methylation of polycomb-regulated regions. (E) Distribution of the lengths of polycomb-regulated regions and PMDs.