Fig. 2.

Genes in PMDs have lower transcript levels. (A) Differences in gene expression between genes in PMDs and HMDs in placenta. Transcript levels are shown as log (FPKM + 1). Only RNA-seq reads that mapped to known transcripts were used for FPKM analysis. (B) Average gene body methylation versus gene expression in placenta. Promoters and CpG islands were removed before computing the average gene body methylation. The histograms to the right show the expression distributions for genes with greater than (red) and less than (black) 70% average gene body methylation. (C) Genomic view of placental data on chromosome 7 showing low levels of transcription within PMDs. The RNA library was not poly-A–selected and reads were mapped to the entire genome using Bowtie.