a, Pearson correlation coefficient of mCG methylation density (y-axis) between H1 and IMR90 at various genomic features. Regions were divided in 20 equally sized bins from 5' to 3'. Pearson correlation was determined in each bin considering all the H1 and IMR90 occurrences of the given genomic region. b, DNA methylation, mRNA, and histone modifications in H1 and IMR90 associated with a PMD. Vertical lines above and below the dotted central line in DNA methylation tracks indicate methylcytosines on the Watson and Crick strands, respectively. Line vertical height indicates the methylation level. The H1 > IMR90 mC track indicates methylcytosines significantly more methylated in H1 than IMR90 at a 5% FDR (FET). Vertical bars in the mRNA and histone modification tracks represent sequence tag enrichment. A yellow box indicates any gene with ≥30 fold higher mRNA abundance in H1 than IMR90. c, Comparison of transcript abundance between H1 and IMR90 of genes with a transcriptional start site located in or within 10 kb of a PMD. Black dots indicate all genes in the genome; blue, red and green indicate PMD genes expressed ≥3-fold higher in H1, IMR90 or not differentially expressed, respectively. d Mean gene body mCG methylation (at least 10 reads required) as a function of the gene expression rank, 1 being the most expressed. Abbreviations: mC, methylcytosine. PMD, partially methylated domain.