Biology of methylation. (A) Methylation state of CpG probed in both forward and reverse strand amplicons (read depth ≥ 100; no mismatches; n = 433) indicates methylation at CpG is symmetric across DNA strands. (B) Methylation of CpG islands (CGI) is homogeneous and predictive of expression. In promoters containing an annotated CGI where ≥20 CpG were assayed (open diamonds; n = 24), methylation of CpG in the CGI was either near 100% or near 0%; furthermore, methylated CGI indicated low or no expression, while genes with unmethylated promoter CGI were expressed over a broad dynamic range. For genes with no annotated CGI (n = 23), methylation of all CpG across the 2-kb promoter region showed no strong correlation with expression.
