Ligation-mediated PCR-based in vivo genomic DNA footprinting of the vitamin K–dependent carboxylase gene promoter in H4IIEC3 cells. Guanine methylation patterns in the sense strand of the gene (lanes 1 and 2). Guanine methylation patterns of the antisense strand of the gene (lanes 3 and 4). In vivo methylation patterns of genomic DNA (lanes 1 and 3, left side of each pair of lanes) are compared with in vitro methylation patterns (lanes 2 and 4, right side of each pair of lanes). Relative hypomethylation of guanines in vivo is indicated with a solid dot (•). Relative hypermethylation of guanines in vivo is indicated with a plus sign (+). The nucleotide number is indicated on the left of each footprint. The start site of transcription at + 1 is indicated with an arrow. Vertical lines indicate sequences in the region of the 12-bp upstream promoter element.