Analysis of CpG methylation in human hematopoietic cell lines and in leukemic blood samples using sequencing of bisulfite-treated genomic DNA. The region of DNA analyzed with this technique was from the 5′ CpG-rich region of the Epha3 gene, which normally contains 22 individual CpG sites. (A) The methylation status of each CpG site. The positions of these 22 CpG sites are numbered relative to the TIS. (B) The proportion of CpG sites found methylated, unmethylated, or partially methylated. Methylated cytosines (black) remain unchanged with bisulfite treatment of genomic DNA, whereas unmethylated cytosines (white) are converted to uracil and then amplified as thymic. Some sequences showed both cytosine and thymine nucleotides present in the one position (gray), suggesting that these cytosines were partially methylated. EphA3 expression by FCA is shown as being either strongly positive (++), weakly positive (+/−), or negative (−). LK63, HSB-2, Raji, and Nalm-1 are all hematopoietic cell lines. Other samples were taken from patients with pre-B or T-ALL leukemias.