DNA methylation analysis of the CpG island identified across the BIM genomic locus. (A) The BIM genomic locus is represented by a schematic adapted from the UCSC genome browser (see supplemental Figure 3A), with regions analyzed in the separate assays (ChIP/MeDIP: regions 1-5; SEQUENOM: regions 1a-5a) indicated above the BIM gene, as well as the TSS (bold arrow), translation start site, and CpG island indicated. (B) MeDIP was carried out on 3 glucocorticoid-sensitive (ALL-3, -11, and -16) and 3 glucocorticoid-resistant (ALL-2, -10, -19) xenografts and enrichment for 5′-methyl-cytosine evaluated by qPCR across regions 1-5 indicated previously. (C) Bisulfite sequencing was carried out as described in “Bisulfite sequencing” to confirm MeDIP results for region 5. Open circles represent unmethylated sites, whereas closed circles represent methylated sites. At least 6 clones were sequenced for each xenograft. (D) SEQUENOM assays were carried out to measure methylation at individual CpG sites across BIM regions 1a-5a. Quantified methylation at each site is represented as a heat map ranging from white (0% methylation) to black (100% methylation). Xenografts are arranged vertically in decreasing order of Bim protein induced after treatment with dexamethasone (1μM, 16 hours).