Figure 3

CpG domains coexist with functional chromatin domains in mammalian rDNA. (A) CpG domains of mouse rDNA (GenBank acc. no. BK000964). Two repeats of the tandem rDNA array are shown on the scheme, and different DNA elements are colour coded and labelled as in Figure 1A. CpG dinucleotide frequency distribution is shown at 100-bp resolution. CpG domain transitions are shown enlarged. The threshold is set at 0.0625 (1:16=random distribution). (B) Scheme of the methylation-sensitive ChIP-chop assay. X, Y and Z indicate hypothetical proteins that bind DNA independent of DNA methylation, bind to unmethylated or methylated DNA, respectively. The expected outcome of the precipitation reactions is shown in the scheme. (C) Differential methylation of mouse rDNA domains. The rDNA ruler is labelled as in Figure 1A. Rectangles and letters A–D mark PCR amplicons for the methylation-sensitive ChIP analysis. HpaII cleavage sites are labelled with H. Circle diagrams aid visualization of unmethylated/methylated DNA ratio in different ChIP samples.