Figure 2

Demethylation of the genome by 5-aza-CdR predominantly targets euchromatin. A self-organizing map (SOM) analysis shows clear partitioning of the human genome into distinct compartments, represented by the U matrix of panel (a). This depiction shows increased levels of gray for nodes within the SOM where there is dissimilarity between adjacent nodes in terms of genomic characteristics, illustrating the structure of the partitioning of the information contained within the SOM. In panel (b) we see that the left partition includes the co-localization (yellow) of the highest quantiles of DNA methylation (green) and of gene expression (red), loci we previously showed to represent the euchromatic compartment of the genome [14]. When we overlay the loci with the greatest changes in DNA methylation resulting from the 1.0 μM 5-aza-CdR exposure (red), we see enrichment at the euchromatic compartment represented by the loci with the highest DNA methylation levels (panel (c), green) or gene expression levels (panel (d), green). 5-aza-CdR, 5-aza-2′-deoxycytidine.