Figure 2.

Loss and gain of DNA methylation in Hells^−/− MEFs. (A) Scatter plots comparing average DNA methylation values (log₂ MAP/input) from replicate microarrays for all 1-kb promoter regions (left) and 1-kb upstream regions (right) in wild-type (y-axis) versus Hells^−/− MEFs (x-axis). The red spots indicate sequences showing more than twofold reduction ([log₂ MAP/input WT] − [log₂ MAP/input Hells^−/−] ≥ 1) of DNA methylation in Hells^−/− MEFs. The blue spots are sequences showing more than twofold gain ([log₂ MAP/input Hells^−/−] − [log₂ MAP/input WT] ≥ 1) of DNA methylation in Hells^−/− MEFs. “n” indicates the number of promoters/upstream regions displaying loss or gain of DNA methylation. “ρ” is the Spearman correlation coefficient. (B) Methylated promoters in wild-type and Hells^−/− MEFs divided to low (LCP), intermediate (ICP), and high CpG density (HCP) promoters. The numbers and percentage of promoters in each class are indicated. (C,D) Loss of DNA methylation in Hells^−/− MEFs at single genes (C) and clusters of neighboring genes (D). The gray boxes represent tiled 2.5-kb regions. The transcripts originating from these regions are shown above the gray boxes; TSSs are indicated by arrows. The scale represents log₂ MAP/input values. The distances between individual promoters are shown in kilobytes. (E) Gain of DNA methylation at Dbt promoter on chromosome 3 in Hells^−/− MEFs. (F) A histogram showing the number of LSH-dependent clusters and number of genes per cluster. (G) A heath map comparison of DNA methylation patterns between wild-type ES cells, wild-type MEFs, and Hells^−/− MEFs. The three groups of LSH-dependent hypo- and hypermethylated promoters are indicated together with the most significant representative biological functions of the genes in each group (Gene Ontology, P < 0.0001).