Figure 3.

KDM2A Binds to Nonmethylated CpG Islands

(A) A schematic of the imprinted Gnas gene, which has a CpG island (CGI) promoter (upper panel). KDM2A binds the Gnas CpG island as indicated by ChIP with a KDM2A-specific antibody followed by qPCR with promoter and body primer sets (lower panel). ChIP with an HA-specific antibody was used as a negative control. Data are from two biological replicates, and error bars represent SEM.

(B) The Gnas CpG island is methylated on the maternal allele and nonmethylated on the paternal allele (upper panel) with the bisulfite PCR amplicon indicated (BA). Bisulfite sequencing performed on ChIP input DNA (left panel) and KDM2A ChIP DNA (right panel) indicates that KDM2A preferentially binds the nonmethylated paternal allele. Empty and filled circles represent nonmethylated and methylated CpG dinucleotides, respectively.

(C) KDM2A binds to other CpG island promoters. A schematic of each gene is shown, and ChIP data are presented as in (A).

(D) KDM2A is not enriched at genes with non-CpG island promoters. ChIP data are presented as in (A).