Figure 4.

DNA methylation is specifically associated with PTENP1 and not the PTEN CpG island. A, Representative sequencing data of region 6 from the haematological and colorectal cancer cell lines Raji and RKO. Only PTENP1 derived alleles showed DNA methylation. Each line represents a single allele. Circles indicate the positions of CpG dinucleotides; black circles indicate methylated CpG dinucleotides; white circles indicate unmethylated CpG dinucleotides; yellow diamonds indicate the positions of nucleotide variations within PTENP1 alleles used to discriminate between PTEN and PTENP1 alleles. B, Representative electropherograms from region 6 showing an unmethylated PTEN allele and a methylated PTENP1 allele from the colorectal cancer cell line RKO. Indicated by the black arrow is the position of a variant nucleotide which was used to discriminate between PTEN and PTENP1 alleles (the same nucleotide indicated by the black arrow in Figure 3B). CpG dinucleotides are boxed in red. C, Allelic bisulphite sequencing of region 5 in the cancer cell lines Raji and RKO. Again, only PTENP1 derived alleles showed methylation. Sequence variations used to discriminate between PTEN and PTENP1 alleles are indicated by yellow diamonds. Black diamonds indicate the positions of additional CpG dinucleotides specific to PTENP1 alleles that were also methylated. D, Representative electropherograms from region 5 showing an unmethylated PTEN allele and a methylated PTENP1 allele from the cell line Raji. Indicated by the black arrow is the position of a nucleotide variation used to discriminate the PTEN and PTENP1 alleles.