The PTEN CpG island and locations of the regions assayed for methylation in this study. The PTEN CpG island (green bar) encompasses a bidirectional promoter from which the KLLN (blue bar) and PTEN (brown bar) genes are transcribed from the same transcription start site. The PTEN gene is transcribed from the positive strand whereas the KLLN gene is transcribed from the negative strand in the opposite direction. The black bars indicate the regions analysed for methylation using bisulphite based PCR assays (see Table 1 for assays, exact position of amplicons and primer sequences). The red vertical lines within the black bars indicate restriction endonuclease sites used to assay for methylation by COBRA. Indicated by the thin black vertical lines are the locations of CG dinucleotides. Also indicated is a region of the PTEN CpG island encompassing 921 bp which shows 91% sequence identity with the 5' region of the PTENP1 pseudogene located at 9p13.3. * For region 5, primers were taken from Bennett et al. . These primers bind sequence that are identical in both the PTEN and PTENP1 genes producing 283 bp and 291 bp amplicons respectively and the HpyCH4IV restriction site used assay for methylation using COBRA is conserved.
Hesson et al. Biological Procedures Online 2012 14:5 doi:10.1186/1480-9222-14-5