Illustration of the genomic organization (A), methylation, and deamination (B) of CpG sites within Alu. The 17 CpG sites are marked with the capital letters (A-Q) above the Alu consensus sequence (Ref. ) and highlighted in the colour pink. The arrowed-line point to the recognition sequence (including the sites H and J) of restriction enzyme Cac8I; Rectangles, primer matching sequences; The arrowed-boxes, primer F-1, F-2, and R-1 were used to amplify the bisulfite-converted templates, and F-w and R-w were used to amplify the templates without bisulfite treatment. The primer F-2 and R-1 were the same as described (Ref. ). The sites A-B-C were included within the probe sequence of MethyLight (Ref. ). The sites H-I-J were the target CpGs in pyrosequencing assay and the site P was the target CpG in MboI-COBRA (Ref. ). The site M was the target CpG used for quantification of unmethylated Alu (Ref. ). The capital letter T in the colour pink was resulted from evolutionary deamination of cytosine. The underlined CpG and TpA represent the methylated CpG site and antisense-deaminated CpG site, respectively.
Xiang et al. BMC Cancer 2010 10:44 doi:10.1186/1471-2407-10-44