MethylCap^®-sequencing allows detection of genomic regions with different CpG density

Figure 1 shows elution patterns of the methylated CDH1 genomic region.
MethylCap assays were performed using DNA from NB4 cells and the MethylCap kit (Diagenode). Differential fractionation of double stranded DNA based on CpG methylation density was performed using increasing salt concentration during the elution steps. (A) qPCR results in a methylated (CDH1-CpG) region show the % of recovery of immunoprecipitated DNA compared to the input in the different fractions. (B) Sequencing of the elution fractions shows that the methylated CpG islands of CDH1 promoter are eluted in the medium and high elution fractions, confirming the qPCR results

MethylCap^®-sequencing (Illumina) confirms qPCR results

Figure 2 shows MethylCap^®-seq results for two different genomic regions.
Using MethylCap^®-seq, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to different elution fractions with increasing salt concentration. Methylated patterns of these two different regions were validated by bisulfite sequencing assay (B).