Heterogeneity in the methylation status of genomic DNA fragments demonstrating similar elution profiles in methyl-CpG binding domain column chromatography

Methyl-CpG binding domain column chromatography enables the separation of DNA fragments on the basis of the number of methylated CpG sites within the fragment. However, the exact elution profile of a specific DNA fragment is unpredictable. In order to address this problem, we have investigated the methylation status of genomic DNA fragments having similar elution profiles. We found that genomic DNA fragments that had high affinity to the column included those with high-density methylation, moderate methylation, and monoallelic methylation. Some DNA fragments associated with both bona fide CpG islands, which are methylation-free, and methylated Alu repeated sequence had high affinity to the column. These results suggest that methylation status of DNA fragments having high affinity to the column is heterogeneous and caution is required for the interpretation of the results.