Add 1 part enriched methylated DNA to 2 parts sequencing lanes, and you have a cocktail that delivers key insights without a data hangover. Last week, a team of Ohio scientists added the latest research recipe that is destined to become a lab fav in Nucleic Acids Research. The crew took the benefits of methylation binding protein (MBD) isolation of methylated DNA and combined it with the muscle of advanced sequencing to create MBD-isolated Genome Sequencing (or MiGS for the acronym enthusiasts). MiGS puts the MDB2 protein to work on enriching methylated DNA for downstream deep sequencing.
The researchers validated the MiGS approach by running three cell-lines, HCT116 (intermediate methylation), plus 2 variants, DICER-EX5 (high methylation) and DKO (low methylation). They found MiGS accurately identified highly methylated genomic loci, and could map DNAm distribution across the genome, as expected.
By digging into the data a little further, they noticed that around 90% of DNAm occurs outside of promoter regions, and determined that a significant portion of that mapped to CTCF binding sites or miRNA coding sequences, pointing out a likely functional role for all of that non-promoter methylation that other methods might have missed.
After all of the test runs the team found that MiGS had some nice advantages over more traditional DNAm profiling methods:
- You can get nearly complete coverage of a genome using two sequencing lanes; bisulfite sequencing requires over 100…so it’s faster, cheaper, and you can run multiple samples.
- There is no context, sequence or probe bias as found with array-based protocols.
- There is higher specificity than with enzymatic digestions or 5-MeC antibody methods, reducing background and false positive / negative results.
The authors did note that MiGS doesn’t have the single base resolution of bisulfite sequencing so you’ll want to hold on to those bisulfite conversion kits if that’s what you need. MiGS might even help you focus your bisulfite sequencing efforts on key regions of interest.
Get all of the MiGS details in Nucleic Acids Research, November 2009.