In the Feb. 20 issue of the journal Nature Methods, team members from Johns Hopkins University, the Ontario Institute for Cancer Research and the University of Toronto detailed their promising new method of detecting the presence of an extra mark on DNA called cytosine methylation.
Cytosine is one of the four main genetic building blocks, or nucleotides, that make up DNA. Methylation simply refers to the presence of a biochemical (methyl) group attached to a nucleotide, in this case cytosine. This altered version of cytosine can affect the way important genes are switched on or off. Such genetic miscues can play havoc with healthy activity within cells.
Examining these marks is important to researchers who are trying to pin down methylation’s precise role in various health problems. But current methods of mapping methylation each have stubborn shortcomings, such as harsh handling of the DNA sample and the need to use particularly large and pre-treated tissue samples.
The new software described in Nature Methods is used with a commercially available nanopore sequencing device. The authors say this technique will directly characterize DNA methylation from smaller tissue samples. “We show that with careful analysis of nanopore sequencing data we can extract this extra layer of information,” said lead author Jared T. Simpson, a principal investigator in the Informatics and Bio-computing Program at the Ontario Institute for Cancer Research and an assistant professor of computer science at the University of Toronto.
Dr. Stegall’s Comments: The science behind methylation has increased in recent years, and in the alternative medicine community this has resulted in a greater awareness of methylation status. The marker measured is MTHFR, and mutations in MTHFR can have a wide range of negative effects in the body which impact the immune, cardiovascular, and gastrointestinal systems, to name a few. The gene sequencing program mentioned in this article is designed to evaluate methylation. While much still needs to be learned about methylation, identifying better ways of measuring methylation has the potential to greatly improve our overall health.