Phenotypic diversity and epigenomic variation – The utility of mass spectrometric analysis of DNA methylation

Epigenomic variation may underlie phenotypic diversity that is not attributable to differences in genomic sequence. Such processes provide an organism the flexibility to respond to changing environmental cues within its lifetime, and perhaps its offspring's lifetime, and would therefore be expected to confer a selective advantage in evolutionary terms. Analysis of epigenomic variation within a population may be both a useful measure of developmental exposures and an indicator of future phenotype. A key molecular indicator of epigenomic variation in organisms is the chemical modification of DNA by methylation at specific nucleotide residues in the genome. Here we discuss how mass spectrometry can be utilised to provide quantitative analysis of DNA methylation patterns across populations. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.

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► We provide a broad conceptual framework for modern epigenetic thinking.
► We discuss the role of MALDI-TOF MS in the analysis of key epigenetic markers, namely DNA methylation.
► We outline the benefits and practical considerations for the use of MALDI-TOF in this context.