One method cells use to modulate the level of a gene's expression is chemically attaching a methyl group (-CH3) to cytosine residues in the DNA of a gene or in the regulatory regions surrounding it. Cytosine methylation has been correlated with diminished gene expression, but it has also been observed in actively transcribed genes. Most of our data about cytosine methylation has come from only four species: humans, mice, one plant, and one fungus. Thus, its global significance has been difficult to determine.

A recent study in Science Express aimed to reveal the evolutionary history of DNA methylation by analyzing it in seventeen eukaryotic genomes: five plants (rice, two land plants, and two green algae); seven animals (puffer fish and six invertebrate species); and five fungi. The authors found that methylation within the body of a gene is conserved between plants and animals, but methylation of mobile genetic parasites called transposons is not.

Transposons are pieces of DNA that can jump around within a genome—wreaking havoc if they jump into the wrong spot and disrupt an important gene. Transposons were methylated in the plants and puffer fish, which will inactivate them and keep them from jumping. Transposons were not, however, methylated in the invertebrates. The authors conclude that the methylation of transposons evolved independently in plants and vertebrates. Transposons can interfere with the recombination that takes place between chromosomes during sexual reproduction; as fungi and unicellular animals often reproduce asexually, it is not as useful for them to suppress transposons.

But methylation for the regulation of gene transcription was used far more widely, indicating that it is ancient. It predates the divergence of plants and animals, which occurred roughly 1.6 billion years ago. These researchers did not try to explain the methylation of actively transcribed genes that has been found in mammals, plants, and one fungus. Apparently that story will have to wait for another day.

Science Express, 2010. DOI: 10.1126/science.1186366 (About DOIs).