Evolution and Diversity of DNA Methylation in Eukaryotes

DNA methylation (DNAm) is an important and well characterized epigenetic process which regulates gene expression, plays a vital role in embryonic development, genomic imprinting, silencing of transposons and tissue specific expression. The present chapter discusses evolution of DNA methyltranferases and compares DNA methylation patterns across eukaryotes with focus on fungi, plants, and animals. DNAm evolution traces back to prokaryotes. Prokaryotes primarily use DNA methylation as genome defense mechanism composed of restriction-modification systems. In mammals, DNAm occurs exclusively at fifth carbon of the cytosine residue (5mC) with the cytosines on both strands being usually methylated, whereas, in plants and fungi, both CpG and CHG or CHH (where H correspond to A, T or C) methylation is documented. DNAm process is conserved in the five kingdoms of life: bacterias, protists, fungi, plants, and animals, however, Schizosaccharomyces pombe and Caenorhabditis elegans lack 5mC, but latter shows presence of adenine N6-methylation (6 mA). Drosophila melanogaster and Saccharomyces cerevisiae, exhibits very low levels of DNAm. DNAm also plays a pivotal role in driving adaptive evolution due to the accumulation of mutations at the methylated CpG sites. The dynamic nature of DNAm is further linked to genetic diversification. In addition, DNAm aberrations are associated with human diseases such as reduction in methylation levels have been observed in human cancers. The ongoing research is gradually unearthing how the genome, environmental factors and disease, shape and modify the methylome and hence eukaryotic phenotype.