Evolution of DNA-methylation machinery: DNA methyltransferases and methyl-DNA binding proteins in the amphioxus Branchiostoma floridae

DNA methylation is an epigenetic mark associated with gene regulation and cell memory, silencing of transposable elements, genomic imprinting, and repression of spurious transcription of duplicated sequences. These roles have varied widely during animal evolution and current functions depend on the specific methylation pattern of the species under consideration. The patterns of methylation are established, maintained, and translated into appropriate functional states by the DNA-methylation machinery, which includes three groups of methyltransferase enzymes, Dnmt1, Dnmt2 and Dnmt3, and five methyl-DNA binding proteins, Mbd1, Mbd2, Mbd3, Mbd4, and MeCP2. In this study, I have identified the members of the Dnmt and the Mbd gene families in the cephalochordate amphioxus (Branchiostoma floridae), the most basal extant chordate and one of the closest sister groups of vertebrates. Database searches, phylogenetic studies and protein domain analyses revealed the presence of the three major groups of Dnmt enzymes in the cephalochordate genome, whereas only two Mbd members, Mbd2/3 and Mbd4, were found. Analysis of the amphioxus methylation machinery suggested that the complexity and the structural organization of cephalochordate methyltransferases do not differ substantially from those of current vertebrate enzymes, while new Mbd proteins arose in vertebrates, which perhaps minimized certain collateral effects associated with the major genomic changes that occurred during the invertebrate-vertebrate transition.