Eukaryotic Methyl-CpG-Binding Domain Proteins and Chromatin Modification

Gene regulation in eukaryotic cells is in part mediated through programs of chromatin methylation. On the DNA level, the presence of m5C, mostly at the CpG positions in the vertebrate genomes, allows the recruitment of multisubunit complex(es) consisting of the histone deacetylases and the so-called methyl-CpG-binding domain (MBD) proteins (2). These proteins each contain the MBD motif. Previously, a group of MBD proteins conserved in vertebrates have been identified, and they include MBD1, MBD2, MBD3, MBD4, and MeCP2 (15). In Drosophila melanogaster, an MBD protein, dMBD2/3, has been characterized that shares significant ho- mology with the vertebrate MBD2 and MBD3 (30, 39). On the other hand, methylation of the histones, in particular at Lys-9 of H3, also plays essential role in the modification of the chromatin structure (20, 42). The Pre-SET and SET do- mains within a group of histone methyltransferases are respon- sible for their intrinsic activities of Lys methylation (18). In- terestingly, genetic evidence from studies of Neurospora spp. suggests that DNA cytosine methylation is downstream of the H3 methylation (37). Consistent with this, an Arabidopsis CpNpG DNA methyltransferase (CMT3) was shown to inter- act with the H3 Lys-9-binding protein, HP1, and thus provides a physical link between the sequential events of histone and DNA methylation in the plants (17). A similar event has re- cently been suggested to exist in the mammals (11). An MBD motif has been located in the human histone H3K9 methylase SETDB1 (34). This implies that DNA methylation might also be located upstream of histone methylation. The following questions could be asked. How many eukaryotic MBD proteins also contain motifs required for histone modi- fication, in particular the H3K9 methylation? How widespread are these proteins in different species? When the conserved MBD motif was used as the bait for search (1), a total of eleven, three, five, two, and twelve MBD-containing genes were found to exist in the genomes of humans, tunicates (Ciona intestinalis), D. melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana, respectively. The same number of MBD proteins as in humans is found in the mouse genome, each representing the respective human ortholog (32). In con- trast, none could be identified in the Archaea, protozoa, and fungus genomes (Table 1). Archaea has been placed as a dis- tinct domain from the bacteria and eukaryotes in evolution, with their metabolic features closer to bacteria and informa- tion processing machinery closer to the eukaryotes (4). Quite a few Archaea species have been fully sequenced. Although pu- tative methyltransferases have been proposed in Methanococ-