A plant cytosine methyltransferase cDNA was isolated using degenerate 
oligonucleotides, based on homology between prokaryote and mouse 
methyltransferases, and PCR to amplify a short fragment of a methyltransferase 
gene. A fragment of the predicted size was amplified from genomic DNA from 
Arabidopsis thaliana. Overlapping cDNA clones, some with homology to the PCR 
amplified fragment, were identified and sequenced. The assembled nucleic acid 
sequence is 4720 bp and encodes a protein of 1534 amino acids which has 
significant homology to prokaryote and mammalian cytosine methyltransferases. 
Like mammalian methylases, this enzyme has a C terminal methyltransferase domain 
linked to a second larger domain. The Arabidopsis methylase has eight of the ten 
conserved sequence motifs found in prokaryote cytosine-5 methyltransferases and 
shows 50% homology to the murine enzyme in the methyltransferase domain. The 
amino terminal domain is only 24% homologous to the murine enzyme and lacks the 
zinc binding region that has been found in methyltransferases from both mouse 
and man. In contrast to mouse where a single methyltransferase gene has been 
identified, a small multigene family with homology to the region amplified in 
PCR has been identified in Arabidopsis thaliana.