Histone methyltransferase. Methylates in vitro both 'Lys-9' and 'Lys-27' of histone H3. Required for in vivo dimethylation of 'Lys-9'. H3 'Lys-9' methylation represents a specific tag for epigenetic control for plant development and transcriptional repression. N(6)-methyl-L-lysyl(27)-[histone H3] + S-adenosyl-L-methionine = H(+) + N(6),N(6)-dimethyl-L-lysyl(27)-[histone H3] + S-adenosyl-L-homocysteine L-lysyl(9)-[histone H3] + 2 S-adenosyl-L-methionine = 2 H(+) + N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + 2 S-adenosyl-L-homocysteine L-lysyl(27)-[histone H3] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl(27)-[histone H3] + S-adenosyl-L-homocysteine Interacts with LHP1. Associated with chromatin. Expressed in roots, stems, leaves and flowers. The SET domain is required for methyltransferase activity and ectopic effect on plant growth. In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster. Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.