Histone methyltransferase that converts monomethylated 'Lys-9' of histone H3 (H3K9me1) to dimethylated 'Lys-9' (H3K9me2) in the absence of bound ubiquitin, and to trimethylated 'Lys-9' (H3K9me3) in the presence of bound ubiquitin. Acts in a locus-specific manner and contributes to the transcriptional silencing of pseudogenes and transposons. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. N(6)-methyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = H(+) + N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-homocysteine N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-homocysteine Interacts with ubiquitin. Associates with euchromatic regions. A number of isoforms are produced. According to EST sequences. 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.