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SUV39H1 is one of two homologues of the Drosophila Supressor-of-variegation 3(9) protein (aka Su(var)3-9). SUV39H1 is a SET domain-containing histone methyltransferase specific for lysine 9 of histone H3. Lysine 9 methylation of histone H3 is found at regions of the genome that are transcriptionally silenced, such as centromeres, repetitive elements and inactive genes. H3 lysine 9 methylation is a hallmark of heterochromatin, regions of the genome that are in a tightly compacted state and relatively devoid of gene expression. HP1 proteins recognize and bind lysine 9 methylation and this contributes to maintaining heterochromatin in its compact and inactive state. SUV39H1 also contains a chromodomain, which may bind to lysine 9 methylation and contribute to the regional spreading of lysine 9 methylation and the establishment of heterochromatin over broader domains of the genome.