SU(VAR)3-9 proteins are key regulators of heterochromatin structure and function in plants, mammals, Drosophila, and yeast. In contrast to animals and fungi, plants contain numerous Su(var)3-9 homologues (SUVH), the members of which form a discrete subfamily. The SU(VAR)3-9 and SUVH proteins associate with heterochromatin and possess histone methyltransferase activity, indicating that they participate in the organization of transcriptionally repressive chromatin. The Arabidopsis thaliana genome contains 10 SUVH genes, belonging to four phylogenetically distinct subgroups: SUVH1, SUVH2, SUVH4, and SUVH5. The structure and expression of SUVH3, a member of the SUVH1 subgroup was investigated. SUVH3 was shown to be broadly expressed during plant development with the highest levels found in proliferating cells. The encoded protein localized in subnuclear foci and remained associated with condensed chromosomes throughout mitosis. A deletion analysis of the SUVH3 upstream region further revealed that an intron located in the 5′ UTR is a key regulator of strong and constitutive SUVH3 expression. © The Author [2006]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved.