Probably mediates the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Required for histone H3 'Lys-9' deacetylation. Involved in rRNA gene silencing in nucleolar dominance. Seems to be implicated in the regulation of genes involved in seeds development. Interacts with DNMT2 (PubMed:20331964). Interacts with DEK3 (PubMed:25387881). A number of isoforms are produced. According to EST sequences. Expressed in leaves, roots, stems, young plantlets, flowers and siliques. Highest levels in ovules, embryos, shoot apical meristems and first leaves. Also expressed in somatic embryos. Loss-of-function mutant (antisense inhibition) induces increased methylation of histone H3 'Lys-4' and hypomethylation of DNA at rDNA repeats. Belongs to the histone deacetylase HD2 family.