Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Might remove acetyl residues only from specific targets, such as rDNA repeats or complex transgenes. Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Required for rRNA gene silencing in nucleolar dominance. Plays a role in transgene silencing, but this effect seems to bee independent of the histone deacetylase activity (PubMed:11340181, PubMed:12486004, PubMed:15037732, PubMed:16648464). Part of the AS1 repressor complex to regulate the KNOX expression in leaf development (PubMed:23271976). Binds to KNAT1, KNAT2, and KNATM chromatin (PubMed:23271976). Involved in the regulation of flowering time (PubMed:21398257, PubMed:25922987). Forms a histone deacetylase complex with HDA5, FLD and MSI4/FVE that represses FLC gene expression to control flowering time (PubMed:21398257, PubMed:25922987). H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl-[histone] Binds 1 zinc ion per subunit. Inhibited by trichostatin A. Interacts with Coi1, which functions in an SCF complex that recruits regulators for ubiquitination (PubMed:12445118). Interacts with AHL22 (PubMed:12445118, PubMed:22442143). Interacts with AS1 (PubMed:23271976). Part of the AS1 repressor complex composed of AS1, LBD6/AS2 and HDA6 (PubMed:23271976). Binds to EBS and SHL (PubMed:25281686). Interacts with MBD6 (PubMed:28229965). Interacts with HDA5 (PubMed:25922987). Interacts with FLD (PubMed:21398257). Not detected in leaves, stems, flowers and young siliques. By jasmonic acid and ethylene. Curling and serrated leaves. Down curling phenotype on both the distal and lateral axis. HDA6 mutations induce high acetylation of histone H4, increased methylation of histone H3 'Lys-4' and hypomethylation of DNA at particular loci, such as the rDNA repeats. Belongs to the histone deacetylase family. HD type 1 subfamily.