HDAC9 (Histone Deacetylase 9) catalyses the deacetylation of lysine residues on the core histones (H2A, H2B, H3 and H4). It belongs to the Class IIa HDAC family, which are key regulators of several developmental and differentiation processes such as cardiac growth. HDAC9 represses MEF2 (myocyte enhancer factor 2)-dependent transcription, playing an important role in cardiac hypertrophy.

The HDAC9 isoform MITR/HDRP lacks active site residues and is therefore catalytically inactive. It represses MEF2-dependent transcription by interacting with HDAC1 and/or HDAC3. MITR/HDRP is thought to play a role in skeletal myogenesis and in heart development. It also protects neurons from apoptosis by inhibiting c-Jun phosphorylation by MAPK10 and by repressing c-Jun transcription through recruitment of HDAC1 to the c-Jun promoter.