Immunoprecipitation of HDAC6 and Interacting Proteins

Methods Mol Biol. 2023;2589:493-508. doi: 10.1007/978-1-0716-2788-4_32.


The lysine deacetylase HDAC6 has unique structural and functional properties: It contains tandem catalytic domains that can deacetylate a variety of proteins and a zinc finger domain that binds ubiquitin. HDAC6 has been implicated in a variety of biological processes, normal or pathological, such as cellular motility, stress response, cancer, neurodegeneration, or viral infection. Due to this, HDAC6 is considered an attractive therapeutic target, and there is a major interest to identify small molecule inhibitors. To gain a mechanistic understanding of how HDAC6 impacts these different biological processes, there is a continued need to discover additional substrates as well as interacting proteins in different paradigms. One approach to achieve this is to perform HDAC6 immunoprecipitations to identify partner proteins. We describe here our optimized protocols to immunoprecipitate HDAC6 with the goal to identify or validate interacting proteins.

Keywords: HDAC6; Immunoblotting; Immunoprecipitation; Interacting partners; Mass Spectrometry; Ubiquitin.

MeSH terms

  • Histone Deacetylase 6 / metabolism
  • Histone Deacetylase Inhibitors
  • Histone Deacetylases* / metabolism
  • Immunoprecipitation
  • Lysine*
  • Ubiquitin / metabolism


  • Histone Deacetylase 6
  • Histone Deacetylases
  • Lysine
  • Ubiquitin
  • Histone Deacetylase Inhibitors