Epigenetic changes play an important role in the pathophysiology of autoimmune diseases
such as allergic asthma, multiple sclerosis, lung diseases, diabetes, cystic fibrosis, atherosclerosis,
rheumatoid arthritis, and COVID-19. There are three main classes of epigenetic alterations:
post-translational modifications of histone proteins, control by non-coding RNA and DNA methylation.
Since histone modifications can directly affect chromatin structure and accessibility, they can
regulate gene expression levels. Abnormal expression and activity of histone deacetylases (HDACs)
have been reported in immune mediated diseases. Increased acetylated levels of lysine residues
have been suggested to be related to the overexpression of inflammatory genes. This review focuses
on the effect of HDAC modifications on histone and non–histone proteins in autoimmune diseases.
Furthermore, we discuss the potential therapeutic effect of HDAC inhibitors (HDACi) used in these
diseases.