Some autoimmune diseases show a positive correlation with dramatically decreased expression of histone deacetylase 9 (HDAC9, an enzyme that removes acetyl groups from histones). Why would the decreased expression of HDAC9 cause immune cells to produce inflammatory genes at inappropriate times?

Autoimmune disease refers to a medical condition in which a person's immune system attacks its own body cells, tissue, or organs instead of protecting them.

Histone acylation protein reduces the positve charge of histone protein as a result DNA wrapped around histone protein losses. Those loose DNA interacts with the transcriptional factors to express genes found in that region.

In normal condition when the gene is no longer needed the histone deacetylase enzyme removes the acetyl group and DNA is again wrapped tightly and become inaccessible.

But when there is a defect in histone deacetylase enzyme then deacetylation does not takes place. As a result in an immune system, the inflammatory genes that were accessible during infection do not wrap around histone protein.