Some autoimmune diseases show a positive correlation with dramatically decreased expression of histone deacetylase (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?

The positive charge of the histone proteins get reduced due to the process of histone acetylation, thus making the wrapping of DNA around the histones less tightened. The loose connected DNA afterward associates with the transcription factors for the articulation of the genes situated in that area.  

Generally, when there is no requirement of gene anymore, the acetyl groups from the histones get withdrawn by the activity of histone deacetylase enzyme (HDAC9) that makes the DNA tightly wrapped and inaccessible again. In case, when less expression of histone deacetylase enzyme occurs, the process of deacetylation fails to take place. This indicates that within an immune cell, at the time of infection, the inflammatory gene, which was made available does not get re-wrapped firmly around the histones.  

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i believe it is "they are not used up by reactions" as the answer to your question, text me back if this is correct because i just learned this.