Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa .

, are currently unknown, but histone post-translational modifications may be involved. Histone proteins can be acetylated to form active euchromatin while histone deacetylases (HDACs) remove acetyl marks to form silent heterochromatin; heterochromatic regions cluster and strongly interact in Neurospora genome organization. Here, we show that mutants lacking components of a heterochromatin- specific HDAC (HCHC) causes histone acetylation gains in heterochromatin genome-wide and increases contacts between distant heterochromatic loci. HCHC loss also impacts cytosine methylation, and in strains lacking both the HCHC and cytosine methylation, heterochromatic regions interact more with euchromatin. Our results suggest cytosine methylation normally functions to segregate silent and active loci when heterochromatic acetylation increases.