As inferred from mouse cell models, histones in silenced rRNA gene copies are deacetylated by HDAC1 (and possibly HDAC2), which is part of the SIN3-HDAC complex bound to NoRC. The PHD domain of the TIP5 (BAZ2A) component of NoRC binds acetylated lysine-16 of histone H4. The residues of histone H4 that are deacetylatd are lysine-5, lysine-8, and lysine-12.
In the main promoters of silenced rRNA gene copies, histone H3 is methylated on lysine-9 (H3K9) by an unknown histone methyltransferase. H3K9 methylation is still observed when deacetylation is inhibited, therefore histone methylation does not depend on deacetylation. However histone deacetylation is required for DNA methylation. Significantly more dimethylation than trimethylation is observed.