Histones in silenced rRNA gene copies are deacetylated by Hdac1 (and possibly Hdac2), which is part of the SIN3-HDAC complex bound to NoRC (Santoro et al. 2002, Zhou et al. 2002). The PHD domain of the Tip5 (Baz2a) component of NoRC binds acetylated lysine-16 of histone H4 (Zhou and Grummt 2005). The residues of histone H4 that are deacetylatd are lysine-5, lysine-8, and lysine-12 (Zhou and Grummt 2005).
In the main promoters of silenced rRNA gene copies, histone H3 is methylated on lysine-9 (H3K9) by an unknown histone methyltransferase (Santoro and Grummt 2005). H3K9 methylation is still observed when deacetylation is inhibited, therefore histone methylation does not depend on deacetylation (Santoro and Grummt 2005). However, histone deacetylation is required for DNA methylation. Significantly more H3K9 dimethylation than trimethylation is observed (Santoro and Grummt 2005).
It is unknown if deacetylation precedes methylation or vice versa.