The packaged mode of heterochromatin is epigenetically inherited, in that the packaging state is typically maintained after replication and mitosis, independent of the underlying DNA sequence. This property implies a that a biochemical mark exists together with cellular machinery that can recognize and maintain the mark locally.
The heterochromatin of all eukaryotes is characterized by histone hypoacetylation, and by methylation of histone H3 on lysine 9 in higher eukaryotes. Some single-celled eukaryotes such as Saccharomyces lack methylation of H3. Heterochromatin Protein 1 (HP1) binds H3 methylated at lysine 9 (H3-mK9). HP1 is a highly conserved protein that directly associated with pericentric heterochromatin.
A Unified Mode of Epigenetic Gene Silencing RNA Meets Polycomb Group Proteins A Unified Mode of Epigenetic Gene Silencing: Article Abstract: "Recently, an essential role for RNA in the epigenetic silencing of genes packaged within heterochromatin in animals has been recognized. The RNA appears to be involved in targeting chromatin remodeling activity to specific loci and in later maintaining the repressed state of the gene. Epigenetic silencing of Hox cluster genes by the Polycomb group proteins also involves the formation of a stably inherited repressive chromatin structure. Recent studies of the C. elegans PcG gene sop-2 revealed an evolutionarily conserved property of PcG proteins in the binding of RNA, suggesting an important role for RNA in PcG-mediated Hox gene repression."