[citation needed] Heterochromatin protein-1 (HP1) has an N-terminal domain that acts on methylated lysines residues leading to epigenetic repression.

The CD binds with histone 3 through a methylated lysine residue at position 9 (H3K9) while the C-terminal CSD homodimerizes and interacts with a variety of other chromatin-associated, non-histone related proteins.

[9] The charges on the β sheets are negative thus making it difficult for it to bind to the DNA as a DNA-binding motif.

[9] The CSD readily homodimerizes in vitro and as a result forms a groove which can accommodate HP1 associated proteins that have a specific consensus sequence: PxVxL, where P is Proline, V is Valine, L is Leucine and x is any amino acid.

While the exact mechanism of how gene silencing is done is unknown, experimental data concluded the rapid exchange of biological macromolecules in and out of the heterochromatin region.

[9] HP1α is a highly evolutionarily conserved protein, existing in species such as Schizosaccharomyces pombe, a type of yeast, all the way to humans.