The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.

Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th position in histones H3 tail is di- or tri-methylated. This attracts a specialized nonhistone protein called heterochromatin protein 1 (HP1) to the methylated site. It represents the repressed region of chromatin. The human chromosomes 1,9,16 and Y chromosome in human males contain a large portion of constitutive heterochromatin.

Facultative heterochromatin: This region is denser than euchromatin, but, unlike constitutive heterochromatin, the lysine at the 27th position of histone H3 tail is di- or tri-methylated (H3K27me3). These regions are characterized by the binding of Polycomb repressive complexes: PRC1 and PRC2. The PRC2 domain is thought to bind first and initiate heterochromatin formation. The PRC2 complexes contain histone deacetylases enzymes that inhibit transcription and cause chromatin repression. In addition, the PRC2 complex also contains the catalytic domain of several histone methyltransferases generating di-trimethyl lysines. PRC 1 then binds to the methylated nucleosomes and condenses the chromatin into a compact structure, inhibiting transcription.