In eukaryotes, chromatin exists in three major forms based on its compaction level - euchromatin, constitutive heterochromatin, and facultative heterochromatin.
Euchromatin is a gene-rich, less compact, and actively transcribed region of the chromatin. When fixed and viewed under a microscope, it appears as lightly stained regions, because it can retain fewer stain particles.
The histone tail amino acids of euchromatin are extensively acetylated. Acetylation increases the negative charge on histone proteins, locally reducing the histone-DNA affinity. This reduces the chromatin compaction, allowing easier access to DNA.
Constitutive heterochromatin is a repeat-rich, gene-poor, and highly compacted region. Under a microscope, constitutive heterochromatin appears darkly stained, as the compaction allows it to take up more DNA binding dye.
A methylated histone tail characterizes constitutive heterochromatin. Methylation increases the affinity between histones and DNA, thereby increasing the chromatin compaction and inhibiting access to DNA.
The methylated histones are also bound by a nonhistone protein called Heterochromatin Protein 1, which facilitates chromatin compaction and spread of constitutive heterochromatin.
Facultative heterochromatin is a repeat-poor and gene-silent region. Under the microscope, it also appears darkly stained due to its higher compaction. The key distinction between facultative and constitutive heterochromatin is that the genes contained within facultative heterochromatin regions are flexible.
For example, in one cell, the genes in facultative heterochromatin may be repressed, while in another, the genes in the same locus may be expressed and wouldn’t be stored in the facultative state.
The facultative heterochromatin regions are often bound by a non-histone protein called Polycomb repressive complex 2 that can di- or tri-methylate H3 histones and contribute to transcriptional repression.
X-chromosome inactivation in female mammals is an example of facultative heterochromatin. Mammalian females have two X chromosomes, and males have only one.
One of the X chromosomes in females comprises highly condensed heterochromatin, resulting in the repression of all genes present on that chromosome. This ensures that genes on the X-chromosome of both males and females are expressed at the same level. Under the microscope, this inactivated X chromosome appears as a Barr body - a dense, darkly-stained spot at the periphery of the nucleus.