Eukaryotic chromosomes undergo DNA packaging in order to allow the genome to fit within the nucleus. This is important, as eukaryotic genomes can be very long, and so packaging is necessary to ensure the DNA fits.
DNA is wound around histone proteins, condensing the long molecule. The winding can be modified to control the transcriptional activity of a given region of DNA, with condensation leading to the silencing of the genes in that region. This leads to the formation of heterochromatin (transcriptionally silent) and euchromatin (more transcriptionally active). The transfers between these states are catalysed by histone acetylases (HATs), histone deacetylases (HDACs), histone methyltransferases (HMTs). Boundary and insulator elements prevent heterochromatin from forming (or spreading) in actively transcribed regions, allowing a chromosome to be in euchromatic and heterochromatic states at the same time. Histone proteins combine into nucleosomes, an octamer.
Non-histone proteins can also influence chromosomal packaging. Gene loops can be used to selectively decondense specific sections of DNA within heterochromatin, to allow expression of relevant genes. This is controlled by CTCF and cohesin. Cohesin forms boundary elements, preventing the entire chromosome from decondensing. This is common on topologically associated domains (TADs), where DNA is looped out of lamina associated domains (LADs) for expression.