Each chromosome is specifically anchored through its telomeres to a discrete place on the nuclear envelope by the proteins of the nuclear lamina. Thus each occupies a geographically distinct nuclear space called a chromosomal territory (Figure 2). The homologous chromosomal pairs (matching chromosomes derived from mother and father) do not necessarily lie next to each other.
Chromosomal territories are separated by channels of open nucleoplasm called the interchromatin compartment. Within each territory, DNA can be highly condensed (heterochromatin) or less condensed (euchromatin). Heterochromatin, defined as DNA that is not currently undergoing active transcription, can contain important chromosomal elements such as centromeres. Euchromatin are those chromosomal areas more likely to be active in gene transcription. The heterochromatin of any given chromosome is found within its territory close to the nuclear envelope (Figure 1), but can often project into the interior of the nucleus as patches and/or surround the nucleolus. The euchromatin of each territory extends into the center of the nucleus. In addition, those specific areas of euchromatin undergoing active RNA transcription (gene expression) are typically found on the very periphery of the chromosomal territory, at its juncture with the interchromatin channels.
Chromosomal territories contain at least one other known functional subdomain. Those portions of the DNA that replicate late are found near the nuclear envelope, while earlier-replicating DNA is found in the interior of each territory, projecting into the center of the nucleus. Thus each chromosome not only occupies a discrete place in the nucleus, but each is additionally highly organized into different functional subcompartments. The DNA in each chromosome is highly contorted, looping back and forth within its territory. Chromosomes appear capable of shuffling segments to the correct spot within their territories to carry out gene expression or DNA replication. Indeed, painting of chromosomal segments, including specific genes, with fluorescent tags clearly indicates that chromosomes are constantly shifting around within their territories. Thus the architecture of the chromosomal territories, although highly organized, has a considerable degree of flexibility that is closely tied to both gene expression and DNA replication.