Nuclear Organization

Linear DNA and chromosome basics

The first level of genome organization concerns how DNA is arranged linearly, and how it is packaged into chromosomes. DNA is composed of two antiparallel strands of nucleic acids, with two bound and opposing nucleic acids referred to as DNA base pairs.

Chromosomal domains

Self-interacting domains

Self-interacting (or self-associating) domains are found in many organisms – in bacteria, they are referred to as Chromosomal Interacting Domains (CIDs), whereas in mammalian cells, they are called Topologically Associating Domains (TADs). Self-interacting domains can range from the 1–2 mb scale in larger organisms to 10s of kb in single celled organisms.

Lamina-associating domains and nucleolar-associating domains

Lamina-associating domains (LADs) and nucleolar-associating domains (NADs) are regions of the chromosome that interact with the nuclear lamina and nucleolus, respectively. Making up approximately 40% of the genome, LADs consist mostly of gene poor regions and span between 40kb to 30Mb in size. There are two known types of LADs: constitutive LADs (cLADs) and facultative LADs (fLADs).

A/B compartments

A/B compartment-associated regions are on the multi-Mb scale and correlate with either open and expression-active chromatin or closed and expression-inactive chromatin . A compartments tend to be gene-rich, have high GC-content, contain histone markers for active transcription, and usually displace the interior of the nucleus. B compartments, on the other hand, tend to be gene-poor, contain histone markers for gene silencing, and lie on the nuclear periphery.

Chromosome territories

The last level of organization concerns the distinct positioning of individual chromosomes within the nucleus. The region occupied by a chromosome is called a chromosome territory . CTs have several common properties. Although chromosomal locations are not the same across cells within a population, there is some preference among individual chromosomes for particular regions.