Nuclear organization refers to the spatial organization and dynamics of
chromatin within a
cell nucleus during
interphase. There are many different levels and scales of nuclear organization.
At the smallest scale,
DNA is
packaged into units called
nucleosome
A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone, histone proteins and resembles thread wrapped around a bobbin, spool. The nucleosome ...
s, which compacts DNA about 7-fold. In addition, nucleosomes protect DNA from damage and carry
epigenetic information. Positions of nucleosomes determine accessibility of DNA to
transcription factor
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription (genetics), transcription of genetics, genetic information from DNA to messenger RNA, by binding t ...
s.
At the intermediate scale, DNA looping can physically bring together DNA elements that would otherwise be separated by large distances. These interactions allow regulatory signals to cross over large genomic distances—for example, from
enhancers to
promoters.
At a larger scale, chromosomes are organized into two compartments labelled A ("active") and B ("inactive"), which are further subdivided into sub-compartments. At the largest scale, entire
chromosomes segregate into distinct regions called
chromosome territories.
Chromosome organization is dynamic at all scales. Individual nucleosomes undergo constant thermal motion and
nucleosome breathing. At intermediate scales, an active process of
loop extrusion creates dynamic loops and
Topologically Associating Domains (TADs).
Importance
Each human
cell contains around two metres of
DNA, which must be tightly folded to fit inside the
cell nucleus
The cell nucleus (; : nuclei) is a membrane-bound organelle found in eukaryote, eukaryotic cell (biology), cells. Eukaryotic cells usually have a single nucleus, but a few cell types, such as mammalian red blood cells, have #Anucleated_cells, ...
. However, in order for the cell to function,
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
s must be able to access the sequence information contained within the DNA, in spite of its tightly-packed nature. Hence, the cell has a number of mechanisms in place to control how DNA is organized.
Moreover, nuclear organization can play a role in establishing cell identity. Cells within an organism have near identical
nucleic acid sequences, but often exhibit different
phenotypes. One way in which this individuality occurs is through changes in
genome architecture, which can alter the
expression of different sets of
gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s. These alterations can have a downstream effect on cellular functions such as
cell cycle
The cell cycle, or cell-division cycle, is the sequential series of events that take place in a cell (biology), cell that causes it to divide into two daughter cells. These events include the growth of the cell, duplication of its DNA (DNA re ...
facilitation,
DNA replication,
nuclear transport, and alteration of
nuclear structure. Controlled changes in nuclear organization are essential for proper cellular function.
History and methodology
The organization of chromosomes into distinct regions within the nucleus was first proposed in 1885 by
Carl Rabl. Later in 1909, with the help of the microscopy technology at the time,
Theodor Boveri coined the termed chromosome territories after observing that chromosomes occupy individually distinct nuclear regions. Since then, mapping genome architecture has become a major topic of interest.
Over the last ten years, rapid methodological developments have greatly advanced understanding in this field.
Large-scale DNA organization can be assessed with DNA imaging using fluorescent tags, such as
DNA Fluorescence in situ hybridization (FISH), and specialized microscopes. Additionally,
high-throughput sequencing technologies such as
Chromosome Conformation Capture-based methods can measure how often DNA regions are in close proximity. At the same time, progress in
genome-editing techniques (such as
CRISPR/Cas9,
ZFNs, and
TALENs) have made it easier to test the organizational function of specific DNA regions and proteins. There is also growing interest in the rheological properties of the interchromosomal space, studied by the means of
Fluorescence Correlation Spectroscopy and its variants.
Architectural proteins
Architectural proteins regulate chromatin structure by establishing physical interactions between DNA elements. These proteins tend to be highly
conserved across a majority of eukaryotic species.
In mammals, key architectural proteins include:
*
Histones: DNA is wrapped around histones to form
nucleosome
A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone, histone proteins and resembles thread wrapped around a bobbin, spool. The nucleosome ...
s, which are basic units of chromatin structure. Each nucleosome consists of 8 histone protein subunits, around which roughly 147 DNA base pairs are wrapped in 1.67 left-handed turns. Nucleosomes provide about 7-fold initial linear compaction of DNA. The concentration and specific composition of histones used can determine local chromatin structure. For example,
euchromatin is a form of chromatin with low nucleosome concentration - here, the DNA is exposed, promoting interactions with gene expression, replication, and organizational machinery. In contrast,
heterochromatin has high nucleosome concentration and is associated with repression of gene expression and replication, as the necessary proteins cannot interact with the DNA.
*
Chromatin remodeling enzymes: These enzymes are responsible for promoting euchromatin or heterochromatin formation by a number of processes, particularly modifying histone tails or physically moving the nucleosomes. This in turn, helps regulate gene expression, replication, and how the chromatin interacts with architectural factors. The list of chromatin remodeling enzymes is extensive and many have specific roles within the nucleus. For example, in 2016 Wiechens et al. identified two human enzymes, SNF2H and SNF2L, that are active in regulating
CTCF binding and therefore affect genome organization and transcription of many genes.
*
CCCTC-binding factor (CTCF), or 11-zinc finger protein, is considered the most prominent player in linking genome organization with gene expression.
CTCF interacts with specific DNA sequences and a variety of other architectural proteins, chiefly cohesin - these behaviours allow it to mediate DNA looping, thus acting as transcriptional repressor, activator, and
insulator. Furthermore, CTCF is often found at self-interacting domain boundaries, and can anchor the chromatin to the nuclear lamina.
CTCF is also involved in
V(D)J recombination
V(D)J recombination (variable–diversity–joining rearrangement) is the mechanism of somatic recombination that occurs only in developing lymphocytes during the early stages of T and B cell maturation. It results in the highly diverse repertoire ...
.
*
Cohesin: The cohesin complex was initially discovered as a key player in
mitosis
Mitosis () is a part of the cell cycle in eukaryote, eukaryotic cells in which replicated chromosomes are separated into two new Cell nucleus, nuclei. Cell division by mitosis is an equational division which gives rise to genetically identic ...
, binding sister chromatids together to ensure proper segregation. However, cohesin has since been linked to many more functions within the cell. It has been found to help facilitate DNA repair and recombination, meiotic chromosome pairing and orientation, chromosome condensation, DNA replication, gene expression, and genome architecture. Cohesin is a heterodimer composed of the proteins SMC1 and SMC3 in combination with the SCC1 and SCC3 proteins. The entire complex is loaded onto DNA by the NIPBL-MAU2 complex in a ring-like fashion.
Levels of nuclear organization
Nucleosome fiber
The organization of DNA within the nucleus begins with the 10 nm fiber, a "beads-on-a-string" structure made of nucleosomes connected by 20-60bp
linkers. A fiber of nucleosomes is interrupted by regions of
accessible DNA, which are 100-1000bp long regions devoid of nucleosomes. Transcription factors bind within accessible DNA to displace nucleosomes and form
cis-regulatory elements. Sites of accessible DNA are typically probed by
ATAC-seq or
DNase-Seq experimental methods.
A 30 nm fiber has long been proposed as the next layer of chromatin organization. While 30 nm fiber is often visible in vitro under high salt concentration, its existence in vivo has been questioned in many recent studies. Instead, these studies point towards a disordered fiber with a width of 20 to 50 nm.
Loop extrusion and DNA loops
The process of loop extrusion by
SMC complexes dynamically creates chromatin loops ranging in size from 50-100kb in yeast to up to several Mb in mammals.
There is strong support for loop extrusion in yeast, mammals, and
nematodes.
In mammals, loop extrusion is responsible for the formation of
topologically associating domains and loops between
CTCF sites, as well as for bringing promoters and enhancers together. CTCF sites serve as boundaries of
insulated neighborhoods or
topologically associating domains.
The presence of loop extrusion in
fruit flies is debated and the formation of DNA loops may be mediated by a different process of boundary element pairing.
Chromosomal domains
Topologically associating domains
Self-interacting (or self-associating) domains are found in many organisms. In eukaryotes, they have been usually referred to as
TADs irrespective of the mechanism of their formation. TADs have a higher ratio of chromosomal contacts within the domain than outside it. They are formed through the help of architectural proteins. In many organisms, TADs correlate with regulation of gene expression, and enhancers and promoters within a TAD interact at higher frequency.
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
The nucleolus (; : nucleoli ) is the largest structure in the cell nucleus, nucleus of eukaryote, eukaryotic cell (biology), cells. It is best known as the site of ribosome biogenesis. The nucleolus also participates in the formation of signa ...
, 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). cLADs are A-T rich heterochromatin regions that remain on lamina and are seen across many types of cells and species. There is evidence that these regions are important to the structural formation of interphase chromosome. On the other hand, fLADs have varying lamina interactions and contain genes that are either activated or repressed between individual cells indicating cell-type specificity. The boundaries of LADs, like self-interacting domains, are enriched in transcriptional elements and architectural protein binding sites.
NADs, which constitutes 4% of the genome, share nearly all of the same physical characteristics as LADs. In fact, DNA analysis of these two types of domains have shown that many sequences overlap, indicating that certain regions may switch between lamina-binding and nucleolus-binding.
NADs are associated with nucleolus function. The nucleolus is the largest sub-organelle within the nucleus and is the principal site for rRNA transcription. It also acts in signal recognition particle biosynthesis, protein sequestration, and viral replication. The nucleolus forms around rDNA genes from different chromosomes. However, only a subset of rDNA genes is transcribed at a time and do so by looping into the interior of the nucleolus. The rest of the genes lay on the periphery of the sub-nuclear organelle in silenced heterochromatin state.
A/B compartments
A/B compartments were first discovered in early
Hi-C studies.
Researchers noticed that the whole genome could be split into two spatial compartments, labelled "A" and "B", where regions in compartment A tend to interact preferentially with A compartment-associated regions than B compartment-associated ones. Similarly, regions in compartment B tend to associate with other B compartment-associated regions.
A/B compartment-associated regions are on the multi-Mb scale and correlate with either open and expression-active chromatin ("A" compartments) or closed and expression-inactive chromatin ("B" compartments).
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. As well, they are typically made up of self-interacting domains and contain early replication origins. B compartments, on the other hand, tend to be gene-poor,
compact, contain histone markers for gene silencing, and lie on the nuclear periphery. They consist mostly of LADs and contain late replication origins.
In addition, higher resolution Hi-C coupled with
machine learning
Machine learning (ML) is a field of study in artificial intelligence concerned with the development and study of Computational statistics, statistical algorithms that can learn from data and generalise to unseen data, and thus perform Task ( ...
methods has revealed that A/B compartments can be refined into subcompartments.
The fact that compartments self-interact is consistent with the idea that the nucleus localizes proteins and other factors such as
long non-coding RNA (lncRNA) in regions suited for their individual roles. An example of this is the presence of multiple
transcription factories throughout the nuclear interior. These factories are associated with elevated levels of transcription due to the high concentration of transcription factors (such as transcription protein machinery, active genes, regulatory elements, and nascent RNA). Around 95% of active genes are transcribed within transcription factories. Each factory can transcribe multiple genes – these genes need not have similar product functions, nor do they need to lie on the same chromosome. Finally, the co-localization of genes within transcription factories is known to depend on cell type.
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 (CT). Among eukaryotes, CTs have several common properties. First, although chromosomal locations are not the same across cells within a population, there is some preference among individual chromosomes for particular regions. For example, large, gene-poor chromosomes are commonly located on the periphery near the nuclear lamina while smaller, gene-rich chromosomes group closer to the center of the nucleus. Second, individual chromosome preference is variable among different cell types. For example, the X-chromosome has shown to localize to the periphery more often in liver cells than in kidney cells. Another conserved property of chromosome territories is that homologous chromosomes tend to be far apart from one another during cell interphase. The final characteristic is that the position of individual chromosomes during each cell cycle stays relatively the same until the start of mitosis.
The mechanisms and reasons behind chromosome territory characteristics is still unknown and further experimentation is needed.
References
External links
*{{Commons category-inline
Cell nucleus
Cellular processes