It has been discovered via a wide range of distinct types of research that the position of a gene in the nucleus shifts if that gene's protein-coding potential is significantly activated. As a consequence of this, it is possible for a section of a chromosome that is highly actively transcribed to expand beyond the boundaries of its own chromosome, creating what is essentially an extended loop.

Even though it was discovered in the nineteenth century, microscopists were already familiar with the nucleolus since it is the largest and most conspicuous of them. The nucleolus, which is made up of a network of RNAs and proteins concentrated around ribosomal RNA genes that are actively being transcribed, is the location of many other specialized reactions in addition to the formation of the cell's ribosome subunits. This is because the nucleolus is made up of a network of RNAs and proteins that are concentrated around ribosomal RNA genes that are actively being transcribed. Although the ribosomal RNA genes are frequently found together in a single nucleolus, they are also frequently found on various different chromosomes. This is because the ribosomal RNA genes are found in multiple copies across the entirety of the eukaryotic genome.

Additionally, the nucleus is home to a variety of organelles that are not readily visible. For instance, the vast majority of plant and animal cells include interchromatin granule clusters and spherical Cajal bodies. These organelles, such as the nucleolus, are composed of certain protein and RNA molecules that come together to form networks. These networks are extremely permeable to other protein and RNA molecules in the nucleoplasm that surrounds them.

Structures like this one, as well as other networks of proteins and RNA molecules coupled to nuclear pores and the nuclear envelope, are able to establish their own distinct biochemical environments because of the immobilization of certain groups of macromolecules.

In theory, this makes it possible for any extra molecules that find their way into these spaces to be efficiently processed through any number of sophisticated reaction pathways. Therefore, processes that take place in particular regions of the nucleus can take advantage of many of the kinetic benefits of compartmentalization if they are contained inside highly permeable fibrous networks of the type being discussed here. On the other hand, in contrast to the membrane-bound compartments found in the cytoplasm, these nuclear subcompartments do not possess a lipid bilayer membrane, which means that they are unable to concentrate or exclude some extremely small molecules.

The cell possesses a remarkable capacity for the building of many different habitats, which allows it to carry out the complicated biochemical processes that it needs to. Structures that are necessary for the proper functioning of several elements of gene expression can be found in the nucleus. One of these subcompartments is called the nucleolus, and it appears to arise only when it is absolutely necessary. It is responsible for producing a significant local concentration of the various RNA molecules and enzymes that are necessary for particular processes. In a manner comparable to this, it has been demonstrated that the collection of enzymes necessary to carry out DNA repair congregate in specific foci inside the nucleus to form "repair factories" when DNA is damaged as a result of irradiation. These "repair factories" then go on to repair the DNA damage. In addition, nuclei usually feature hundreds of different foci that act as factories for the creation of DNA or RNA. These foci can be found throughout the nucleus.

Is the arrangement of chromosomes and other elements related to the nucleus carried out on an intranuclear framework that is analogous to the cytoskeleton? Nuclear matrix, also known as the nuclear scaffold, is the name given to the insoluble material that is still present in the nucleus after a series of biochemical extraction steps have been completed. It is likely that many of the proteins and RNA molecules that make up this insoluble material come from the fibrous regions of the nucleus that were discussed earlier. On the other hand, other proteins may be involved in the formation of the base of chromosomal loops or the attachment of chromosomes to other structures in the nucleus.

Following our discussion on the dynamic shape of the chromosomes during interphase, we will now move on to the chromosomes during the mitotic phase of the cell cycle. During the process of mitosis, the chromosomes will coil up and generate very condensed structures. These structures are almost always straightforward to spot using light microscopy. Even while a normal interphase chromosome is only around ten times shorter as a result of this condensation, the appearance of the chromosomes is significantly altered.

As was mentioned before, the two DNA molecules that are produced as a byproduct of DNA replication during the interphase of the cell-division cycle are what give rise to the two sister chromosomes, also known as sister chromatids, which are held together by their respective centromeres. These chromosomes are often covered in substantial amounts of RNA-protein complexes, in addition to a variety of other chemicals. After this covering has been removed, electron micrographs of each chromatid reveal that it is composed of chromatin loops that radiate from a core framework. These loops are structured in this manner because each chromatid contains a central framework. Tests that used DNA hybridization to identify specific DNA sequences demonstrated that the order of the observable features along a mitotic chromosome largely corresponds to the order of the genes along the DNA molecule. This was determined by comparing the results of the experiments. Therefore, it is possible to think of mitotic chromosome condensation as being at the pinnacle of the hierarchy of chromosomal packaging.

The process of chromosome compaction that occurs during mitosis is one that is both highly structured and dynamic. It is designed to achieve at least two important purposes. When condensation is complete, the first step is for sister chromatids to get untangled from one another and to position themselves next to one another (during metaphase). As a consequence of this, when the mitotic apparatus begins to pull the sister chromatids apart, they may be able to do so with relative ease. Second, when the chromosomes are separated to generate daughter cells, the compacted chromosomes prevent the relatively fragile DNA molecules from fracturing. This happens because the compacted chromosomes are closer together. Early M phase is the point in the cell cycle when the process that converts interphase chromosomes into mitotic chromosomes starts. This transformation is intimately connected to the maturation of the cell cycle. During the M phase, gene expression is silenced, and certain alterations to histones contribute to the remodeling of the chromatin as it becomes more compact. Two different kinds of ring-shaped proteins called cohesins and condensins work together to help achieve this compaction.

Because the chromosomes are normally more spread out during interphase, it is more difficult to observe the finer details of their structure at this time. Notable outliers include the one-of-a-kind lampbrush chromosomes that are located in the oocytes of vertebrates and the polytene chromosomes that are located in the vast secretory cells of insects. The results of studies conducted on these two separate types of interphase chromosomes testify to the fact that each lengthy DNA molecule is broken up into a number of discrete domains, which are then arranged as loops of chromatin before being compacted by additional folding. The expression of the genes contained within a loop results in the unfolding of the loop, allowing the cell's machinery to gain access to the DNA.

Chromosomes that are in the interphase stage of their life cycle reside in various regions of the nucleus of the cell and are not very tightly intertwined. It is believed that euchromatin exists as tightly folded fibers of compacted nucleosomes when it is not being transcribed and that the bulk of interphase chromosomes are made up of euchromatin. However, euchromatin can sometimes be broken up by sections of heterochromatin. These are places in which the nucleosomes undergo additional packing, which normally renders the DNA unresponsive to gene expression. There are several distinct kinds of heterochromatin, and some of them are found in significant chunks in the region around centromeres and in close proximity to telomeres. However, heterochromatin can also be found in a wide variety of other places on chromosomes, and in these places it can help to regulate the expression of genes that are essential for the development of the organism.

It is common for heterochromatin to be found in close proximity to the nuclear envelope on the inside of the nucleus. This is because high levels of gene expression induce loops of chromatin to shift away from their respective chromosome regions. This is a reflection of the existence of nuclear compartments in which certain proteins and RNAs are concentrated in higher levels to encourage particular sets of metabolic activities. These compartments exist in every cell. The component pieces of a subcompartment have the ability to either self-assemble into unique organelles such as nucleoli or Cajal bodies, or they have the ability to attach themselves to permanent structures such as the nuclear envelope.

During the process of mitosis, the two DNA molecules that make up each duplicated chromosome are packaged as two independently folded chromatids. This takes place during the process of shutting down gene expression. During the early stages of the M phase, this procedure begins. Condensation occurs concurrently with histone modifications that aid in chromatin packing; however, the presence of other proteins is necessary for the successful completion of this ordered process, which reduces the distance between each DNA molecule's ends-to-ends by an additional factor of ten compared to the length of the molecule during interphase.