Nucleoplasm: Characteristics, Structure And Functions

The nucleoplasm is the substance in which DNA and other nuclear structures, such as nucleoli , are embedded . It is separated from the cell cytoplasm through the membrane of the nucleus, but can exchange materials with it through the nuclear pores.

Its components are mainly water and a series of sugars, ions, amino acids, and proteins and enzymes involved in gene regulation, among these more than 300 proteins other than histones. In fact, its composition is similar to that of the cell cytoplasm.

Within this nuclear fluid are also nucleotides, which are the “building blocks” used for the construction of DNA and RNA, with the help of enzymes and cofactors. In some large cells, such as acetabularia , the nucleoplasm is clearly visible.

The nucleoplasm was previously thought to consist of an amorphous mass enclosed in the nucleus , excluding chromatin and nucleolus. However, inside the nucleoplasm there is a protein network in charge of organizing the chromatin and other components of the nucleus, called the nuclear matrix.

New techniques have been able to better visualize this component and identify new structures such as intranuclear sheets, protein filaments emerging from nuclear pores, and the RNA processing machinery.

General characteristics

The nucleoplasm, also called “nuclear juice” or karyoplasm, is a protoplasmic colloid with properties similar to the cytoplasm, relatively dense and rich in different biomolecules, mainly proteins.

Chromatin and one or two corpuscles called nucleoli are found in this substance. There are also other immense structures in this fluid such as Cajal bodies, PML bodies, spiral bodies or  nuclear speckles , among others.

The structures necessary for the processing of messenger preRNA and transcription factors are concentrated in the Cajal bodies.

The speckles  nuclear appear to be similar to Cajal bodies are very dynamic and move to regions where transcription is active.

PML bodies appear to be markers for cancer cells, as they incredibly increase their numbers within the nucleus.

There is also a series of spherical nucleolar bodies that range between 0.5 and 2 µm in diameter, composed of globules or fibrils that, although they have been reported in healthy cells, their frequency is much higher in pathological structures.

The most relevant nuclear structures that are embedded in the nucleoplasm are described below:


The nucleolus is an outstanding spherical structure located inside the nucleus of cells and is not delimited by any type of biomembrane that separates them from the rest of the nucleoplasm.

It is made up of regions called NORs ( chromosomal nucleolar organizer regions ) where the sequences that code for ribosomes are located . These genes are found in specific regions of the chromosomes.

In the specific case of humans, they are organized in the satellite regions of chromosomes 13, 14, 15, 21 and 22.

A series of essential processes occurs in the nucleolus, such as transcription, processing, and assembly of the subunits that make up ribosomes.

On the other hand, leaving aside its traditional function, recent studies have found that the nucleolus is related to cancer cell suppressor proteins, cell cycle regulators, and proteins from viral particles.

Subnuclear territories

The DNA molecule is not randomly dispersed in the cell nucleoplasm, it is organized in a highly specific and compact way with a set of highly conserved proteins throughout evolution called histones.

The process of organizing DNA allows the introduction of almost four meters of genetic material into a microscopic structure.

This association of genetic material and protein is called chromatin. This is organized in regions or domains defined in the nucleoplasm, and two types can be distinguished: euchromatin and heterochromatin.

Euchromatin is less compact and encompasses genes whose transcription is active, since transcription factors and other proteins have access to it in contrast to heterochromatin, which is highly compact.

Heterochromatin regions are found in the periphery and euchromatin more to the center of the nucleus, and also close to the nuclear pores.

Similarly, chromosomes are distributed in specific areas within the nucleus called chromosomal territories. In other words, chromatin is not randomly floating in the nucleoplasm.

Nuclear matrix

The organization of the various nuclear compartments seems to be dictated by the nuclear matrix.

It is an internal structure of the nucleus composed of a sheet coupled to nuclear pore complexes, nucleolar remains and a set of fibrous and granular structures that are distributed throughout the nucleus, occupying a significant volume of it.

Studies that have attempted to characterize the matrix have concluded that it is too diverse to define its biochemical and functional makeup.

The lamina is a kind of layer composed of proteins that ranges from 10 to 20 nm and is juxtaposed to the inner face of the nucleus membrane. The protein constitution varies depending on the taxonomic group studied.

The proteins that make up the lamina are similar to the intermediate filaments and, in addition to nuclear signaling, possess globular and cylindrical regions.

As for the internal nuclear matrix, it contains a high number of proteins with a binding site for messenger RNA and other types of RNA. In this internal matrix, DNA replication, non-nucleolar transcription and post-transcriptional messenger preRNA processing occurs.


Inside the nucleus there is a structure comparable to the cytoskeleton in cells called the nucleoskeleton, made up of proteins such as actin, αII-spectrin, myosin, and the giant protein called titin. However, the existence of this structure is still debated by researchers.


The nucleoplasm is a gelatinous substance in which various nuclear structures, mentioned above, can be distinguished.

One of the main components of the nucleoplasm are ribonucleoproteins, made up of proteins and RNA made up of a region rich in aromatic amino acids with an affinity for RNA.

The ribonucleoproteins found in the nucleus are specifically called small nuclear ribonucleoproteins.

Biochemical composition

The chemical composition of the nucleoplasm is complex, including complex biomolecules such as nuclear proteins and enzymes, and also inorganic compounds such as salts and minerals such as potassium, sodium, calcium, magnesium, and phosphorus.

Some of these ions are indispensable cofactors of enzymes that replicate DNA. It also contains ATP (adenosine triphosphate) and acetyl coenzyme A.

A series of enzymes necessary for the synthesis of nucleic acids, such as DNA and RNA, are embedded in the nucleoplasm. Among the most important are DNA polymerase, RNA polymerase, NAD synthetase, pyruvate kinase, among others.

One of the most abundant proteins in the nucleoplasm is nucleoplastim, which is an acidic and pentameric protein that has unequal domains in the head and tail. Its acidic characteristic manages to shield the positive charges present in the histones and manages to associate with the nucleosome.

Nucleosomes are those bead-like structures on a necklace, formed by the interaction of DNA with histones. Small lipid molecules have also been detected floating in this semi-aqueous matrix.


The nucleoplasm is the matrix where a series of essential reactions take place for the proper functioning of the nucleus and the cell in general. It is the site where the synthesis of DNA, RNA and ribosomal subunits occurs.

It works as a kind of “mattress” that protects the structures immersed in it, in addition to providing a means of transporting materials.

It serves as a suspension intermediate for subnuclear structures and, in addition, helps to keep the shape of the nucleus stable, giving it rigidity and hardness.

The existence of several metabolic pathways in the nucleoplasm, as in the cell cytoplasm, has been demonstrated. Within these biochemical pathways are glycolysis and the citric acid cycle.

The pentose phosphate pathway, which contributes the pentoses to the nucleus, has also been reported. In the same way, the nucleus is a synthesis zone for NAD + , which functions as coenzymes of dehydrogenases.

Messenger preRNA processing

Processing of pre-mRNA takes place in the nucleoplasm and requires the presence of the small nucleolar ribonucleoproteins, abbreviated as snRNP.

Indeed, one of the most important active activities that occurs in the eukaryotic nucleoplasm is the synthesis, processing, transport and export of mature messenger RNAs.

The ribonucleoproteins group together to form the spliceosome or splicing complex, which is a catalytic center responsible for removing introns from messenger RNA. A series of RNA molecules high in uracil is responsible for recognizing introns.

The spliciosome is composed of about five small nucleolar RNAs called snRNA U1, U2, U4 / U6 and U5, in addition to the participation of other proteins.

Let us remember that in eukaryotes, genes are interrupted in the DNA molecule by non-coding regions called introns that must be eliminated.

The splicing reaction integrates two consecutive steps: the nucleophilic attack in the 5 ′ cut zone by interaction with an adenosine residue adjacent to the 3 ′ zone of the intron (step that frees the exon), followed by the union of the exons.


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