Eukaryotic cells contain a vast amount of genetic material that must be organized within the microscopic nucleus. This organizational challenge is solved by a system of DNA packaging, with the nucleosome core at its center. The nucleosome core is the fundamental, repeating unit of chromatin, the substance that makes up chromosomes. It acts as a building block, allowing the cell’s long strands of DNA to be condensed.
Functionally, the nucleosome core can be visualized as a spool around which DNA is wound. This mechanism is the first step in a multi-level process of compaction. By wrapping DNA into these discrete units, the cell can manage its genetic library. This organization is not merely for storage; it also plays a role in how genetic information is accessed by the cell.
Composition of the Nucleosome Core
The nucleosome core is a particle composed of two main types of molecules: DNA and a set of proteins called histones. The protein component, known as the histone octamer, is a complex made of eight individual histone proteins. It contains two copies each of four different core histones: H2A, H2B, H3, and H4. These histone proteins are relatively small and are among the most conserved proteins in eukaryotes, indicating their importance.
A key chemical characteristic of histones is their high content of positively charged amino acids, such as lysine and arginine. This positive charge is fundamental to the structure of the nucleosome core. It allows the histone octamer to form a strong electrostatic attraction with the DNA molecule, which is negatively charged due to the phosphate groups in its sugar-phosphate backbone. This attraction facilitates the wrapping of the DNA around the protein spool.
Around this histone octamer, a segment of DNA measuring approximately 147 base pairs in length makes about 1.67 left-handed turns. The interaction is stabilized by over 100 hydrogen bonds between the histone proteins and the DNA. The resulting structure is a compact, disc-shaped particle that forms the most basic level of DNA organization within the nucleus.
The Role in DNA Compaction
The primary physical function of the nucleosome core is to compact the DNA molecule into a much smaller volume. The DNA from a single human cell would be about two meters long, yet it must fit inside a cell nucleus that is typically only a few micrometers in diameter. The formation of nucleosomes is the initial and most significant step in achieving this compression.
This first level of organization creates a structure often described as “beads on a string.” The nucleosome core particles are the “beads,” and the DNA that connects them is the “string,” referred to as linker DNA. This linker DNA can vary in length, typically ranging from about 10 to 80 base pairs, depending on the species and cell type.
The “beads on a string” fiber, which is about 10 nanometers in diameter, undergoes further coiling to achieve higher levels of compaction. This next stage is facilitated by another histone protein called H1, or the linker histone. H1 binds to the linker DNA and interacts with the DNA wrapped around the histone octamer, helping to pull adjacent nucleosomes closer together. This action coils the 10-nanometer fiber into a more condensed 30-nanometer fiber, a structure that prepares the DNA for its eventual arrangement into a chromosome.
Controlling Access to Genes
Beyond its structural role in DNA packaging, the nucleosome core is a dynamic structure that regulates access to the genetic code. The tight wrapping of DNA around the histone octamer can physically obstruct the cellular machinery responsible for reading genes and synthesizing proteins. For a gene to be expressed—or turned “on”—its DNA sequence must be accessible to enzymes like RNA polymerase, which initiate transcription.
The cell has developed mechanisms to modify chromatin structure and expose specific DNA regions as needed. This process is carried out by large protein machines called chromatin remodeling complexes. These complexes can bind to nucleosomes and use the energy from ATP hydrolysis to physically alter their position. They can slide a nucleosome along the DNA, eject it from the DNA to expose a gene, or even replace standard histones with histone variants that change the nucleosome’s properties.
This ability to reposition or remove nucleosomes is not random. Chromatin remodelers are recruited to specific locations on the genome by other proteins, known as transcription factors, which recognize and bind to particular DNA sequences. This targeted action ensures that only the necessary genes are made accessible for transcription at any given time. The dynamic nature of the nucleosome core allows the cell to control gene expression in response to its changing needs and external signals.
Epigenetic Influence on the Core
The dynamic behavior of nucleosomes is largely directed by chemical signals in a system known as epigenetics. These are modifications that alter gene activity without changing the underlying DNA sequence itself. Many of these epigenetic marks are placed on the histone proteins of the nucleosome core, on their flexible “tails” that extend outward from the central, structured region. These tails are accessible to various enzymes that can add or remove a variety of chemical groups.
Two of the most well-understood histone modifications are acetylation and methylation. Acetylation, the addition of an acetyl group, is typically carried out by enzymes called histone acetyltransferases (HATs). This modification neutralizes some of the positive charge on the histone tails, weakening their interaction with the negatively charged DNA. This loosening of the DNA’s grip on the histone core generally makes the DNA more accessible, promoting gene transcription.
Conversely, methylation involves the addition of a methyl group to histone tails by enzymes called histone methyltransferases. The effect of methylation is more complex and context-dependent than acetylation. Depending on which specific amino acid on the histone tail is methylated and how many methyl groups are added, the modification can either signal for gene activation or gene repression. These chemical modifications act as a code, read by other proteins to determine how a particular region of chromatin should be handled.