Structure Of Nucleosome

The nucleosome is the most basic repeating unit of chromatin, which allows for the compact packaging and organization of genomic DNA (deoxyribonucleic acid) within cells. The nucleosome consists of DNA wrapped around an octamer of four homodimerized canonical histones (H2A, H2B, H3, and H4), which are highly basic globular proteins with a primary protein sequence rich in arginine and lysine residues.

There are three levels of chromatin organization which finally form an assembly that is positioned within the cell nucleus.

DNA wraps around histone proteins forming nucleosomes; the "beads on a string" structure (euchromatin).
Multiple histones fold the DNA into a 30 nm fibre consisting of nucleosome arrays in their most compact form (heterochromatin).
Higher-level DNA packaging of the 30 nm fibre into a looped structure which folds to form the metaphase chromosome (during mitosis and meiosis).

1.0Structure Of Nucleosome

A nucleosome structure is the fundamental unit of chromatin, which is the structure that packages DNA into the nucleus of a cell. The nucleosome consists of a segment of DNA wound around a core of histone proteins. The structure of the nucleosome can be described in more detail as follows:

Histone Core: The core is made up of eight histone proteins, which include two copies each of H2A, H2B, H3, and H4. These histones are highly conserved proteins that have a positive charge, allowing them to interact with the negatively charged DNA. The core histones come together to form a histone octamer.

DNA: Approximately 147 base pairs of DNA wrap around this histone core 1.65 times in a left-handed superhelical turn. This wrapped DNA is known as core DNA.

Linker DNA: Adjacent nucleosomes are connected by stretches of linker DNA, which can vary in length from about 10 to 80 base pairs, depending on the organism and the cell type. The H1 histone, or linker histone, binds to the linker DNA between nucleosomes, helping to compact the chromatin further and stabilize the structure of the nucleosome.

2.0Chromatin Structure

The repeating units of nucleosomes and linker DNA form a "beads-on-a-string" structure known as the 10 nm fiber. This fiber can further fold and coil into more compact structures, forming the 30 nm fiber, and eventually higher-order structures that make up the chromosomes visible during cell division.

The Basic unit of Chromatin: The Nucleosome

The primary level of organization of eukaryotic chromosomes comprises of DNA and associated protein, the histones, which together form a structure termed as chromatin. The orderly packaging of eukaryotic DNA depends on histone proteins. Histones are a group of small proteins that have a high content of the basic amino acids, arginine and lysine. Histones are divided into five classes, H1, H2A, H2B, H3 and H4 based on the relative amounts of these amino acids, that is, the arginine/lysine ratio.

The amino acid sequences of histones, H3 and H4, have und The amino acid sequences of histones, H3 and H4, have undergone very little change over long periods of evolutionary time and are therefore said to be conserved. The reason why these proteins are conserved is because histones interact with the main chain of the DNA molecule, which is identical in all organisms. In addition, nearly all of the amino acids in a histone molecule interact with another molecule, either DNA or another histone. As a result, the amino acid sequence in a histone protein must be constant. If an amino acid is replaced by another amino acid, the structure and function of the protein would be altered. This would then upset the DNA-protein interaction.

In the early 1970s, it was found that when chromatin was treated with nonspecific nuclease enzymes, most of the DNA was converted to fragments of approximately 200 base pairs in length. This means that such pieces of DNA were protected from nuclease attack.

In contrast, a similar treatment of naked DNA (i.e. DNA not bound to any protein) produced randomly sized fragments, since the entire DNA was available for enzymatic lysis. This finding also suggested that chromosomal DNA was protected from enzymatic attack, except at certain sites along its length. Therefore, the proteins which bind to DNA protect it from nuclease digestion. In 1974, using the data from nuclease digestion, Roger Kornberg proposed that DNA and histones are organized into repeating subunits, called nucleosomes. To form this basic nucleosome unit, the DNA must bind firmly to the histone proteins.

DNA and core histones are held together by several types of noncovalent bonds, including ionic bonds between negatively charged phosphates of the DNA backbone and positively charged amino acids of the histones. The two molecules make contact at sites where the minor groove of the DNA faces inward toward the histone core, which occurs at approximately 10 base-pair intervals. In between these points of contact, the two molecules are seen to be separated by considerable space, which might provide access to the DNA for transcription factors and other DNA-binding proteins. For many years, histones were thought of as inert, structural molecules but these small proteins play critically important roles in determining the activity of the DNA with which they are associated. It has also become evident that chromatin is a dynamic cellular component in which histones, regulatory proteins and a variety of enzymes move in and out of the nucleoprotein complex to facilitate the complex functions of DNA transcription, compaction, replication, recombination and repair.

3.0The Structure of A Nucleosome

The nucleosome is the fundamental packaging unit of the DNA which serves to reduce its length so that an extremely long molecule of DNA can be sensed to fit into a very small nucleus. The nucleus which is 10 mm in diameter can pack 200,000 times this length of DNA within its boundaries due to this phenomenon of compaction starting with nucleosomes. The assembly of nucleosomes is the first important step in the compaction process.

Each nucleosome contains a nucleosome core particle consisting of 146 base pairs of supercoiled DNA wrapped almost twice around a disk-shaped complex of eight histone molecules, which form the core.
The histone core of each nucleosome consists of two copies each of histones H2A, H2B, H3 and H4 assembled into an octamer.
The histone H1 resides outside the nucleosome core particle and is called a linker histone because it binds to part of the linker DNA that connects one nucleosome core particle to the next.
Fluorescence studies indicate that H1 molecules continuously dissociate and reassociate with chromatin. Together the H1 protein and the histone octamer interact with about 168 base pairs of DNA.
H1 histone molecules can be selectively removed from the chromatin fibres by subjecting the preparation to solutions of low ionic strength. When chromatin is treated to remove H1, under the electron microscope the nucleosome core particles and naked linker DNA can be seen as separate elements, and together appear like “beads on a string”.

The formation of the nucleosome helps to wrap-up the DNA and reduces its length, so that it can be accommodated within the tiny cell nucleus. We know that the nucleotide-nucleotide spacing is 0.34 nm, and each nucleosome comprises of approximately 200 base pairs, which would require a length of 0.34 nm x 200 bp equal to 68 nm. Hence, a single nucleosome, 10 nm in diameter, would stretch to nearly 70 nm if fully extended. Consequently, it is said that the packing ratio of the DNA of nucleosomes is approximately 7:1 or the length of the DNA is reduced 7 times.

Studies carried out using X-ray crystallography have shown that the eight histone molecules that comprise a nucleosome core particle are organized into four heterodimers: two dimers of histones H2A-H2B and two dimers of H3-H4.
Each histone dimer binds 27 to 28 base pairs of DNA, with contacts occurring where the minor groove of the DNA faces the histone core.
The two H3-H4 dimers are associated with one another in the center of the core particle to form a tetramer, whereas the two H2A-H2B dimers are positioned on each side of the (H3-H4)2 tetramer.

Each core histone consists of:

A globular region, called the “histone fold,” consisting of three helices and
A flexible, extended N-terminal tail that projects out of the histone disk and past the DNA double helix.

These histone dimers are formed because the C-terminal ends consist of helices which are folded into a compact mass in the core of the nucleosome. In contrast, the N-terminal segment of each core histone (and also the C terminal segment of H2A) takes the form of a long, flexible tail that extends past the DNA helix and into the surroundings. It is this tail region that gets modified by addition of specific groups. This process of modification is related to the regulation of expression of the DNA through transcription.

Higher Levels of Chromatin Structure A DNA molecule wrapped around nucleosome core particles of 10-nm diameter is the lowest level of chromatin organization. Chromatin does not, however, exist within the cell in this relatively extended, “beads-on-a-string” state.
When chromatin is released from nuclei and prepared at physiologic ionic strength, a fibre of approximately 30-nm thickness is observed. Electron micrographs have shown the occurrence of a 30-nm chromatin fibre released from a nucleus following lysis of the cell in a hypotonic salt solution.

Two models have been proposed in which the nucleosomal filament is coiled into the higher order, thicker fibre.

In the “zig-zag” model, the linker DNA is present in a straight, extended state that criss-crosses between consecutive core particles, which are organized into two separate stacks of nucleosomes. The two stacks of nucleosomes are coiled into a higher-order helical structure.
In the “solenoid” model, the linker DNA gently curves as it connects consecutive core particles, which are organized into a single, continuous helical array containing about 6–8 nucleosomes per turn.

These models differ in the relative positioning of nucleosomes within the fibre. Recent research favors the “zig-zag” model depicted in which successive nucleosomes along the DNA are arranged in different stacks and alternating nucleosomes become interacting neighbors.

The assembly of the 30-nm fibre increases the DNA-packing ratio an additional 6-fold, or about 50-fold altogether. This higher order packaging of the DNA is then thrown into a well-defined loop structure which finally is packaged to form the chromatid, a unit of the chromosome.

Thus the association of DNA and specific proteins, forming Chromatin determines the nuclear integrity of a cell. Any alteration in this assembly would affect cell function and survival.