How a 2 meters long DNA is fitted into a 2 micrometers Nucleus?

An average Human cell (diploid) contains about 6.4 billion base pairs of DNA divided among 46 chromosomes. The length of each base pair is about 0.34 nm. Therefore, if the DNA molecule in a diploid cell were laid out end to end, the total length of DNA would be approximately 2 meters.

Since the diameter of a typical cell nucleus is only 10 μm, it is obvious for us to know that how is it possible to fit 2 meters of DNA in such a small space without getting tangled up. The answer lies in the remarkable manner in which a DNA molecule is packaged.

Eukaryotic cells have many levels of packaging of the DNA within the nucleus involving a variety of DNA binding proteins.

First Order of Packaging

It involves the winding of DNA around histones to form structures called Nucleosomes. The formation of nucleosomes is the foremost step and a vital step in the packaging of DNA that allows DNA to be folded into much more compact structures. So, let us briefly discuss what histones and nucleosomes are all about.

Histones:

Histones are by far the most abundant proteins associated with eukaryotic DNA. These are a remarkable group of small proteins that possess an unusually high content of the basic amino acids arginine and lysine. Histones are divided into five classes: H1, H2A, H2B, H3, and H4, which can be distinguished by their arginine/lysine ratio.

Nucleosome:

In 1974, Roger Kornberg proposed that DNA and histones are organized into repeating subunits, called nucleosomes. Each nucleosome contains a disk-shaped core complex consisting of two copies each of histone H2A, H2B, H3, and H4 assembled into an octamer. The remaining histones H1 is found associated with the outer surface of the core particle.

The H1 protein is referred to as a linker histone because it binds to part of the linker DNA that connects one nucleosome core particle to the next. If H1 protein is removed then the nucleosome core particles and naked linker DNA can be seen together as “beads on a string”.

Figure: Electron Micrograph of Chromatin Fibers showing “beads on string” structures.

Together the H1 protein and the histone octamer interact with about 168 base pairs of DNA. DNA and core histones are held together by several types of non-covalent bonds, including ionic bonds between negatively charged phosphates of the DNA backbone and positively charged residues of the histones.

We began this article by wondering how a nucleus of 10μm diameter can pack 2 m long DNA (200000  times bigger) within its boundaries. But now, we know that a nucleosome contains around 180 base pairs associated with it and a single nucleosome is 10 nm in length. Thus, if we fully extend the 180 base-pair long DNA then it would stretch to nearly a length of 61 nm.

From the above discussion, we can conclude that the compacting effect of the nucleosome reduces the length of the DNA by a factor of six.

Second-Order of Packaging

It involves the association to form a 30nm Chromatin Fiber. Despite more than two decades of investigation, the structure of the 30nm fiber remains a subject of debate. Two models in which the nucleosomal filament is coiled have been proposed.

1. The Zig-Zag model.

2. The Solenoid model.

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

Figure: Naked DNA molecules are wrapped around histones to form nucleosomes. Nucleosomes are organized into 30 nm fibers, which in turn are organized into looped domains. When cells prepare for mitosis, the loops become further compacted into mitotic chromosomes.

Regardless of how it is accomplished, the assembly of 30nm fibers further reduces the length of DNA by a factor of seven, or by a factor of 42 altogether (i.e. nucleosome + 20nm chromatin fiber). That means a 30nm fiber would contain 1.26μm (1260nm) long DNA.

This is still insufficient to fit 1-2 meters of DNA into a nucleus approximately 10^-5 meters across. Additional folding of the 30nm fiber is required to compact the DNA further. Although the exact nature of this folded structure remains unclear, one popular model proposes that the 30nm fiber forms loops of 40-90kb that are held together at their bases by a proteinaceous structure referred to as the nuclear scaffold.

Two classes of proteins that contribute to the nuclear scaffold have been identified. One of them is topoisomerases II and other is structural maintenance of chromosome (SMC) protein. Topoisomerase II is abundant in both scaffold preparations and purified mitotic chromosomes. Topo II regulates the degree of supercoiling and is also expected to untangle the DNA molecules of different loops when they get intertwined.