DNA packaging in eukaryotes

Molecular organization of eukaryotic chromosome

“The DNA wrapped around histone octamer is called as a nucleosome”

Image credit: www.emilianoponzi.com

In the previous article “ story of chromosome” we had covered the history and structure of the chromosome in brief. The chromosomes are the basic unit of hereditary. DNA is arranged on the chromosome and made up of nitrogenous bases, phosphate and sugar.


For more detail on the structure of DNA read the article: Story of DNA


A haploid genome is consist of 3.7 billion base pairs per cells. If we consider the DNA of all body cells and make a single long chain we can reach to the sun and believe me it is longer than that distance.

The DNA folded 104 times to its original length and become a metaphase chromosome. Here at the different stage of arrangement, DNA is arranged in a different structure with several proteins.

The folding of DNA is started when the proteins called Histones interact with DNA. The eukaryotic DNA packaging is organized into 3 major structures;

  • Nucleosome assembly
  • 30nm fiber
  • Chromatid

The nucleosome assembly

H1, H2A, H2B, H3 and H4 are 5 major types of histone protein involved eukaryotic DNA arrangement in which histones H2A, H2B, H3 and H4 creates nucleosome assembly. “When the  DNA wrapped around histones (H2A, H2B, H3 and H4) the structure is called as nucleosome assembly.” These proteins help in assembling DNA into the nucleus.

Nucleosome structure

Each nucleosome is made up of eight Histone molecules (each H2A, H2B, H3, H4 two times in a single nucleosome) wrap around DNA molecule.

Image credit: www.wikipedia.org

Histone proteins are positively charged protein molecules which interact with negatively charged phosphate of DNA and makes a tight wrap. The H1 histone is not involved in the nucleosome assembly. Hence the remaining four histones are called as core element or nucleosome core particles.

DNA molecules wrap around the Octamer of 4 histones and create the nucleosome core.

The nuclease enzyme helps to cut DNA into small pieces. The enzyme is used in the study of nucleosome properties. Particularly, this types of nuclease enzyme only cut the DNA which links two nucleosome assembly.

However, the enzyme is unable to cut the tightly wrapped DNA and the nucleosome assembly remains intact. “The short stretch of DNA which connects the two nucleosome assembly is called as a linker DNA”.

The linker DNA is a variable. The length of linker DNA varies from organism to organism. Typically, it is ranging from 20 to 60bp. Moreover, the DNA in the nucleosome assembly is invariable remain intact in every eukaryote. The length of the nucleosome DNA is 147bp.

Noticeably, H1 is not a part of histone core assembly, it binds to histone DNA and hence called as linker histone. Only single H1 histone is present on each linker DNA therefor the H1 histone is half in number as compared to other histones.

H1 histone is slightly larger than other histones. The histones in nucleosome core assembly have a histone fold domain which facilitates the binding of DNA to histones. 

Each histone molecule from the core histone assembly has the amino terminus tail of amino acids. The nucleosome core along with the linker DNA is called as chromatosome.

For performing replication, it is very crucial to release histones from DNA thus the DNA in nucleosome core assembly is negatively supercoiled. It wrapped left-handedly which allows DNA to perform replication.


For more detail on DNA replication read the article: The General process of DNA replication


We had discussed earlier that the only linker DNA can be digested with the nuclease and the DNA in histone core assembly is protected by nuclease activity. This function is served by the H1 histone protein.

The H1 Histone binds to the DNA in two distinct regions. The one end of the H1 histone binds near the linker DNA and another end of H1 binds in the middle of the 147bp DNA of nucleosome assembly, asymmetrically.

Thus the H1 histone protects the nucleosome core DNA from the nuclease attack and helps nucleosome core DNA to wrap tightly into the assembly.

The long sequences of nucleosome assembly and linker DNA is called as a chromatin. The chromatin is,

Nucleosome core assembly (147bp DNA + histone octamers) + linker DNA + H1 histone

The addition of the Histone H1 gives the next level of compaction to the DNA by creating the 30nm fiber.

30nm fiber

The 30nm fiber organized further into one of the two described models: solenoid model and the zigzag model.

In the solenoid model, the 11nm fiber of nucleosome is arranged as like solenoids in which the linker DNA is arranged in the centre. However, the linker DNA never passes through the central axis.

In the zigzag model of 30nm fiber, the linker DNA is passed through the central axis of the fiber and creates a zigzag pattern of arrangement.

Solenoid and zigZag manner of nucleosome arrangement. Image credit: www.mechanobio.info

 

The entire process of this next level of compaction depends on the length of the linker DNA. As we discussed earlier the length of the linker DNA is variable. If the linker DNA is long enough to passes through the axis, it will arrange in a zigzag manner otherwise it will arrange in the solenoid.

Till now our DNA is arranged from a double helix to nucleosome and from nucleosome to 30nm fiber. Two nucleosomes are bound by linker DNA and arrangement of 6 nucleosomes with a linker DNA creates the 30nm fiber.

Depending upon the length of linker DNA, the nucleosome assembly will be organized as solenoid or zigzag. But how the nucleosome assembly in 30nm fiber remains intact?

Remember the histone tail?

The 30nm fiber cannot be formed without the Histone tail. The amino-terminal histone tail is capable of binding with adjacent histones into a 30nm fiber. This will stabilize the 30nm fiber in a compact form.

Different nanometer fibers of DNA. Image credit: www.csls-text.c.u-tokyo.ac.jp

The tail of Histones H2A, H3 and H4 are more specifically involved in the formation of 30nm fiber. Interestingly, the negatively charged histone fold domains of histone H2A interact with the positively charged amino terminus tail of adjacent nucleosomes histone H4.

The nucleosome and 30nm fiber results in the compaction of DNA by 40 folds. Still, this level of packaging is not sufficient to fit DNA into a nucleus. Another group of protein help in further packaging. These proteins are the scaffold protein. The scaffold protein helps in looping of 30nm fiber further and forms the Nuclear scaffold.

The image represents eukaryotic DNA organization. Image credit: www.slideplayer.com

 

Chromatid

Finally, the loop creates chromatid (not chromatin). The chromatid is now attached with one centromere and becomes a chromosome. Each chromosome has two sister chromatids.

the chromatid contains the euchromatin and heterochromatin regions. More detail on euchromatin and heterochromatin region click here,

Histone proteins play important role in the maintenance of gene expression. Histone remodelling and modification regulate the replication and transcription.

During the replication, polymerase only accesses the DNA which is not bound by histones. Histone acetylation, methylation, phosphorylation and other modification allows DNA replication and transcription.

Image credit: www.ib.bioninja.com.au

Tightly packed DNA looks darker on the chromosome and called as heterochromatin region while transcriptionally accessible regions are loosely packed and are called as euchromatin region. 

In the heterochromatin region, the nucleosome assembly is organized into higher order structure as compared to euchromatin region. 

We can not observe DNA under the microscope but we can see chromosome under the microscope even we can count the number of chromosomes.

 

Article written by: Tushar Chauhan

Article reviewed by: Ravi Parmar

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