DNA Packaging: Definition
In 1974, Reger Kornberg discovered that chromosomes are made up of DNA and protein. In eukaryotes, DNA arrangement is significantly more complicated. Each chromosome has a single DNA molecule that runs the length of the chromosome from one end to the other. The DNA molecule is coiled and folded many times, then linked to numerous proteins to form chromatin, which is made up of nearly equal numbers of DNA and proteins.
Histone proteins and Non-Histone proteins are two types of chromosomal proteins. Histones are proteins that help DNA fit into chromatin fibers more easily. Histone proteins are positively charged and include a large number of arginine and lysine amino acids, which bind to negatively charged DNA.
There are two types of histones:
Core Histones
Linker Histones
H2A, H2B, H3, and H4 are the four basic or core histones. An octamer is made up of two H3, H4 dimers, and two H2A, H2B dimers. Linker histones hold the DNA in place on the nucleosome, allowing it to be released for transcription.
Histones can be changed to change the amount of DNA packed. Histones become more hydrophobic when the methyl group is added. This leads to very tight DNA packaging. Acetylation and phosphorylation loosen DNA packing by making it more negatively charged.
Non-histone proteins are a heterogeneous set of structural and regulatory proteins found in the structure of chromatin and present in small amounts. Non-histone proteins have a wide range of roles since they contain:
Structural proteins penetrate the structure of specific portions of the DNA molecule and serve a key role in the spatial organization of DNA within the nucleus, as they are responsible for shortening DNA by 100,000 times through the formation of packed chromatin. Regulatory proteins control whether or not the DNA code is used to make RNA, proteins, and enzymes.
Packaging of DNA:
The DNA double helix is packaged into so-called Nucleosomes at the first level of packaging: sets of around 200 base pairs of DNA are twisted around a nucleus of eight proteins, the histones. Histone proteins are positively charged due to their amino acid makeup, but they can be changed by enzymes to change their total charges. Histone acetyl transferases, for example, cause acetyl moieties to be linked to histones, neutralizing the inherent charge of the histones. Histone deacetylases are a class of enzymes that can remove these acetyl moieties and restore the positive inherent charge of histones. Because the DNA’s constituents, the nucleotides, are negatively charged, the charge state of the histones is thought to have a significant impact on the DNA’s packaging density in the chromatin.
DNA can be further packed by generating chromatin fibers, which are nucleosome coils. During mitosis or cell division, these fibers are condensed into chromosomes. The packing of chromatin into chromosomes that we are most familiar with, on the other hand, happens only during a few phases of mitosis.
The majority of the time, DNA is packaged randomly. The beads are around 10 nm in diameter, compared to the 2-nm diameter of a DNA double helix. A DNA molecule in this form is about seven times shorter than a double helix without histones. The nucleosomes and the linker DNA between them are coiled into a 30-nm chromatin fiber during the next step of compaction. The chromosome is now around 50 times shorter than the expanded form as a result of this coiling. Several fibrous proteins are utilized to pack the chromatin at the third level of packing. These fibrous proteins also ensure that each chromosome in a non-dividing cell occupies a distinct nucleus region that does not overlap with the nucleus of any other chromosome.
During the S phase of interphase, DNA replicates. The chromosomes are made up of two connected sister chromatids after replication. Cohesion proteins bind the pairs of identically packed chromosomes together when they are fully compacted. In a region known as the centromere, the sister chromatids are most connected. Under a light microscope, the conjoined sister chromatids with a diameter of roughly 1 m are evident. Because the centromeric region is thick, it will seem like a confined area.
Euchromatin refers to loosely packed regions that are required for protein synthesis and are crucial to the cell. Because euchromatin has a loose packing of DNA, transcription proteins can easily get in and create RNA. Heterchromatin, on the other hand, is a type of DNA that is firmly packed through DNA as well as good ol’ histone methylation.
Why is it necessary to package DNA?
The DNA is around 3 meters long and must fit into the nucleus, which is only a few micrometers in diameter. The DNA molecules must be packed into an incredibly compressed and compact structure called chromatin to fit into the nucleus. The DNA is reduced to an 11 nm fiber during the earliest phases of packaging, which represents approximately 5-6 folds of compaction. This is accomplished by packaging nucleosomes in a specific order. DNA packaging is divided into three categories.
1. The nucleosome is the first-order DNA packing.
2. Solenoid fiber is a type of second-order DNA packing.
3. Scaffold loop Chromatids Chromosome is the third order DNA packaging.