Packaging of DNA into Microscopic Nucleus
Human DNA is 2 billion nanometers in length and fits into a small nucleus which is about 2000-6000 nanometers in diameter. DNA passes through various stages to get accommodated within the nucleus. Let us explore the stages of organization of DNA.
Journey of DNA
Central dogma proposed by FrancisCrick in 1958, proves that the information flows from DNA to RNA and then to proteins.
Fig1 – Flow of genetic information
The first step of this dogma is the replication where the information within the DNA gets replicated. The second step is transcription wherein the information within the DNA gets copied to RNA. The third step is translation where the information within the RNA is utilized to synthesize proteins.
Packing ratio
It is the ratio obtained by dividing the length of DNA with the length into which it is packaged. The measurement of the packing ratio gives us an idea about the level to which DNA gets condensed. The DNA moves through several hierarchies of organization to obtain different packing ratios.
For example – There are 4.6 x 10^7 bp present in the shortest human chromosome. To obtain the length of DNA the number of base pairs is multiplied with .34nm which is the distance between the two base pairs. The length of DNA so obtained comes to 14,000 µm. The most condensed form of DNA during mitosis measures 2 µm in length. Hence the packing ratio comes to 7000 (14,000/2).
Organization of DNA within prokaryotes -
The prokaryotic organisms lack a well defined nucleus however the DNA is organized with the help of some positively charged groups into a structure named as nucleoid.
The DNA is negatively charged due to the phosphate groups and the repulsion due to this negative charge is counteracted by the association of DNA with positively charged polyamines such as spermine and spermidine. These positively charged groups shield the negative charges of the DNA phosphate groups.
Along with polyamines there are abundant small proteins which give the DNA a compact structure (ex. H-NS). The DNA finally attains a supercoiled structure which gets opened with the help of enzymes like DNA gyrase during replication.
Organization of DNA within eukaryotes
In eukaryotic organisms DNA is present along with some basic proteins in the form of chromosomes within the nucleus and chromatin is a unit of analysis of a chromosome which gives a general idea of the nature of a chromosome
What are Histones?
They are the positively charged basic proteins.They are of 5 major types and contain amino acids residues like lysine and arginine. The five major types are H1, H2A, H2B, H3 and H4.
Formation of nucleosome
The association of the DNA with histone proteins starts from the formation of nucleosomes.
A neucleosome is a fundamental unit of chromatin which is made up of a histone octamer wrapped around by duplex DNA. The histone octamer acts like a core and consists of two copies of each of these histone proteins H2A, H2B, H3 and H4. This octamer is wrapped around by the duplex DNA which is approximately 147bp in length. During the coiling process DNA takes one full turn and covers ¾ th of the histone octamer in the next turn. Large number of repeating units of neucleosomes forms chromatin. Nucleosomes together with DNA appear like beads on a string. At this stage the DNA is 10nm in diameter and attains a packing ratio of about 6.
Fig 1 – Structure of a single neucleosome
Role of Histone 1 or H1-
It holds the DNA which is wrapped around the nucleosome in a proper position. The linker DNA is made up of approximately 20-60 bp and the H1 binds to the linker DNA. This gives the stability to the zig-zagged 30 nm chromatin fiber which is the next level of organization.
Formation of chromatin fiber or solenoid fiber
This stage is seen during interphase in the cell cycle. After the beads on a string stage the DNA coils in such a way that at least 6 nucleosomes are packed per coil. In this stage DNA attains a diameter of 30 nm and this level of organization is known as 30 nm fiber or solenoid fiber. When the chromatin is extracted from isotonic buffers it appears like a 30 nm fiber. At this stage it attains a packing ratio of 10.
Stages after solenoid fiber
Later the solenoid fiber get further coiled and condensed and is organized into loops, scaffolds and domains to obtain cytologically visible threads known as chromatids. The looping is such that the base of the loops is attached to the same protein skeletal work. Some metallic ions like calcium and copper along with non histone proteins help in the looping process. This increases the packing ratio to about 1000 in interphase chromosomes and about 10,000 in mitotic chromosomes.
Fig3 - Levels of organization of DNA
What are non Histone proteins ?
Chromosomal proteins which are not histones are grouped under non histone proteins. They can be acidic, basic or neutral. Their mol. wt varies from 10 KD to many million Daltons.
There are about 750-2000 different kinds of non histone proteins and examples of most abundant ones are Topoisomerases and High mobility group of proteins (HMGs). Functions mostly served by them are
Histone modifications
The primary structure of all the histone proteins remains the same but they vary from each other due to the chemical modifications which occur at a later stage. Some of these modifications are:
Acetylation:
During this modification, acetyl groups (CH3CO-) are added to the lysine residues of histone proteins. The core of the nucleosomes, is made up of lysine rich N terminal residues of the histone proteins. Being positively charged these residues interact with the negatively charged phosphate groups of the DNA. Enzymes like histone acetyl transferase (HAT) acetylate the lysine residues hence inhibiting their interaction with the phosphate groups of DNA. As a result DNA is inhibited from getting further condensed and this leads to active transcription of the genes.
However enzymes like histone deacetylases (HDACs), remove the acetyl groups from the lysine residues leaving them free to interact with DNA. This interaction helps in further condensation of DNA so that it attains a fully coiled structure which is less exposed to the transcription enzymes.
Phosphorylation :
This modification involves the addition of phosphate groups to serine and threonine residues which makes the chromosomes more compact and prepares them for mitosis and meiosis.
Methylation:
This modification involves the addition of methyl groups to lysine and arginine residues. Methylation of some residues either stimulates or inhibits gene transcription at that region.
Euchromatin and Heterochromatin
The folding of DNA is not uniform throughout. In some regions the folding is highly compact and intricate giving rise toheterochromatic regions and the others are called euchromatin regions.
Some general characters of heterochromatin
It is densely packed and is found in the regions of chromosomes where there are few or no genes such as
Some general characters of euchromatin
Most parts of the chromosomes which are rich in transcriptionally active genes are termed as euchromatin regions.They are made up of loosely packed 30nm fibers. These regions are separated from heterochromatin by insulators. The histone proteins in this region show increased acetylation.
What happens to nucleosomes during transcription?
The neucleosome blocks the promoter region of a gene hence inhibiting the transcription factors from accessing it. During transcription of a gene either the nucleosome is expelled or in some other cases it slides along the DNA so that the transcription factors can bind the promoter region.
A set of proteins remove the neucleosome in front of the DNA to be transcribed and allow the RNA polymerase II (RNAP II) to travel down the DNA. After completion of transcription of that fragment of DNA the proteins replace the necleosome back into its position.
References
Fig1 – http/library.thinkquest.org/C0122429/intro/genetics.htm
Fig2 - http/www.accessexcellence.org/RC/VL/GG/nucleosome.php
Fig3 - http/plantcellbiology.masters.grkraj.org/html/Plant_Cell_Genetics1-Chromosomes.htm
Human DNA is 2 billion nanometers in length and fits into a small nucleus which is about 2000-6000 nanometers in diameter. DNA passes through various stages to get accommodated within the nucleus. Let us explore the stages of organization of DNA.
Journey of DNA
Central dogma proposed by FrancisCrick in 1958, proves that the information flows from DNA to RNA and then to proteins.
Fig1 – Flow of genetic information
The first step of this dogma is the replication where the information within the DNA gets replicated. The second step is transcription wherein the information within the DNA gets copied to RNA. The third step is translation where the information within the RNA is utilized to synthesize proteins.
Packing ratio
It is the ratio obtained by dividing the length of DNA with the length into which it is packaged. The measurement of the packing ratio gives us an idea about the level to which DNA gets condensed. The DNA moves through several hierarchies of organization to obtain different packing ratios.
For example – There are 4.6 x 10^7 bp present in the shortest human chromosome. To obtain the length of DNA the number of base pairs is multiplied with .34nm which is the distance between the two base pairs. The length of DNA so obtained comes to 14,000 µm. The most condensed form of DNA during mitosis measures 2 µm in length. Hence the packing ratio comes to 7000 (14,000/2).
Organization of DNA within prokaryotes -
The prokaryotic organisms lack a well defined nucleus however the DNA is organized with the help of some positively charged groups into a structure named as nucleoid.
The DNA is negatively charged due to the phosphate groups and the repulsion due to this negative charge is counteracted by the association of DNA with positively charged polyamines such as spermine and spermidine. These positively charged groups shield the negative charges of the DNA phosphate groups.
Along with polyamines there are abundant small proteins which give the DNA a compact structure (ex. H-NS). The DNA finally attains a supercoiled structure which gets opened with the help of enzymes like DNA gyrase during replication.
Organization of DNA within eukaryotes
In eukaryotic organisms DNA is present along with some basic proteins in the form of chromosomes within the nucleus and chromatin is a unit of analysis of a chromosome which gives a general idea of the nature of a chromosome
What are Histones?
They are the positively charged basic proteins.They are of 5 major types and contain amino acids residues like lysine and arginine. The five major types are H1, H2A, H2B, H3 and H4.
Formation of nucleosome
The association of the DNA with histone proteins starts from the formation of nucleosomes.
A neucleosome is a fundamental unit of chromatin which is made up of a histone octamer wrapped around by duplex DNA. The histone octamer acts like a core and consists of two copies of each of these histone proteins H2A, H2B, H3 and H4. This octamer is wrapped around by the duplex DNA which is approximately 147bp in length. During the coiling process DNA takes one full turn and covers ¾ th of the histone octamer in the next turn. Large number of repeating units of neucleosomes forms chromatin. Nucleosomes together with DNA appear like beads on a string. At this stage the DNA is 10nm in diameter and attains a packing ratio of about 6.
Fig 1 – Structure of a single neucleosome
Role of Histone 1 or H1-
It holds the DNA which is wrapped around the nucleosome in a proper position. The linker DNA is made up of approximately 20-60 bp and the H1 binds to the linker DNA. This gives the stability to the zig-zagged 30 nm chromatin fiber which is the next level of organization.
Formation of chromatin fiber or solenoid fiber
This stage is seen during interphase in the cell cycle. After the beads on a string stage the DNA coils in such a way that at least 6 nucleosomes are packed per coil. In this stage DNA attains a diameter of 30 nm and this level of organization is known as 30 nm fiber or solenoid fiber. When the chromatin is extracted from isotonic buffers it appears like a 30 nm fiber. At this stage it attains a packing ratio of 10.
Stages after solenoid fiber
Later the solenoid fiber get further coiled and condensed and is organized into loops, scaffolds and domains to obtain cytologically visible threads known as chromatids. The looping is such that the base of the loops is attached to the same protein skeletal work. Some metallic ions like calcium and copper along with non histone proteins help in the looping process. This increases the packing ratio to about 1000 in interphase chromosomes and about 10,000 in mitotic chromosomes.
Fig3 - Levels of organization of DNA
What are non Histone proteins ?
Chromosomal proteins which are not histones are grouped under non histone proteins. They can be acidic, basic or neutral. Their mol. wt varies from 10 KD to many million Daltons.
There are about 750-2000 different kinds of non histone proteins and examples of most abundant ones are Topoisomerases and High mobility group of proteins (HMGs). Functions mostly served by them are
- Helping in the structural organization of chromatin fibers
- Maintaining stability of the chromatin fibers
- Involved in gene regulation
Histone modifications
The primary structure of all the histone proteins remains the same but they vary from each other due to the chemical modifications which occur at a later stage. Some of these modifications are:
Acetylation:
During this modification, acetyl groups (CH3CO-) are added to the lysine residues of histone proteins. The core of the nucleosomes, is made up of lysine rich N terminal residues of the histone proteins. Being positively charged these residues interact with the negatively charged phosphate groups of the DNA. Enzymes like histone acetyl transferase (HAT) acetylate the lysine residues hence inhibiting their interaction with the phosphate groups of DNA. As a result DNA is inhibited from getting further condensed and this leads to active transcription of the genes.
However enzymes like histone deacetylases (HDACs), remove the acetyl groups from the lysine residues leaving them free to interact with DNA. This interaction helps in further condensation of DNA so that it attains a fully coiled structure which is less exposed to the transcription enzymes.
Phosphorylation :
This modification involves the addition of phosphate groups to serine and threonine residues which makes the chromosomes more compact and prepares them for mitosis and meiosis.
Methylation:
This modification involves the addition of methyl groups to lysine and arginine residues. Methylation of some residues either stimulates or inhibits gene transcription at that region.
Euchromatin and Heterochromatin
The folding of DNA is not uniform throughout. In some regions the folding is highly compact and intricate giving rise toheterochromatic regions and the others are called euchromatin regions.
Some general characters of heterochromatin
It is densely packed and is found in the regions of chromosomes where there are few or no genes such as
- Centromeres
- Telomere
Some general characters of euchromatin
Most parts of the chromosomes which are rich in transcriptionally active genes are termed as euchromatin regions.They are made up of loosely packed 30nm fibers. These regions are separated from heterochromatin by insulators. The histone proteins in this region show increased acetylation.
What happens to nucleosomes during transcription?
The neucleosome blocks the promoter region of a gene hence inhibiting the transcription factors from accessing it. During transcription of a gene either the nucleosome is expelled or in some other cases it slides along the DNA so that the transcription factors can bind the promoter region.
A set of proteins remove the neucleosome in front of the DNA to be transcribed and allow the RNA polymerase II (RNAP II) to travel down the DNA. After completion of transcription of that fragment of DNA the proteins replace the necleosome back into its position.
References
Fig1 – http/library.thinkquest.org/C0122429/intro/genetics.htm
Fig2 - http/www.accessexcellence.org/RC/VL/GG/nucleosome.php
Fig3 - http/plantcellbiology.masters.grkraj.org/html/Plant_Cell_Genetics1-Chromosomes.htm
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