Chromatin Organization: 7 Interesting Facts To Know


Chromatin contains DNA and Proteins

The cell division or cell cycle in eukaryotes cells induces significant changes in the chromosomal structure. In the eukaryotic cells present in the G0 phase (non-dividing phase) and those in the initial phases of the cell cycle, such as G1, S, and G2 phase (stages of interphase), the chromatin (chromosomal material) is amorphous and randomly scattered in specific portions of the nucleus.

In the S phase, DNA replication (duplication) occurs, which is already present in the amorphous state. Thus every chromosome produce two sister chromatids (called sister chromosomes) that remain joined with one another even after replication is finished.

The chromatin becomes significantly more condensed during the prophase of mitosis, appearing in a specific number of sister chromatids specific to species.

Chromatin comprises thread-like structures containing protein, and DNA is roughly equivalent to masses. A small quantity of RNA is usually present in chromatin. In chromatin, the proteins are tightly bound with the DNA. These proteins are known as histones. DNA sticks across histone proteins to form building blocks of chromatin structure known as a nucleosome.

chromatin organization
Figure: Chromatin organization is supported by the structures composed of DNA and Histone proteins

Likewise, numerous non-histone proteins are also found in chromatin. Histone proteins are generally involved in gene expression regulation along with the integral maintenance of chromosomal structure.

Starting with nucleosomes, eukaryotic chromosomal DNA is packed into a progression of higher-level structures that finally yield a compact design known as chromosome that can be seen with the help of a low magnifying power microscope (light microscope). We can easily compare this easily visible compact structure with the DNA of a bacterium.

Histones consists of Basic Proteins

  • Histones exist in the chromatin of almost every eukaryotic cell.
  • Histones have a molecular weight between 11,000 and 21,000 kilodaltons.
  • Histones have abundance of amino acids like lysine and arginine (about 25%) which are basic in nature.
  • The histone proteins present in eukaryotic cells are classified into five different classes based on their amino acid composition and molecular weight. These are namely: H1, H2A, H2B, H3 and H4. 

Histones proteins like H1, H2A, and H2B exhibits the least sequence similarity among eukaryotes.

Figure: Nucleosome is made up of DNA and Histone protein complex (core). Histone core is made of various subunits of proteins

The H4 histone proteins have conserved functions, and only 2 out of 102 residues of amino acids are different among the amino acid residues of H4 histone proteins of peas and cows. Only eight amino acid residues differ in the amino acid residues of yeast and humans. The amino acid sequence is almost identical in all eukaryotes.

Every kind of histone has variations in structures and amino acid sequence; it is because the side chains of amino acid are enzymatically manipulated by glycosylation, phosphorylation, ADP-ribosylation, and acetylation or methylation. These chemical modifications may affect the shape, net electric charge and various other properties of histones. They also affect the functional and structural properties of the chromatin and regulate transcription.

Nucleosomes Are the Structural Units of Chromatin

A eukaryotic chromosome is highly compact form of DNA molecule having length of approximately 105 micrometres, which is going to fit into the nucleus of size approximately 10 micrometres. This compaction includes various levels of continuous folding and supercoiling events.

Treating chromosomes for partial unfolding reveals that some tightly bound beads of proteins like structures are present regularly.

These “beads on-a-string” structures are actually the complexes of histone proteins and DNA. The Bead (DNA and histones) and the connecting DNA between the two beads form a nucleosome. A nucleosome is the structural unit of the higher-order chromatin (chromosomes) present in a cell.

Every bead of a nucleosome consists of eight histone molecules: two duplicates every one of H4, H3, H2A and H2B. A single nucleosome contains 200 bp of DNA, out of which 146 bp DNA are tightly wrapped around the histone core.

In contrast, the remaining DNA acts as a linker DNA between two nucleosomes beads and binds to the H1 subunit of the histone protein.

Figure: Tight packing of nucleosomes and the presence of active and silent forms are a part of Chromatin organization,_which_comprises_147_bp_of_DNA_wrapped_ar.jpg# /media/File:The_basic_unit_of_chromatin_organization_is_the_nucleosome,_which_comprises_147_bp_of_DNA_wrapped_ar.jpg

When chromatin is treated with DNA digesting enzymes, it causes selective digestion of linker DNA, resulting in the detachment of histone particles containing 146 bp of bound DNA that has been protected from DNA digesting enzymes.

Scientists have successfully purified nucleosome and after x-ray diffraction studies, it is observed that a nucleosome comprised of the eight histone molecules with some wrapped DNA around it which is present in the form of a left-handed solenoidal supercoil.

Later studies justified the underwound eukaryotic DNA despite of the presence of proteins that underwind DNA. This depicts that nucleosomes with solenoidal wrapping of DNA is actually one type of supercoiling that can be possessed by the underwound (negatively supercoiled) DNA. For tight wrapping of DNA on the histone proteins needs to eliminate around one turn in the DNA.

When the nucleosome core proteins bind to a circular DNA in a relaxed state, it induces negative supercoiling in the closed circular DNA. Since this binding process doesn’t break the DNA or alters the linking number, the development of negative solenoidal supercoiling should have some positive supercoiling for compensation in the unbound area of the DNA.

The eukaryotic topoisomerases can deal with positive supercoiling by relaxing the positive supercoil (unbound) and leaving the negative supercoil fixed (by the site from where it is linked with the core proteins of the histone), which results in a net decrement in the linking number. For sure, topoisomerases have been proved essential for associating chromatin obtained from histones and the circular DNA in vitro.

The sequence of the DNA binding to the histone proteins also affects the binding strength and other parameters of DNA binding with histones. Histone proteins do not randomly bind with the DNA. Although the mechanism is not clearly understood until now, the Histone proteins prefer to bind with the DNA from the AT-rich sequence (sequence having a lot of AT base pairs).

The tight binding of the DNA over the nucleosome’s histone centre needs minor groove compression in the DNA at binding points. Also, there should be some (2 or 3) AT base pairs for making the compression process more feasible.

Several other proteins are also needed to position DNA on nucleosomal histone core accurately. In a few organisms, several proteins interact with a particular DNA sequence and help form a complex with nucleosomal histone core. This process also modulates the gene expression in eukaryotes.

Nucleosomes to Higher Order Structures

Winding of DNA around a histone core of nucleosome shortens the DNA length for about seven-folds. The compaction in a chromosome is as high as 10,000 folds supported by adequate proof for the presence of the higher-order chromosomal organization. Some isolated chromosomes show that nucleosomes exist in highly organized structures known as 30 nm fibre.

That kind of packaging needs one molecule of H1 histone per nucleosome. Nucleosome organization into 30 nm fibres are not present over the whole chromosome set is interspersed by areas where DNA is bound with sequence-specific non-histone proteins. The 30 nm structure additionally appears in the region where transcriptional activity is going on.

Areas in which genes are under expression or transcription are obviously in a less-ordered condition containing very little or low H1 histone subunit. The 30 nm fibre is considered the second degree of chromatin association, giving 100 fold compactness to the DNA.

Although the exact mechanism of higher-level supercoiling is still not clearly understood, it looks like some regions of DNA interact with the nuclear scaffold.

The scaffold region (where DNA binds with the histone of a nucleosome) rare separated by a 20 to 100 kbp long DNA loop. This loop DNA may contain some related genes as well. For instance, in Drosophila, histone-coding genes group together in loops and bind to the scaffold.

The scaffold seems to contain few other proteins, a lot of histone H1 (situated in the inside structure of the fibre) and topoisomerase II. The presence of topoisomerase II further points out towards the relation between chromatin structure and DNA underwinding.

Topoisomerase II is so vital for maintaining the chromatin structure that inhibitors of topoisomerase II enzyme are capable of killing dividing cells. These inhibitors promote strand breakage but do not allow topoisomerase II to seal these breaks.

Proof exists for extra layers of association in eukaryotic chromosomes, each layer significantly upgrading the level of compaction.

Figure: Different levels of chromatin organization

Higher-level chromatin structure presumably changes from chromosome to chromosome, within a chromosome, and from condition to condition the existence of a cell. However, not a single model is capable of explaining these structures. Although, the rule is clear: in eukaryotic chromosomes, DNA compaction has coils upon coils type of condensation.

The word “chromosome” is in reference to a nucleic acid, which is the reservoir of the genetic information of an organism. Similarly, this term is also used for the compactly packed coloured structures visible in the nucleus of a stained dye cell visible under a microscope.

Maintenance of Condensed Chromosome Structures by SMC Proteins

The third class of chromatin proteins, along with the histones and topoisomerases, is the SMC (structural maintenance of chromosomes) proteins. The structure construction of SMC proteins contains five particular domains.

The carboxyl-terminal amino-terminal of the globular domain plays a role in ATP hydrolysis and is associated with the α-helical coiled motifs attached with the hinge domain. These are dimeric protein which forms a V-shape complex which is also connected to the hinge domain.

The C and N domain comes in proximity to finalize the formation of ATP hydrolytic site at both the ends of the V complex. Proteins listed in the SMC family are generally found in many living organisms, from microbes to mammals. Eukaryotes have broadly two types of SMC proteins, namely condensins and cohesins.

The cohesins are assumed to have an important role in joining sister chromatids after replication till they condense to form chromosome at metaphase. This interaction is important because chromosomes need to detach properly during cell division.

Although well-explained mechanisms through which cohesins connect sister chromosomes and the importance of ATP hydrolysis are not clearly understood. As the cell prepares itself to enter mitosis, condensin plays a significant role in the chromosomal condensation.

Under In-vitro conditions, condensins interact with the DNA and makes positive supercoils; restricting condensin causes the DNA to become overwound, instead of underwinding initiated by the nucleosome binding. The exact mechanisms through which condensin promotes the compacting of chromatin is not clearly understood yet.

Level of Organization in Bacterial DNA

We are about to discuss the detailed structure of bacterial chromosomes. The bacterial DNA is present in the form of a compact structure known as a nucleoid. It occupies a huge part of the cell volume (Figure). The DNA joins the inner membrane of plasma membrane at several locations.

In comparison with the eukaryotic chromatin, fewer details are known about the nucleoid. In E. coli, a scaffold-like structure seems to arrange the closed circular chromosome into an arrangement of loops, as depicted above for chromatin. However, bacterial DNA doesn’t appear to have any structure similar to the eukaryotic nucleosomes.

Although E. coli has several proteins similar to the eukaryotic histones (they are usually dimeric (Mw 19,000 KDa), they are not much stable and degrades within few minutes. Thus, they are not found in the form of a DNA histone complex. The bacterial chromosome provides more accessible genetic information; therefore, it is considered a much dynamic bio-macromolecule.  

Figure: Bacterial DNA is present in the form of single chromosome known as nucleoid and plasmids (extra chromosomal DNA)

The bacterium divides through binary fission (a type of cell division), and it takes about 15 min. In contrast, a common eukaryotic cell does not enter into the division cycle for hours or even months. Similarly, a much significant part of prokaryotic DNA is utilized for encoding RNA and protein.

Increased rates of cellular metabolism in microbes imply that a high proportion of the DNA undergoes transcription or replication at a given time compared to eukaryotic cells.


In this article we have discussed about the crucial aspects of DNA packaging and higher order structures. To gain better understanding for this topic please go through our article on DNA supercoiling.

Interview Q&A

Q1. What are the functions and structure of a chromosome?

Answer:  Chromosomes have a shape like thread and are placed inside the nucleus of a eukaryotic cell. Prokaryotes do not have multiple chromosomes. Instead, they generally have a single circular chromosome known as a nucleoid. Chromosomes are DNA (usually a single DNA molecule) and proteins (histones and some non-histone proteins). The exclusive function of chromosomes is that they carry genes responsible for the inheritance of genetic traits and the transfer of genetic information to off-springs.

Q2. How can changes in the structure of chromosomes affect an individual?

Answer: There are a lot of factors that are responsible for the structural changes in the chromosomes. These changes could bring about differences in the gene expression of an individual, which eventually cause changes in protein expression and the body functions as well. 

Q3. How is a very long DNA structure fitted into the small nuclei?

Answer: DNA is present in the chromosomes has a length of centimeters. It fits in the nucleus having the radii of the order of micrometers with the help of nucleic acids binding histone proteins. The DNA of chromosomes is negatively charged, which binds to the positively charged histone proteins to form nucleosomes. A single nucleosome wraps around 146 base pairs of DNA, making 1.65 turns on the histone core. 

Q4. What are the two types of chromosomes?

Answer: Based on the sex of an individual, chromosomes are divided into two categories

  1. 1- Autosomes (responsible for the functioning of the body. They are 44 in number, 22 pairs)
  2. 2- Allosomes (Sex chromosomes, responsible for the functioning of the secondary sexual characteristics they are 2 in number, one pair)

Humans have autosomes (22 pairs) and allosomes (one pair) or sex chromosomes.

Q5. Name the components of eukaryotic chromosomes.

Answer: The chromosomes in eukaryotes are mainly composed of protein components (histones and non-histones), nucleic acid components (DNA and small amount of RNA), and some metal ions, etc.

Q6. What would happen if a person has an extra chromosome?

Answer: Extra chromosomes in the cells of a person leads to chromosomal abnormalities.

The presence of an extra copy of the 21st chromosome (trisomy) leads to down syndrome. Klinefelter’s syndrome is caused by an extra X chromosome in the individual, making its genotype 44+XXY.

Q7. What are the types of chromosomes based on the position of the centromere?

Answer: there are four types of chromosomes based on the position of the centromere

  1. Metacentric
  2. Sub-metacentric
  3. Acrocentric
  4. Telocentric

Q8. Mention two ways to classify chromosomes.

Answer: Chromosomes are classified based on several criteria:

  1. Based on the position of centromere:
  • Metacentric: Centromere is present in the middle of chromosome
  • Sub-metacentric: Centromere is present near the middle of chromosome
  • Acrocentric: Centromere is present near the one end of the chromosome
  • Telocentric: Centromere is present at the terminal position of the chromosome 
  • Based on sex chromosomes:
  • Autosomes: Responsible for the normal functions of the body
  • Allosomes: responsible for the secondary sexual characteristics

Q9. What are histones? What are their important functions?

Answer: Histones are basic and positively charged DNA binding proteins (since DNA is negatively charged) that helps in the supercoiling of DNA. Histones form a core that promotes the DNA to wrap around. Thus, histone binding is responsible for regulating the expression of genes.

Q10. How many types of histones are present in eukaryotic cells?

Answer: Five types of histone proteins are found in eukaryotic cells. Out of five, four are involved in forming the histone core of nucleosome (H2A, H2B, H3, and H4), while H1 binds with DNA on the nucleosome surface.

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