What is the structure of heterochromatin?

What is the structure of heterochromatin?

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A short article about euchromatin and heterochromatin mentions that the structure of heterochromatin usually depicted in images "has never been visualized in vivo, and its existence is questionable". Obviously, heterochromatin exists, since you can see it on photomicrographs, but what about its structure?

Is it true that the structure is not confirmed? Are there any other candidate structures?

Heterochromatin structure

Figure 1. Association of the Sir3 silencing protein with mono- and di-nucleosomes. (A) Biolayer Interferometry Assay (BLI) for assessing the binding of Sir3 to reconstituted nucleosomes. The nucleosome is immobilized on the sensor using a biotin linker. Association of Sir3 results in a change in refractive index of reflected light which is measured in real time. (B) binding curves for the association of the BAH domain of Sir3 (Sir3BAH) and full-length Sir3 with mono- and di-nucleosomes (MonoN and DiN, respectively), showing greatly increased affinity of full-length Sir3 for DiN. From Behrouzi, Lu, et al., 2016, eLife.

Figure 2. Model for association of the SIR complex with chromatin based on the nucleosome-binding properties of the Sir3 and the SIR complex. From Behrouzi, Lu, et al., 2016, eLife

Figure 3. Crystal structures of the yeast nucleosome in complex with the BAH domain of Sir3. Sir3 binds to the tail of histone H4 via contacts with K16 and H18, and induces contacts between R17 and R19 with nucleosomal DNA. The resulting arginine “clamp” is required for silencing. From Wang et al., 2013, PNAS.


Model for heterochromatic underreplication and the structure of polytene chromosomes.

Fig. 6 . Model for heterochromatic underreplication and the structure of polytene chromosomes. Double-stranded DNA in a hypothetical region of Drosophila pericentromeric heterochromatin is shown, with NotI restriction sites (N) and a region of probe homology indicated. Satellite repeats inhibit their own replication by blocking fork elongation. The barrier formed by satellite repeats could reflect an intrinsic property of highly repetitious sequences or could result from the compaction of satellite repeats into a chromatin structure distinct from other heterochromatic sequences. The first polytene S phase ends before replication forks stalled at satellite barriers are resolved, causing heterochromatic underreplication. Truncated linear DNAs are generated in the second polytene S phase, when replication forks extend to the same barriers where forks were left unresolved in the first polytene S phase. DNAs are shown with blunt ends for clarity, but they would probably have staggered ends, particularly on lagging strands. Once produced, truncated DNAs would be replicated in each subsequent S phase.

Heterochromatin and Euchromatin

The terms “heterochromatin” and “euchromatin” were given by Heitz in 1928-29, although they had been discovered much earlier. Heterochromatic blocks observed during interphase were earlier termed as pro-chromosomes. The substance of which eukaryotic chromosomes are composed is known as chromatin it contains DNA, protein and a small amount of RNA.

During interphase most of the chromatin is in diffuse (de-coiled) state, but some segments are visible because of their condensed or coiled state.

The condensed segments stain deeply during interphase this phenomenon is called positive heteropycnosis in contrast, the phenomenon of negative heteropycnosis denotes the absence of condensation, hence lack of or poor staining, in certain chromosome parts during cell division (especially during prophase and metaphase), when the rest of the chromosome is highly condensed.

Thus the chromatin that follows the normal coiling and de-coiling cycle is called euchromatin whereas the chromatin that deviates from the normal is called heterochromatin. The heterochromatic regions take more stain (dark stained) than euchromatic regions. Pachytene is the most suitable stage for locating the heterochromatic regions.

There are three kinds of heterochromatic regions in the chromosomes observed during interphase and prophase stages:

Chromocentres are the heterochromatic regions which occur near the centromeres. Dipteran salivary gland cells contain one large chromo-centre formed by the fusion of the chromocentres of all the chromosomes present in the cell. Knobs are spherical and heterochromatic structures and are observed more clearly in some species, such as, maize, during pachytene.

Heterochromatin is classified into the following two types:

(1) Constitutive heterochromatin:

It forms a permanent structural characteristic of a particular chromosome and it does not revert to euchromatin. Examples of this type of heterochromatin occur in the centromeric and telomeric regions. Constitutive heterochromatin contains repetitive DNA, and non-repetitive A-T rich main band DNA.

Satellite DNA is also localized in the centromeric heterochromatin. Repetitive DNA contains many to a million copies of base sequences each of which is few to hundreds of base pairs in length.

(2) Facultative heterochromatin:

It represents the inactivated and condensed segments of euchromatin it is expressed under certain conditions. Heterochromatinization of one of the two X chromosomes of human females is a common example of facultative heterochromatin. This type of heterochromatin can revert back to euchromatin and thus it is an important means of genetic regulation.

Euchromatin is known to contain genes which are active, whereas, the genes located in heterochromatic regions are repressed. This inactivity of the genes is chiefly due to the highly condensed state of the chromatin.

Replication of heterochromatin occurs late in the S-phase. Certain genes have been located in the heterochromatic regions of Drosophila and tomato. The Y chromosome of Drosophila is heterochromatic but it carries the gene for bobbed bristles (bb).

The Y chromosome, which is heterochromatic, is also necessary for male fertility in the fly. Cytological observations have revealed that a part of the Y chromosome becomes euchromatic in the spermatocytes. Lima-de-Faria in 1969 reported the occurrence of gene amplification for ribosomal cistrons in the heterochromatic DNA body of Acheta domesticus (house cricket).

The heterochromatic regions contain more DNA as compared to the euchromatin and, therefore, they must contain more genes than euchromatic regions of the same size. In the intact interphase lymphocyte nuclei, Frenster and coworkers in 1963 found that DNA content was 74% in heterochromatin and 13% in euchromatin.

Specific template activity of heterochromatin fraction was 26 and 28% for DNA and RNA syntheses, respectively, while that of euchromatin fraction was 400 and 470%, for DNA and RNA syntheses, respectively.

Thus most of the newly synthesized RNA and DNA were localized with in the euchromatin fraction. It has been found that gross differences do not exist between DNA from euchromatin and heterochromatin with respect to the base composition.

DNA Packaging in Cells

When comparing prokaryotic cells to eukaryotic cells, prokaryotes are much simpler than eukaryotes in many of their features (Figure). Most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid.

A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid.

In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together?

The size of the genome in one of the most well-studied prokaryotes, E.coli, is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure.

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus (Figure). At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the “beads on a string” structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage, the chromosomes are at their most compact, are approximately 700 nm in width, and are found in association with scaffold proteins.

In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin. Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted.

These figures illustrate the compaction of the eukaryotic chromosome.

Genomics and Gene Expression

David P. Clark , Nanette J. Pazdernik , in Biotechnology (Second Edition) , 2016

Gaps Remain in the Human Genome

Although the sequence of the genome is considered complete, there are still gaps. One method of finding the sequence of any gaps is called chromosome walking. In this method, a particular clone is sequenced to start the process. Then the new sequence data is used to find overlapping clones ( Fig. 8.10 ). After those are identified and sequenced, more overlapping clones are identified. The process goes in order either up or down the chromosome, compiling the sequence piece by piece. Usually, the first clone is located relative to a particular marker, such as an STS or RFLP.

FIGURE 8.10 . Chromosome Walking

Researchers identify the downstream and upstream regions of a gene using chromosome walking. In this example, the end of library clone 1 is converted into a probe. The probe is used to screen a library, and a second clone is identified. The two clones overlap and are linked to form a complete gene.

Most of the gaps fall in highly condensed regions of repetitive DNA, known as heterochromatin , which is difficult to sequence. Three features characterize heterochromatin: hypoacetylation (i.e., lack of acetyl groups on the histones) methylation of histone H3 on a specific lysine and methylation on CpG or CpNpG sequence motifs. Heterochromatin is not transcribed and comes in two forms: facultative heterochromatin and constitutive heterochromatin ( Fig. 8.11 ). The amount of methylation on lysine-9 in histone H3 determines whether or not heterochromatin is considered facultative or constitutive. The constitutive form is found around the centromeres and telomeres of the chromosome and does not change from one generation to the next.

FIGURE 8.11 . Facultative versus Constitutive Heterochromatin

The amount of methylation on lysine-9 in histone H3 determines whether or not heterochromatin is considered facultative or constitutive.

Facultative heterochromatin is found in other regions of the chromosomes, and its presence is cell-specific. Once a specific region of a chromosome becomes heterochromatin, all of the cells’ descendants will maintain this pattern. The border for facultative heterochromatin is not static, and each cell in a tissue might have a little more DNA condensed than other cells. This is exemplified by the classic inactivation of the white gene in Drosophila, where the fly will have a mottled red and white eye color because the gene is silenced into facultative heterochromatin in some cells and not others. This genetic variation is called position effect variegation (PEV).

Gaps in genomes can often be sequenced by chromosome walking, where one end of a library clone is used to find other overlapping clones. Most gaps result from heterochromatin, highly condensed repetitive DNA found in specific sites throughout the genome. The physical nature of heterochromatin makes it difficult to sequence.

What is Heterochromatin

The tightly packed form of DNA in the nucleus is referred to as heterochromatin. However, heterochromatin is less compact than metaphase DNA. The staining of non-dividing cells in the nucleus under the light microscope exhibits two distinct regions depending on the intensity of the staining. Lightly stained areas are considered as euchromatin, whereas the darkly stained areas are considered as heterochromatin. Heterochromatin organization is more compact in such a way that their DNA is inaccessible to the proteins which are involved in the gene expression. Genetic events like chromosomal crossing over are avoided by the compact nature of heterochromatin. Hence, heterochromatin is considered as transcriptionally and genetically inactive. Two heterochromatin types can be identified in the nucleus: constitutive heterochromatin and facultative heterochromatin.

Constitutive Heterochromatin

Constitutive heterochromatin contains no genes in the genome, hence it can be retained in its compact structure also during the interphase of the cell. It is a permanent feature of the cell’s nucleus. DNA in the telomeric and centromeric regions belong to the constitutive heterochromatin. Some regions in the chromosomes belong to the constitutive heterochromatin for example, most of the regions of Y chromosome is constitutionally heterochromatic.

Facultative Heterochromatin

Facultative heterochromatin contains the inactive genes in the genome hence, it is not a permanent feature of the cell’s nucleus but it can be seen in the nucleus some of the time. These inactive genes may be inactive either in some cells or during some periods. When those genes are inactive, they form facultative heterochromatin. Chromatin structures, beads on a string, 30 nm fiber, active chromosomes in the interphase are shown in figure 2.

Figure 2: Chromatin Structures

Function of Heterochromatin

Heterochromatin is mainly involved in maintaining the integrity of the genome. The higher packaging of heterocromatin allows the gene expression to be regulated by keeping the DNA regions inaccessible to proteins in gene expression. The formation of heterochromatin prevents the DNA end damage by endonucleases due to its compact nature.

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