Euchromatic and heterochromatic region of

chromosome

By Abin ghosh10111001

Not only are the genomes of most eukaryotes much more complex than those of prokaryotes, but the DNA of eukaryotic cells is also organized differently from that of prokaryotic cells.

The genomes of prokaryotes are contained in single chromosomes, which are usually circular DNA molecules. In contrast, the genomes of eukaryotes are composed of multiple chromosomes, each containing a linear molecule of DNA.

The DNA of eukaryotic cells is tightly bound to small basic proteins (histones) that package the DNA in an orderly way in the cell nucleus.

Nucleic acid in eukaryotes

The complexes between eukaryotic DNA and proteins are called chromatin, which typically contains about twice as much protein as DNA.

The major proteins of chromatin are the histones—small proteins containing a high proportion of basic amino acids (arginine and lysine) that facilitate binding to the negatively charged DNA molecule.

There are five major types of histones—called H1, H2A, H2B, H3, and H4—which are very similar among different species of eukaryotes

In addition, chromatin contains an approximately equal mass of a wide variety of nonhistone chromosomal proteins

Chromatin

o When interphase nuclei are broken open very gently and their contents examined under the electron microscope, most of the chromatin is in the form of a fiber with a diameter of about 30 nm

o If this chromatin is subjected to treatments that cause it to unfold partially, it can be seen under the electron microscope as a series of "beads on a string" (The string is DNA, and each bead is a "nucleosome core particle" that consists of DNA wound around a protein core formed from histones

Electron micrograph of (a)30nm dna strand

and (b) “beads on string structure”

DNA packing in eukaryotes

Having described how DNA is packaged into nucleosomes to create a chromatin fibre, we now turn to the mechanisms that create different chromatin structures in different regions of a cell's genome. We now know that mechanisms of this type are used to control many genes in eukaryotes

certain types of chromatin structure can be inherited; that is, the structure can be directly passed down from a cell to its decedents. Because the cell memory that results is based on an inherited protein structure rather than on a change in DNA sequence, this is a form of epigenetic inheritance.

Heitz (1929) originally described as heterochromatin that portion of the nuclear chromatin which demonstrated its allocycly by maintaining a condensed state throughout cell interphase while the remainder of the nuclear chromatin was extending to what he termed the euchromatin state. Cooper (1959) was able to summarize the data from Drosophila which suggested that heterochromatin and euchromatin differed in their biophysical conformations and in metabolic expression of their genes but not in their basic structure of DNA arranged within chromosomes.

Heterochromatin and euchromatin

Most of the euchromatin in interphase nuclei appears to be in the form of 30-nm fibres, organized into large loops containing approximately 50 to 100 kb of DNA. About 10% of the euchromatin, containing the genes that are actively transcribed, is in a more decondensed state (the 10-nm conformation) that allows transcription.

In contrast to euchromatin, about 10% of interphase chromatin (called heterochromatin) is in a very highly condensed state that resembles the chromatin of cells undergoing mitosis. Heterochromatin is transcriptionally inactive and contains highly repeated DNA sequences, such as those present at centromeres and telomeres.

when a gene that is normally expressed in euchromatin is experimentally relocated into a region of heterochromatin, it ceases to be expressed, and the gene is said to be silenced. These differences in gene expression are examples of position effects, in which the activity of a gene depends on its position relative to a nearby region of heterochromatin on a chromosome. First recognized in Drosophila, position effects have now been observed in many eukaryotes, including yeasts, plants, and humans.

Heterochromatin and euchromatin boundary is dynamic

The cause of position effect variegation in Drosophila

Regulation of chromatin structure

Barrier to protect euchromatic region

Heterochromatin is condensed Heterochromatin DNA is late replicating Heterochromatin DNA is methylated In heterochromatin, histones are hypo-

acetylated Histones from heterochromatin are

methylated on lysine 9 Heterochromatin is transcriptionally inactive Heterochromatin does not participate in

genetic recombination

Properties of heterochromatin

Constitutive heterochromatin

All cells of a given species will package the same regions of DNA in constitutive heterochromatin, and thus in all cells any genes contained within the constitutive heterochromatin will be poorly expressed. For example, all human chromosomes 1, 9, 16, and the Y-chromosome contain large regions of constitutive heterochromatin.

In most organisms, constitutive heterochromatin occurs around the chromosome centromere and near telomeres.

Two types of heterochromatin

Constitutive HC contains a particular type of DNA called satellite DNA, which consists of large numbers of short tandemly repeated sequences : Alpha-satellite DNA, DNA satellite I, II and III. These satellite DNA sequences are able to fold on themselves and may have an important role in the formation of the highly compact structure of the constitutive HC.

Constitutive HC is stable and conserves its heterochromatic properties during all stages of development and in all tissues.

Constitutive HC is highly polymorphic, probably because of the instability of the satellite DNA. This polymorphism can affect not only the size but also the localisation of the heterochromatin, and apparently has no phenotypic effect.

Constitutive HC is strongly stained by the C-band technique, which is the result of the very rapid renaturation of the satellite DNA following denaturation.

Characteristics of constitutive HC

In many complex organisms, including humans, each centromere is embedded in a stretch of special centric heterochromatin that persists throughout interphase, even though the centromere-mediated movement of DNA occurs only during mitosis

This chromatin contains a centromere-specific variant H3 histone, known as CENP-A (see Figure 4-41), plus additional proteins that pack the nucleosomes into particularly dense arrangements and form the kinetechore, the special structure required for attachment of the mitotic spindle.

The regions of DNA packaged in facultative heterochromatin will not be consistent between the cell types within a species, and thus a sequence in one cell that is packaged in facultative heterochromatin (and the genes within poorly expressed) may be packaged in euchromatin in another cell (and the genes within no longer silenced). However, the formation of facultative heterochromatin is regulated, and is often associated with morphogenesis or differentiation

An example of facultative heterochromatin is X-chromosome inactivation in female mammals

Facultative heterochromatin

Facultative HC is characterised by the presence of LINE-type repeated sequences. These sequences, dispersed throughout the genome, could promote the propagation of a condensed chromatin structure.

Facultative HC is reversible, its heterochromatic state depending on the stage of development or the cell type examined. The inactive X (Barr body) in the somatic cells females and the inactive sex vesicle at the pachytene stage of male meiosis provide two examples of facultative HC.

Facultative HC is not particularly rich in satellite DNA, and is therefore not polymorphic.

Facultative HC is never stained by the C-band technique.

Characteristics of facultative HC

Mammals achieve dosage compensation by the transcriptional inactivation of one of the two X chromosomes in female somatic cells, a process known as X-inactivation.

Early in the development of a female embryo, when it consists of a few thousand cells, one of the two X chromosomes in each cell becomes highly condensed into a type of heterochromatin.

The condensed X chromosome can be easily seen under the light microscope in interphase cells; it was originally called a Barr body and is located near the nuclear membrane

Diffentiating constitutive from facultative HC

For many decades, heterochromatin was thought to be a single entity defined by its highly condensed structure and its ability to silence genes permanently.

Each domain of heterochromatin is thought to be formed by the cooperative assembly of a set of non-histone proteins.

For example, classical pericentromeric heterochromatin contains more than six such proteins, including heterochromatin protein I (HPI)

polycomb form of heterochromatin contains a similar number of proteins in a non-overlapping set (pcc proteins).

other types of heterochromatin must exist whose protein composition is not known

It is likely that each of these types of heterochromatin is differently regulated and has different roles in the cell

There are Multiple forms of Heterochromatin

Role of HC in the organisation of nuclear domains

• Heterochromatin and euchromatin occupy different nuclear domains. HC is usually localised in the periphery of the nucleus and is attached to the nuclear membrane. In contrast, the active chromatin occupies a more central position.

• The preferential localisation of HC against the nuclear membrane may be due to the interaction of the protein HP1 with the lamin B receptor, which is an integral component of the inner membrane of the nucleus.

• The peripheral localisation of HC concentrates the active elements towards the centre of the nucleus, allowing the active euchromatin to replicate and be transcribed with maximum efficiency.

Functions of heterochromatin

Role of HC in the centromeric function In most eukaryotes, the centromeres are loaded with a considerable mass of

heterochromatin. It has been suggested that centromeric HC is necessary for the cohesion of sister chromatids and that it allows the normal disjunction of mitotic chromosomes.

In the yeast Schizosaccharomyces pombe, the homologue of the HP1 protein Swi6 is absolutely essential for efficient cohesion of sister chromatids during cell division.

Moreover, experiments involving the deletion of satellite DNA show that a large region of satellite DNA repeats is indispensable for the correct functioning of the centromere.

It is supposed that centromeric HC might, de facto, create a compartment by increasing the local concentration of the centromeric histone variant, CENP-A, and by promoting the incorporation of CENP-A rather than the histone H3 during replication.

Role of HC in gene repression (epigenetic regulation)

Gene expression may be controlled at two levels:

Firstly, at the local level which is transcription control, thanks to the formation of local transcription complexes. This level involves relatively small DNA sequences linked to individual genes.

At a more global level, in which case it is the transcriptability that is controlled. It involves much larger sequences that represent a large chromatin domain, which can be either in an active or an inactive state. Heterochromatin appears to be involved in controlling the transcriptability of the genome. Genes that are usually located in the euchromatin can, therefore, be silenced when they are placed close to a heterochromatic domain.

The packaging of selected regions of eukaryotic genomes into different forms of chromatin makes possible a type of cell memory mechanism that is not available to bacteria. The crucial feature of this uniquely eukaryotic form of gene regulation is the storage of the memory of the state of a gene on a gene-by-gene basis-in the form of local chromatin structures that can persist for various lengths of time.

condensed chromatin that coats important developmental regulatory genes is maintained by the polycomb group of proteins. The latter type of heterochromatin silences a large number of genes that encode gene regulatory proteins early in embryonic development, covering a total of about 2 per cent of the human genome, and it is removed only when each individual gene is needed by the developing organism

Inherence of epigenetic information

the RNA interference machinery can selectively shut off synthesis of the target RNAs

For this remarkable mechanism to occur, the short siRNAs produced by the Dicer protein are assembled with a group of proteins (including Argonaute) to form the RITS (RNA-induced transcriptional silencing) complex. Using single-stranded siRNA as a guide sequence, this complex binds complementary RNA transcripts as they emerge from a transcribing RNA polymerase II

Positioned on the genome in this manner, the RITS complex attracts proteins that covalently modify nearby histones and eventually directs the formation and spread of heterochromatin to prevent further transcription initiation. In some cases, the RITS complex also induces the methylation of DNA, which, as we have seen, can repress gene expression even further

Rna interfernce heterochromatin formation

RNAi-directed heterochromatin formation is an important cell defence mechanism that limits the accumulation of transposable elements in the genome by maintaining them in a transcriptionally silent form.

The fact that heterochromatin stands at the interface between heritable gene silencing, chromatin fine structure and gross nuclear organisation has made it a powerful and durable concept that continues to excite the interest of researchers who study the mechanisms of gene regulation.

The discovery that the RNAi machinery is directly involved in heterochromatin formation has revealed an entirely new aspect of silent chromatin and a potential mechanism by which small RNAs can target specific regions of DNA for silencing.

Summary and conclusions

Molecular biology of cell ,5th edition

Ncbi book shelf ,Bookshelf ID: NBK9863

Heterochromatin structure and function Niall Dillon

Reference