Heterochromatin and Euchromatin

Depending on the level of compactness, the chromatin gets divided into heterochromatin or euchromatin. The less compact one is known as the euchromatin. It forms an 11nm fiber, representing the nucleosome structure. The heterochromatin looks compact and dense. It is known as the 30 nm fiber. Let us discuss each one in details.

Euchromatin:

It involves the actively transcribing DNA of the chromosome. Thus, the euchromatin consists of normally functioning genes. It is a region of a eukaryotic chromosome that gets diffused during the interphase. The euchromatin consists of the active genomic form and stains lighter. Maximum percentage of the human genome involves the euchromatin (92%). Its structure appears like the beads on a string form. The nucleosomes comprise of proteins and DNA linked together. The proteins are known as histones. There are eight histones in the nucleosome. The methylated lysine 4 is present on the tail of the histone protein. It indicates a marker for the euchromatin.

Image 1: A chromosome with highlighted heterochromatin, euchromatin, and telomere

·        G-Banding: It involves the staining of the chromosome using a Giemsa stain. The stain helps in staining the regions of the DNA consisting of the very high amount of A-T base pairs. Euchromatin appears in the form of light bands after staining the chromosomes with Giemsa stain. Prokaryotes only show the presence of euchromatin and no heterochromatin.

Euchromatin actively involves the DNA undergoing transcription process. All euchromatin genes do not participate in the DNA to RNA processes. Mostly, the euchromatin gets transformed into the heterochromatin. It helps in controlling the gene expression and replication. The examples include the housekeeping genes. It encodes for the proteins involved in cell structure and function. Embryonic stem cells possess a diffused chromatin structure. The formation of condensed euchromatic varies in these cells. The condensation of the euchromatic differs from species to species.

Heterochromatinization of euchromatin: It is a form of repression of euchromatin. Sometimes a segment of a chromosome or the entire chromosome gets inactivated and condensed. It may also remain inactive for many generations. An example includes X inactivation in females. The human females possess two X chromosomes, out of which one gets inactivated. Meaning, certain genes on that particular X chromosome get inactivated. It is a crucial step for preventing lethality due to double dosage of alleles. 
Constitutive heterochromatin:

The constitutive heterochromatin regions occur throughout the chromosomes. Most of it occurs in the pericentromeric regions of the chromosomes. However, it also occurs in the telomeres or throughout the length of the chromosomes. Mainly, the chromosomes 1, 9, 16, 19, and Y consist of constitutive heterochromatin. It consists of tandem repeats such as satellite repeats, minisatellites, and microsatellites. Banding techniques help in visualizing the heterochromatin. Example of banding technique includes C banding. The regions having constitutive heterochromatin stain darker. The peripheral regions of the nucleus show a very high content of constitutive heterochromatin. The euchromatin occurs mostly in the center of the nucleus. Thus, it involves actively transcribing genes. It also manifests the segregation of sister chromatids.

The telomeric sequences involve a higher conservation rate as compared to that of the repeat sequences. Earlier, the biologists thought that the constitutive heterochromatin did not possess any genes. However, later on, total 450 genes got revealed in the Drosophila heterochromatin regions. Hence, they have highly condensed regions with epigenetic modifications. These modifications prevented transcription. The position effect occurs when the genes located near the constitutive heterochromatin get silenced. The replication of the constitutive heterochromatin occurs in the late S phase of the cell cycle. It does not participate in the meiotic recombination. The heterochromatin mainly gets condensed in the interphase and gets repressed transcriptionally. The condensation of the constitutive heterochromatin occurs due to histone modifications as well. The underacetylation of the histone H4 determines the overall status of the heterochromatin. Such modifications occur in both the mitosis and meiosis. Following are the modifications:

•        Histone hypoacetylation

•        Histone H3-Lys9 methylation

•        Cytosine methylation

Image 2: Difference between euchromatin and heterochromatin

Heterochromatin structure in the yeast telomere:

The telomeres are the cell protectors occurring at the end of the chromosomes. It gets packaged into tightly condensed heterochromatin. Not only does it condense tightly, but also extends into the adjacent regions. It prevents the lethal fusions with other chromosomes and protects the chromosomes from the action of nucleases. It helps in responding towards the DNA damage. The model organism for studying the heterochromatin involves budding yeast. It shows epigenetic inheritance of heterochromatin. An important gene in the budding yeast involved in the inheritance of heterochromatin is known as the ADE2 gene. It encodes an enzyme involved in adenine biosynthesis. Loss of the gene activity leads to an accumulation of a red pigment. If the gene moves in the vicinity to the telomeric heterochromatin region, the gene expression gets silenced leading to the synthesis of red pigment. The inheritance of the red pigment-producing genes remains stable due to the stability of the heterochromatin.

Centromeric heterochromatin:

The Centromeric sequences vary widely in different species. Normally, the chromosomes contain a single centromeric region containing the alpha satellite repeats. It gets packaged in the heterochromatin. Mitosis is an important phase of the cell cycle. During mitosis, centromere plays a crucial role in attaching the chromosome to the spindle microtubule. The chromosomal breaks lead to the growth of the fragment having the Centromeric region. A spontaneous inactivation of heterochromatin also leads to the formation of a monocentric chromosome.

Duplication of heterochromatin:

Special proteins in the heterochromatin show an ability to bind to the histones such as H3 or H4. These histones undergo a specific modification process. The enzyme responsible for the modification of histones also occurs in the heterochromatin region. The chromosome duplication leads to the random distribution of parent chromosomes into two daughter strands. Thus, it results in a mixture of old and new nucleosomes. The histone-modifying enzyme always binds to the old nucleosomes. The telomeric heterochromatin consists of three important Sir Proteins. They decide the duplication of the telomeric chromatin. The protein complexes under acetylates with the histone tails. It also shows its ability of binding with the other proteins.

References:

[1] Human Chromosomes, Orlando J. Miller, Eeva Therman, Page 71-72

[2] Heterochromatin: Molecular and Structural Aspects, Ram Sagar Verma

[3] Dictionary of Genetics, Himanshu Arora

[4] Essential Genetics: A Genomics Perspective, Daniel L. Hartl, Elizabeth W. Jones, Hartl Daniel

Copyright, 2019. All Rights Reserved.

Chromatin remodeling

Chromosome involves the fine design of DNA and protein complex. It also involves few non-histone proteins performing various functions. The compact structure of chromosomes fits them in the nucleus of the cell. The eukaryotic chromatin organization includes an inbuilt system of regulation. Hence, it does not require an additional repressor molecule to control the gene expression. It is the main feature of eukaryotic regulation of gene expression. The prokaryotic gene expression consists of operons such as Lac and the tryptophan operons. They require repressors to bind with the respective operators and prevent the transcription of the structural genes. However, the eukaryotic systems have their own mechanisms independent of the repressors. Hence, they save their machinery and material from making the repressor molecules. 

Repression of gene activity:

Image: Chromatin remodeling

The eukaryotic nucleosome organization shows a repressive effect on the gene expression. Hence, it does not include the extra repressors. The eukaryotic genes involve two main types based on the transcription such as the transcriptionally active genes and the transcriptionally inactive genes. The enzymes known as nucleases degrade or interact with the DNA molecules. The transcriptionally active genes show sensitivity to the DNase-I. The transcriptionally inactive genes do not sensitivity to the DNase-I. The transcriptionally active and inactive genes get distinguished by a restriction digest and a southern blot. Process the cells for obtaining the chromatin. Treat the chromatin with the DNase-I enzyme. The process of restriction digestion involves treatment of the DNA with the restriction enzyme. The enzyme cleaves the DNA to form fragments of different sizes. Hence, it targets the restriction sites.

The fragments get separated by gel electrophoresis followed by Southern blotting and autoradiography. The studies reveal two types of genes. One type of genes shows accessibility to the DNase-I. The other type of genes does not allow the DNase-I access. The genes accessible to the DNase-I consists of few fragments or no fragments. These regions involve a less coiled DNA. The less coiled DNA expose more hypersensitive sites near the transcriptionally active sites. These regions show very high sensitivity. They are present upstream of the transcription start site. The non-accessible regions involve more and more coiling. Hence, they show the whole gene. Due to very high coiling, they do not expose the genes to DNase-I.

The histone proteins also repress the gene expression. Suppose DNA gets simultaneously treated with histones and promoter binding protein. In this case, the histones compete more strongly for the promoters. They form nucleosomes at TATA box of the core promoter. The promoter binding proteins do not get a chance to bind with the promoters. Hence, the transcription does not occur. Suppose if the DNA first binds with the promoter binding protein. The proteins get assembled to the TATA box, thereby blocking the nucleosome assembly. Hence, it results in the transcription of the genes. The third possibility involves the treatment of DNA with the promoter binding proteins and activators. The activators bind with the enhancers thereby allowing the promoter binding proteins to bind to the TATA box. Hence, transcription occurs.

Activation of genes by chromatin remodeling:

Gene activation involves a key event related to the chromatin structure. It alters the chromatin structure in the vicinity of the core promoter. It is known as the chromatin remodeling. Two types of chromatin remodelers include nucleosome modifying enzymes and the ATP-dependent nucleosome remodeling complex. The nucleosome modifying enzymes conduct acetylation or deacetylation of the core histones.

Let us consider the nucleosome modifying enzymes. The histone acetyltransferases help in the acetylation process. The histone acetyltransferases get recruited to the chromatin. The activators interact with the DNA binding sites in the presence of the histone acetyltransferases and acetylate the lysine residues. Mainly the amino-terminal tails of the core histones have the lysine residues. Thus, the histones slowly lose the affinity for the DNA. Due to the acetylation, the chromatin structure gets reduced from the 30 nm to the 10 nm. Now the promoters become more accessible for the transcription. The TFIID binds to the site and allows transcription. The acetylated structures get deacetylated by another class of enzymes known as histone deacetylases. These enzymes remove the acetyl groups and restore the 30nm fiber.

ATP-dependent nucleosome remodeling complexes involve a large multiprotein complex. They help in remodeling the chromatin. They use ATP hydrolysis for obtaining energy. The activators interacting with the DNA binding sites recruit nucleosome remodeling complexes. These complexes alter the nucleosome. Thus, the transcription machinery binds to the promoter. An example includes SW1/SNF ATP-dependent nucleosome remodeling complex in yeast.

References:

[1] Epigenetics, Lyle Armstrong
[2] Human Molecular Genetics, Tom Strachan, Andrew Read

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